Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    A comparative analysis of human adult testicular cells expressing stem Leydig cell markers in the interstitium, vasculature, and peritubular layer
    Eliveld, Jitske ; Daalen, Saskia K.M. van; Winter-Korver, Cindy M. de; Veen, Fulco van der; Repping, Sjoerd ; Teerds, Katja ; Pelt, Ans M.M. van - \ 2020
    Andrology 8 (2020)5. - ISSN 2047-2919 - p. 1265 - 1276.
    human testis - markers - propagation - stem Leydig cells

    Background: Origin of human adult Leydig cells (ALCs) is not well understood. This might be partly due to limited data available on the identification and location of human precursor and stem Leydig cells (SLCs) which hampers the study on the development of ALCs. Objectives: The aim of the present study was to investigate whether described human (PDGFRα, NGFR) and rodent (NES, PDGFRα, THY1, NR2F2) SLC markers are expressed by a common cell population within human adult testicular interstitial cells in vivo and before and after in vitro propagation. Materials and methods: Immunohistochemical analyses were used to identify localization of human adult testicular interstitial cells expressing described SLC markers. Next, interstitial cells were isolated and cultured. The percentage of cells expressing one or more SLC markers was determined before and after culture using flow cytometry. Results: NR2F2 and PDGFRα were present in peritubular, perivascular, and Leydig cells, while THY1 was expressed in peritubular and perivascular cells. Although NES and NGFR were expressed in endothelial cells, co-localization with PDGFRα was found for both in vitro, although for NGFR only after culture. All marker positive cells were able to undergo propagation in vitro. Discussion: The partly overlap in localization and overlap in expression in human testicular cells indicate that PDGFRα, NR2F2, and THY1 are expressed within the same ALC developmental lineage from SLCs. Based on the in vitro results, this is also true for NES and after in vitro propagation for NGFR. Conclusion: Our results that earlier described SLC markers are expressed in overlapping human interstitial cell population opens up further research strategies aiming for a better insight in the Leydig cell lineage and will be helpful for development of strategies to cure ALC dysfunction.

    Effect of exercise on apparent total tract digestibility of nutrients and faecal recovery of ADL and TiO2 in ponies
    Schaafstra, F.J.W.C. ; Doorn, D.A. van; Schonewille, J.T. ; Roelfsema, E. ; Westermann, C.M. ; Dansen, O. ; Jacobs, M. ; Lee, J.Y. ; Spronck, E.A. ; Blok, M.C. ; Hendriks, W.H. - \ 2018
    Animal 12 (2018)12. - ISSN 1751-7311 - p. 2505 - 2510.
    digestibility - equines - exercise - markers - total faeces collection
    Exercise and physical training are known to affect gastrointestinal function and digestibility in horses and can lead to inaccurate estimates of nutrient and energy digestibility when markers are used. The effect of exercise on apparent nutrient digestibility and faecal recoveries of ADL and TiO2 was studied in six Welsh pony geldings subjected to either a low- (LI) or high-intensity (HI) exercise regime according to a cross-over design. Ponies performing LI exercise were walked once per day for 45 min in a horse walker (5 km/h) for 47 consecutive days. Ponies submitted to HI exercise were gradually trained for the same 47 days according a standardized protocol. Throughout the experiment, the ponies received a fixed level of feed and the daily rations consisted of 4.7 kg DM of grass hay and 0.95 kg DM of concentrate. The diet was supplemented with minerals, vitamins and TiO2 (3.0 g Ti/day). Total tract digestibility of DM, organic matter (OM), CP, crude fat, NDF, ADF, starch, sugar and energy was determined with the total faeces collection (TFC) method. In addition, DM and OM digestibility was estimated using internal ADL and the externally supplemented Ti as markers. Urine was collected on the final 2 days of each experimental period. Exercise did not affect apparent digestibility of CP, crude fat, starch and sugar. Digestibility of DM (DMD), OM (OMD), ADF and NDF tended to be lower and DE was decreased when ponies received the HI exercise regime. For all treatments combined, mean faecal recoveries of ADL and Ti were 87.8±1.7% and 99.3±1.7%, respectively. Ti was not detected in the urine, indicating that intestinal integrity was maintained with exercise. Dry matter digestibility estimated with the TFC, ADL and Ti for ponies subjected to LI exercise were 66.3%, 60.3% and 64.8%, respectively, while DMD for HI ponies were 64.2%, 60.3% and 65.2%, respectively. In conclusion, physical exercise has an influence on the GE digestibility of the feed in ponies provided with equivalent levels of feed intake. In addition, the two markers used for estimating apparent DMD and OMD indicate that externally supplemented Ti is a suitable marker to determine digestibility of nutrients in horses performing exercise unlike dietary ADL.
    Inzicht en Zichtbaar Weerbaar: meetmethoden nodig voor teelt-zeker weerbaar telen
    Wurff, A.W.G. van der; Streminska, M.A. ; Boer, F.A. de; Cuesta Arenas, Y. ; Janse, J. - \ 2015
    Wageningen UR
    cropping systems - horticulture - plant protection - hydroponics - greenhouse horticulture - conferences - chrysanthemum - soilless culture - substrates - measurement - interactions - markers - plant development - climate - cultivars - tuinbouw - glastuinbouw - teeltsystemen - cultuur zonder grond - substraten - meting - interacties - merkers - plantenontwikkeling - klimaat - cultivars
    Aandacht wordt geschonken aan: voedingswater, micro-leven, rasverschillen, en oud stekmateriaal. Poster van PlantgezondheidEvent 12 maart 2015.
    Using selection index theory to estimate consistency of multi-locus linkage disequilibrium across populations
    Wientjes, Y.C.J. ; Veerkamp, R.F. ; Calus, M.P.L. - \ 2015
    BMC Genetics 16 (2015). - ISSN 1471-2156
    genomic breeding values - genetic-relationship information - quantitative trait loci - dairy-cattle breeds - prediction - accuracy - haplotype - markers - impact - lines
    Background
    The potential of combining multiple populations in genomic prediction is depending on the consistency of linkage disequilibrium (LD) between SNPs and QTL across populations. We investigated consistency of multi-locus LD across populations using selection index theory and investigated the relationship between consistency of multi-locus LD and accuracy of genomic prediction across different simulated scenarios. In the selection index, QTL genotypes were considered as breeding goal traits and SNP genotypes as index traits, based on LD among SNPs and between SNPs and QTL. The consistency of multi-locus LD across populations was computed as the accuracy of predicting QTL genotypes in selection candidates using a selection index derived in the reference population. Different scenarios of within and across population genomic prediction were evaluated, using all SNPs or only the four neighboring SNPs of a simulated QTL. Phenotypes were simulated using different numbers of QTL underlying the trait. The relationship between the calculated consistency of multi-locus LD and accuracy of genomic prediction using a GBLUP type of model was investigated.
    Results
    The accuracy of predicting QTL genotypes, i.e. the measure describing consistency of multi-locus LD, was much lower for across population scenarios compared to within population scenarios, and was lower when QTL had a low MAF compared to QTL randomly selected from the SNPs. Consistency of multi-locus LD was highly correlated with the realized accuracy of genomic prediction across different scenarios and the correlation was higher when QTL were weighted according to their effects in the selection index instead of weighting QTL equally. By only considering neighboring SNPs of QTL, accuracy of predicting QTL genotypes within population decreased, but it substantially increased the accuracy across populations.
    Conclusions
    Consistency of multi-locus LD across populations is a characteristic of the properties of the QTL in the investigated populations and can provide more insight in underlying reasons for a low empirical accuracy of across population genomic prediction. By focusing in genomic prediction models only on neighboring SNPs of QTL, multi-locus LD is more consistent across populations since only short-range LD is considered, and accuracy of predicting QTL genotypes of individuals from another population is increased.
    Low 25-hydroxyvitamin D2 and 25-hydroxyvitamin D3 levels are independently associated with macroalbuminuria, but not with retinopathy and macrovascular disease in type 1 diabetes: the EURODIAB prospective complications study
    Engelen, L. ; Schalkwijk, C.G. ; Eussen, S.J.P.M. ; Scheijen, J.L.J.M. ; Soedamah-Muthu, S.S. ; Chaturvedi, N. ; Fuller, J.H. ; Stehouwer, C.D. - \ 2015
    Cardiovascular Diabetology 14 (2015). - ISSN 1475-2840 - 9 p.
    glomerular-filtration-rate - vitamin-d deficiency - microvascular complications - cardiovascular-disease - risk-factors - 1,25-dihydroxyvitamin d-3 - endothelial function - mortality - markers - determinants
    Background Low circulating levels of total vitamin D [25(OH)D] and 25(OH)D3 have been associated with vascular complications in few studies on individuals with type 1 diabetes. However, these measures are affected by UV light exposure. Circulating 25(OH)D2, however, solely represents dietary intake of vitamin D2, but its association with complications of diabetes is currently unknown. We investigated the associations between 25(OH)D2 and 25(OH)D3 and the prevalence of albuminuria, retinopathy and cardiovascular disease (CVD) in individuals with type 1 diabetes. Methods We measured circulating 25(OH)D2 and 25(OH)D3 in 532 individuals (40¿±¿10 years old, 51 % men) with type 1 diabetes who participated in the EURODIAB Prospective Complications Study. Cross-sectional associations of 25(OH)D2 and 25(OH)D3 with albuminuria, retinopathy and CVD were assessed with multiple logistic regression analyses adjusted for age, sex, season, BMI, smoking, HbA1c, total-HDL-cholesterol-ratio, systolic blood pressure, antihypertensive medication, eGFR, physical activity, alcohol intake, albuminuria, retinopathy and CVD, as appropriate. Results Fully adjusted models revealed that 1 nmol/L higher 25(OH)D2 and 10 nmol/L higher 25(OH)D3 were associated with lower prevalence of macroalbuminuria with ORs (95 % CI) of 0.56 (0.43;0.74) and 0.82 (0.72;0.94), respectively. These vitamin D species were not independently associated with microalbuminuria, non-proliferative and proliferative retinopathy or CVD. Conclusions In individuals with type 1 diabetes, both higher 25(OH)D2 and 25(OH)D3 are associated with a lower prevalence of macroalbuminuria, but not of retinopathy and CVD. Prospective studies are needed to further examine the associations between 25(OH)D2 and 25(OH)D3 and the development of microvascular complications and CVD in type 1 diabetes.
    Empirical and deterministic accuracies of across-population genomic prediction
    Wientjes, Y.C.J. ; Veerkamp, R.F. ; Bijma, P. ; Bovenhuis, H. ; Schrooten, C. ; Calus, M.P.L. - \ 2015
    Genetics, Selection, Evolution 47 (2015). - ISSN 0999-193X
    dairy-cattle breeds - linkage disequilibrium - relationship matrix - complex traits - multi-breed - selection - values - markers - heritability - models
    Background: Differences in linkage disequilibrium and in allele substitution effects of QTL (quantitative trait loci) may hinder genomic prediction across populations. Our objective was to develop a deterministic formula to estimate the accuracy of across-population genomic prediction, for which reference individuals and selection candidates are from different populations, and to investigate the impact of differences in allele substitution effects across populations and of the number of QTL underlying a trait on the accuracy. Methods: A deterministic formula to estimate the accuracy of across-population genomic prediction was derived based on selection index theory. Moreover, accuracies were deterministically predicted using a formula based on population parameters and empirically calculated using simulated phenotypes and a GBLUP (genomic best linear unbiased prediction) model. Phenotypes of 1033 Holstein-Friesian, 105 Groninger White Headed and 147 Meuse-Rhine-Yssel cows were simulated by sampling 3000, 300, 30 or 3 QTL from the available high-density SNP (single nucleotide polymorphism) information of three chromosomes, assuming a correlation of 1.0, 0.8, 0.6, 0.4, or 0.2 between allele substitution effects across breeds. The simulated heritability was set to 0.95 to resemble the heritability of deregressed proofs of bulls. Results: Accuracies estimated with the deterministic formula based on selection index theory were similar to empirical accuracies for all scenarios, while accuracies predicted with the formula based on population parameters overestimated empirical accuracies by ~25 to 30%. When the between-breed genetic correlation differed from 1, i.e. allele substitution effects differed across breeds, empirical and deterministic accuracies decreased in proportion to the genetic correlation. Using a multi-trait model, it was possible to accurately estimate the genetic correlation between the breeds based on phenotypes and high-density genotypes. The number of QTL underlying the simulated trait did not affect the accuracy. Conclusions: The deterministic formula based on selection index theory estimated the accuracy of across-population genomic predictions well. The deterministic formula using population parameters overestimated the across-population genomic accuracy, but may still be useful because of its simplicity. Both formulas could accommodate for genetic correlations between populations lower than 1. The number of QTL underlying a trait did not affect the accuracy of across-population genomic prediction using a GBLUP method
    Genomics and the challenging translation into conservation practice
    Shafer, A.B.A. ; Wolf, J.B.W. ; Alves, P.C. ; Bergstrom, L. ; Bruford, M.W. ; Brannstrom, I. ; Colling, G. ; Dalen, L. van; Meester, L. de; Ekblom, R. ; Vergeer, P. - \ 2015
    Trends in Ecology and Evolution 30 (2015)2. - ISSN 0169-5347 - p. 78 - 87.
    genetic diversity - background selection - population genomics - insular population - dna - divergence - speciation - evolution - sequence - markers
    The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners.
    Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.)
    Koning, C.F.S. ; Esselink, G. ; Vukosavljev, M. ; Westende, W.P.C. van 't; Gitonga, V.W. ; Krens, F.A. ; Voorrips, R.E. ; Weg, W.E. van de; Schulz, D. ; Debener, T. ; Maliepaard, C.A. ; Arens, P.F.P. ; Smulders, M.J.M. - \ 2015
    Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 10 p.
    powdery mildew - markers - tool - identification - resistance - genome - diversity - sequences - platform - plant
    In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.
    Introgression Browser: High throughput whole-genome SNP visualization
    Aflitos, S.A. ; Sanchez Perez, G.F. ; Ridder, D. de; Fransz, P. ; Schranz, M.E. ; Jong, J.H.S.G.M. de; Peters, S.A. - \ 2015
    The Plant Journal 82 (2015)1. - ISSN 0960-7412 - p. 174 - 182.
    in-situ hybridization - alien chromosomes - recombination - tomato - markers - thaliana - potato - identification - organization - improvement
    Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not viable. Here, we present the Introgression Browser (IBROWSER), a bioinformatics tool aimed at visualizing introgressions at nucleotide or SNP accuracy. The software selects homozygous SNPs from Variant Call Format (VCF) information and filters out heterozygous SNPs, Multi-Nucleotide Polymorphisms (MNPs) and insertion-deletions (InDels). For data analysis IBROWSER makes use of sliding windows, but if needed it can generate any desired fragmentation pattern through General Feature Format (GFF) information. In an example of tomato (Solanum lycopersicum) accessions we visualize SNP patterns and elucidate both position and boundaries of the introgressions. We also show that our tool is capable of identifying alien DNA in a panel of the closely related S. pimpinellifolium by examining phylogenetic relationships of the introgressed segments in tomato. In a third example, we demonstrate the power of the IBROWSER in a panel of 597 Arabidopsis accessions, detecting the boundaries of a SNP-free region around a polymorphic 1.17 Mbp inverted segment on the short arm of chromosome 4. The architecture and functionality of IBROWSER makes the software appropriate for a broad set of analyses including SNP mining, genome structure analysis, and pedigree analysis. Its functionality, together with the capability to process large data sets and efficient visualization of sequence variation, makes IBROWSER a valuable breeding tool.
    Effect of a high-protein diet on maintenance of blood pressure levels achieved after initial weight loss: the DiOGenes randomized study
    Engberink, M.F. ; Geleijnse, J.M. ; Bakker, S.J.L. ; Larsen, T. - \ 2015
    Journal of Human Hypertension 29 (2015). - ISSN 0950-9240 - p. 58 - 63.
    risk-factors - controlled-trial - glycemic index - obese women - supplementation - hypertension - overweight - markers - fat
    Randomized trials have shown significant blood pressure (BP) reductions after increased protein compared with carbohydrate intake, but the effect on BP maintenance after initial weight loss is unclear. We examined the effect of a high-protein diet on the maintenance of reduced BP after weight loss in 420 overweight adults from the Diet, Obesity and Genes study. After an 8-week weight-loss period (>8% BW), subjects (42±6 years) were randomized to either a high-protein diet (23–28 en% protein) or a lower-protein control diet (10–15 en% protein) for 26 weeks. BMI after weight loss was 30.3±4.3¿kg¿m-2, BP was 118/73¿mm¿Hg and 28 subjects (6.5%) used antihypertensive agents. Systolic BP during 26 weeks of weight maintenance dietary intervention increased in both treatment groups, but it was 2.2¿mm¿Hg less (95% CI: -4.6 to 0.2¿mm¿Hg, P=0.08) in the high-protein group than in the lower-protein control group. In 191 (pre)hypertensive subjects (baseline systolic BP120¿mm¿Hg), a larger difference was observed (-4.2¿mm¿Hg (-7.7, -0.7), P=0.02). The effect was attenuated after adjustment for initial BP (-3.4¿mm¿Hg (-6.9, -0.03), P=0.048), and after additional adjustment for weight change (-2.7¿mm¿Hg (-6.1, 0.4), P=0.11). Adjustment for 24-h urinary excretion of sodium and potassium did not change the results. Diastolic BP yielded similar results. These findings suggest that a BP reduction after weight loss is better maintained when the intake of protein is increased at the expense of carbohydrates. This effect is partly mediated by body weight.
    Genetic and morphological diversity of okra (Abelmoschus esculentus [L.] Moench.) genotypes and their possible relationships, with particular reference to Greek landraces
    Kyriakopoulou, O.G. ; Arens, P.F.P. ; Pelgrom, K.T.B. ; Karapanos, I. ; Bebeli, P. ; Passam, H.C. - \ 2014
    Scientia Horticulturae 171 (2014). - ISSN 0304-4238 - p. 58 - 70.
    numerical-analysis - germplasm - aflp - collection - cultivars - stability - patterns - distance - markers - plants
    Despite its high economic value in many countries (especially in developing regions of the tropics and sub-tropics), okra has received little attention with respect to its source of origin and genetic diversity, particularly at the molecular level. Phenotypic description (morphology, pod characteristics and seed germination) and AFLP (amplified fragment length polymorphism) analysis were performed on Greek and international genotypes. Whereas morphological descriptors did not separate the accessions according to their geographical origin, AFLP analysis revealed a low level (12%) of polymorphism and distinct geographical groupings. Greek germplasm separated into three distinct groups with no overlap between them on the basis of molecular markers. A higher degree of genetic heterogeneity was found (UPGMA analysis) among the accessions of the Boyiatiou group than in the Pylaias group, whereas the occurrence of some common phylogenetic characteristics made separation on the basis of morphology alone difficult. The results from AFLP markers indicate that Greek germplasm constitutes a significant pool of variation with respect to morphological parameters, pod characteristics and seed germinability. Moreover, differences in seed germination among phenotypes may relate to their geographical origin (mainland or islands).
    Analyses of historical and current populations of black grouse in Central Europe reveal strong effects of genetic drift and loss of genetic diversity
    Segelbacher, G. ; Strand, T.M. ; Quintela, M. ; Axelsson, T. ; Jansman, H.A.H. ; Koelewijn, H.P. ; Hoglund, J. - \ 2014
    Conservation Genetics 15 (2014)5. - ISSN 1566-0621 - p. 1183 - 1195.
    major histocompatibility complex - capercaillie tetrao-urogallus - hamster cricetus-cricetus - balancing selection - allele frequencies - climate-change - mhc - loci - markers - differentiation
    Black grouse (Tetrao tetrix) in Central Europe have undergone a severe contraction of their range in recent decades with only a few small isolated remaining populations. Here we compare genetic diversity of two contemporary isolated populations (Sallandse Heuvelrug, Netherlands and Luneburger Heide, Germany) with historical samples from the same region collected within the last one hundred years. We use markers with both putatively neutral and functional variation to test whether the present small and highly fragmented populations hold lower genetic diversity compared to the former larger population. For this we applied three different types of genetic markers: nine microsatellites and 21 single nucleotide polymorphisms (SNPs), both sets which have been found to be neutral, and two functional major histocompatibility complex (MHC) genes for which there is evidence they are under selection. The contemporary small isolated populations displayed lower neutral genetic diversity compared to the corresponding historical samples. Furthermore, samples from Denmark showed that this now extinct population displayed lower genetic variation in the period immediately prior to the local extinction. Population structure was more pronounced among contemporary populations compared to historical populations for microsatellites and SNPs. This effect was not as distinct for MHC which is consistent with the possibility that MHC has been subjected to balancing selection in the past, a process which maintains genetic variation and may minimize population structure for such markers. Genetic differentiation among the present populations highlights the strong effects of population decline on the genetic structure of natural populations, which can be ultimately attributed to habitat loss following anthropogenic land use changes.
    F1 hybrid of cultivated apple (Malus x domestica) and European pear (Pyrus communis) with fertile F2 offspring
    Fischer, T.C. ; Malnoy, M. ; Hofmann, T. ; Schwab, W. ; Palmieri, L. ; Wehrens, H.R.M.J. ; Schuch, L.A. ; Müller, M. ; Schimmelpfeng, H. ; Velasco, R. ; Martens, S. - \ 2014
    Molecular Breeding 34 (2014)3. - ISSN 1380-3743 - p. 817 - 828.
    nuclear-dna content - genetic-linkage maps - flow-cytometry - japanese pear - s-alleles - borkh. - diversity - rosaceae - markers - genome
    The establishment of intergeneric hybrids for horticultural and agricultural crops is still a demanding task for breeding programmes. The aim of such approaches is to introduce new quality and resistance traits and to enlarge the gene pool. Recently, an F1 hybrid between Malus × domestica and Pyrus communis became available which arose from a breeding approach undertaken in the late 1980s by the breeder Max Zwintzscher (Cologne-Vogelsang). Unlike previous reports, viable and fertile F2 plants were obtained from this F1 hybrid line by author HS, providing a unique perspective not only for genomic, transcriptomic and metabolomic studies but also for advanced breeding strategies. Here, we give the first report on the confirmation and characterization of the F1 hybrid by phenotypic, genetic and biochemical means. The intergeneric hybrid shows an intermediary phenotype of leaves, flowers and fruits, and some disorder of secondary shoot growth. Nuclear DNA content is also intermediary and corresponds to a diploid state. Apple and pear type rDNA as well as SI alleles from each genus were found. At the metabolic level, parallel biosynthesis of the apple dihydrochalcone phloridzin and of arbutin, a p-hydroquinone-glucoside typical for pear, take place leading to considerable concentrations of both in leaves. The overall data allow secure confirmation of the hybrid character and give a first insight into the hybrids genetics and physiology.
    Use of Two-Part Regression Calibration Model to Correct for Measurement Error in Episodically Consumed Foods in a Single-Replicate Study Design: EPIC Case Study
    Agogo, G.O. ; Voet, H. van der; Veer, P. van 't; Ferrari, P. ; Leenders, M. ; Muller, D.C. ; Sánchez-Cantalejo, E. ; Bamia, C. ; Braaten, T. ; Knüppel, S. ; Johansson, I. ; Eeuwijk, F.A. van; Boshuizen, H.C. - \ 2014
    PLoS ONE 9 (2014)11. - ISSN 1932-6203 - 15 p.
    dietary self-report - nutrition - cancer - instruments - outcomes - disease - markers
    In epidemiologic studies, measurement error in dietary variables often attenuates association between dietary intake and disease occurrence. To adjust for the attenuation caused by error in dietary intake, regression calibration is commonly used. To apply regression calibration, unbiased reference measurements are required. Short-term reference measurements for foods that are not consumed daily contain excess zeroes that pose challenges in the calibration model. We adapted two-part regression calibration model, initially developed for multiple replicates of reference measurements per individual to a single-replicate setting. We showed how to handle excess zero reference measurements by two-step modeling approach, how to explore heteroscedasticity in the consumed amount with variance-mean graph, how to explore nonlinearity with the generalized additive modeling (GAM) and the empirical logit approaches, and how to select covariates in the calibration model. The performance of two-part calibration model was compared with the one-part counterpart. We used vegetable intake and mortality data from European Prospective Investigation on Cancer and Nutrition (EPIC) study. In the EPIC, reference measurements were taken with 24-hour recalls. For each of the three vegetable subgroups assessed separately, correcting for error with an appropriately specified two-part calibration model resulted in about three fold increase in the strength of association with all-cause mortality, as measured by the log hazard ratio. Further found is that the standard way of including covariates in the calibration model can lead to over fitting the two-part calibration model. Moreover, the extent of adjusting for error is influenced by the number and forms of covariates in the calibration model. For episodically consumed foods, we advise researchers to pay special attention to response distribution, nonlinearity, and covariate inclusion in specifying the calibration model.
    Vroege detectie van dracht bij koeien door Proteomics Biomerkers in melk = Early pregnancy detection using proteomics biomarkers in milk
    Pas, M.F.W. te; Kruijt, L. ; Wit, A.A.C. de; Hulsegge, B. ; Riel, J.W. van; Heeres-van der Tol, J.J. ; Sulkers, H. ; Woelders, H. - \ 2014
    Lelystad : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research nr. 747) - 10
    melkkoeien - zwangerschap - eiwitexpressieanalyse - merkers - melkproductie - melkveehouderij - rundveehouderij - productiebeperkingen - optimalisatie - voortplantingsefficiëntie - dairy cows - pregnancy - proteomics - markers - milk production - dairy farming - cattle husbandry - production restrictions - optimization - reproductive efficiency
    The aim of this study is to develop an accurate, fast, cheap, and reliable test to detect pregnancy before day 35 on the basis of markers in milk. The ultimate goal is to have a method that can be implemented in a practical setting.
    High level of molecular and phenotypic biodiversity in Jatropha curcas from Central America compared to Africa, Asia and South America
    Montes Osorio, L.R. ; Torres Salvador, A.F. ; Jongschaap, R.E.E. ; Azurdia, C. ; Berduo, J. ; Trindade, L.M. ; Visser, R.G.F. ; Loo, E.N. van - \ 2014
    BMC Plant Biology 14 (2014). - ISSN 1471-2229
    net assimilation rate - relative growth-rate - genetic diversity - leaf-area - germplasm collection - biofuel plant - l. accessions - markers - aflp - variability
    Background The main bottleneck to elevate jatropha (Jatropha curcas L.) from a wild species to a profitable biodiesel crop is the low genetic and phenotypic variation found in different regions of the world, hampering efficient plant breeding for productivity traits. In this study, 182 accessions from Asia (91), Africa (35), South America (9) and Central America (47) were evaluated at genetic and phenotypic level to find genetic variation and important traits for oilseed production. Results Genetic variation was assessed with SSR (Simple Sequence Repeat), TRAP (Target Region Amplification Polymorphism) and AFLP (Amplified fragment length polymorphism) techniques. Phenotypic variation included seed morphological characteristics, seed oil content and fatty acid composition and early growth traits. Jaccard’s similarity and cluster analysis by UPGM (Unweighted Paired Group Method) with arithmetic mean and PCA (Principle Component Analysis) indicated higher variability in Central American accessions compared to Asian, African and South American accessions. Polymorphism Information Content (PIC) values ranged from 0 to 0.65. In the set of Central American accessions. PIC values were higher than in other regions. Accessions from the Central American population contain alleles that were not found in the accessions from other populations. Analysis of Molecular Variance (AMOVA; P¿
    Genetic diversity and linkage disequilibrium analysis in elite sugar beet breeding lines and wild beet accessions
    Adetunji, I. ; Willems, G. ; Tschoep, H. ; Bürkholz, A. ; Barnes, S. ; Boer, M.P. ; Malosetti, M. ; Horemans, S. ; Eeuwijk, F. van - \ 2014
    Theoretical and Applied Genetics 127 (2014)3. - ISSN 0040-5752 - p. 559 - 571.
    beta-vulgaris l. - genome-wide association - yellow-vein-virus - population-structure - ssp maritima - rhizomania resistance - restorer gene - markers - map - dna
    Linkage disequilibrium decay in sugar beet is strongly affected by the breeding history, and varies extensively between and along chromosomes, allowing identification of known and unknown signatures of selection. Genetic diversity and linkage disequilibrium (LD) patterns were investigated in 233 elite sugar beet breeding lines and 91 wild beet accessions, using 454 single nucleotide polymorphisms (SNPs) and 418 SNPs, respectively. Principal coordinate analysis suggested the existence of three groups of germplasm, corresponding to the wild beets, the seed parent and the pollen parent breeding pool. LD was investigated in each of these groups, with and without correction for genetic relatedness. Without correction for genetic relatedness, in the pollen as well as the seed parent pool, LD persisted beyond 50 centiMorgan (cM) on four (2, 3, 4 and 5) and three chromosomes (2, 4 and 6), respectively; after correction for genetic relatedness, LD decayed after
    The domestication and evolutionary ecology of apples
    Cornille, A. ; Giraud, T. ; Smulders, M.J.M. ; Roldán-Ruiz, I. ; Gladieux, P. - \ 2014
    Trends in Genetics 30 (2014)2. - ISSN 0168-9525 - p. 57 - 65.
    wild malus-orientalis - genetic-structure - population-structure - venturia-inaequalis - crop domestication - cultivated apple - fruit - sylvestris - markers - mill.
    The cultivated apple is a major fruit crop in temperate zones. Its wild relatives, distributed across temperate Eurasia and growing in diverse habitats, represent potentially useful sources of diversity for apple breeding. We review here the most recent findings on the genetics and ecology of apple domestication and its impact on wild apples. Genetic analyses have revealed a Central Asian origin for cultivated apple, together with an unexpectedly large secondary contribution from the European crabapple. Wild apple species display strong population structures and high levels of introgression from domesticated apple, and this may threaten their genetic integrity. Recent research has revealed a major role of hybridization in the domestication of the cultivated apple and has highlighted the value of apple as an ideal model for unraveling adaptive diversification processes in perennial fruit crops. We discuss the implications of this knowledge for apple breeding and for the conservation of wild apples.
    Postprandial fatty acid specific changes in circulating oxylipins in lean and obese men after high-fat challenge tests
    Strassburg, K. ; Esser, D. ; Vreeken, R.J. ; Hankemeier, T. ; Müller, M.R. ; Duynhoven, J.P.M. van; Golde, J. van; Dijk, S.J. van; Afman, L.A. ; Jacobs, D.M. - \ 2014
    Molecular Nutrition & Food Research 58 (2014)3. - ISSN 1613-4125 - p. 591 - 600.
    eicosanoid biology - markers - health
    Scope Circulating oxylipins may affect peripheral tissues and are assumed to play an important role in endothelial function. They are esterified in triglyceride-rich lipoproteins that are increased after a high-fat (HF) meal, depending on BMI and fatty acid (FA) type. Yet, it is unclear which oxylipins appear in circulation after HF meals differing in FA composition. Methods and results In a double-blind randomized crossover challenge study, we characterized the postprandial oxylipin response after different HF challenges in lean and obese men receiving HF milkshakes, either high in saturated FAs (SFA), monounsaturated FAs (MUFA), or omega 3 (n-3) polyunsaturated FAs (PUFA). Plasma oxylipin profiles were significantly altered at 2 and 4 h after shake consumption when compared to baseline. Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) derived oxylipins increased after n-3 PUFA shake consumption. MUFA shake consumption increased levels of cytochrome P450 mediated oxylipins. SFA shake consumption led to strong increases in linoleic acid (LA) derived HODEs. No differences were observed between lean and obese individuals at baseline and after any shake consumption. Conclusion e are the first demonstrating acute effects on circulating oxylipins after HF meal challenges. These changes were strongly influenced by different dietary FAs and may affect endothelial function.
    A comparison of microsatellites and SNPs in parental assignment in the GIFT strain of Nile tilapia (Oreochromis niloticus): The power of exclusion
    Trong, T.Q. ; Bers, N.E.M. van; Crooijmans, R.P.M.A. ; Dibbits, B.W. ; Komen, J. - \ 2013
    Aquaculture 388-391 (2013). - ISSN 0044-8486 - p. 14 - 23.
    genotyping errors - computer-program - empirical-evaluation - natural-populations - markers - wild - inference - paternity - sibship - salmon
    In this study, parental assignment was studied in the 10th generation of a pedigreed selected Nile tilapia (Oreochromis niloticus) population (GIFT) and their offspring, by comparing two types of molecular markers, microsatellites and SNPs, using an exclusion-based (Vitassign) and a likelihood-based (Cervus) method. For the experiment, G10 parents were divided in 4 groups (cohorts) and allowed to produce offspring by natural group mating. In total 173 offspring were tested against 238 parents, using either 12 microsatellites (PIC = 0.639; exclusion power 68.0%) or 122 SNPs (PIC = 0.341; exclusion power 99.9%). In this study, more than half of the candidate parents were either full- or half-sibs with other parents. Furthermore, 13.8% of the parents died before being sampled for DNA. When offspring were assigned to parents in the same cohort, using Vitassign, for microsatellites, allowing up to 2 mismatches, 37.6% offspring got unique assignments, 45.1% got multiple assignments, and 17.3% were not assigned; for SNPs with up to 15 mismatches allowed, 83.8% offspring got unique assignments while 13.9% got multiple assignments. Only 2.3% were not assigned. Using Cervus, for microsatellites, the mean ‘strict’ (> 95% CF) assignment rate across the 4 cohorts was 18%, the ‘relax’ (80–95% CF) assignment rate was 43%, and 39% were not assigned; for SNPs, 39% ‘strict’ assignments were obtained (mean across 4 cohorts); the remaining offspring were not assigned. In general assignment rates were higher when cohort offspring were assigned to all parents combined, irrespective of method (Vitassign or Cervus) or marker used. However, consistency of assignments between microsatellites and SNPs was low: 28% with Vitassign and 16% with Cervus. Consistency of assignments between Cervus and Vitassign was high with SNPs (65%), but was low with microsatellites (31%). We conclude that missing parents and relatedness among candidate parents resulted in low assignment rates. Furthermore, low exclusion power of the microsatellite set resulted in low assignment rates and multiple parent pair assignments irrespective of method used. Exclusion methods and likelihood-based methods can be equally good for parental assignments, providing that good marker sets with high exclusion power are available.
    Fruit size QTL indentification and the prediction of parental QTL genotypes and breeding values in multiple pedigreed populations of sweet cherry
    Rosyara, U.R. ; Bink, M.C.A.M. ; Weg, W.E. van de; Zhang, G. ; Sebolt, A. ; Dirlewanger, E. ; Quero-Garcia, J. ; Schuster, M. ; Iezzoni, Amy - \ 2013
    Molecular Breeding 32 (2013)4. - ISSN 1380-3743 - p. 875 - 887.
    quantitative trait loci - plant-populations - bayesian-analysis - quality - cross - map - markers - genes - peach - set
    Large fruit size is a critical trait for any new sweet cherry (Prunus avium L.) cultivar, as it is directly related to grower profitability. Therefore, determining the genetic control of fruit size in relevant breeding germplasm is a high priority. The objectives of this study were (1) to determine the number and positions of quantitative trait loci (QTL) for sweet cherry fruit size utilizing data simultaneously from multiple families and their pedigreed ancestors, and (2) to estimate fruit size QTL genotype probabilities and genomic breeding values for the plant materials. The sweet cherry material used was a five-generation pedigree consisting of 23 founders and parents and 424 progeny individuals from four full-sib families, which were phenotyped for fruit size and genotyped with 78 RosCOS single nucleotide polymorphism and 86 simple sequence repeat markers. These data were analyzed by a Bayesian approach implemented in FlexQTL™ software. Six QTL were identified: three on linkage group (G) 2 with one each on groups 1, 3, and 6. Of these QTL, the second G2 QTL and the G6 QTL were previously discovered while other QTL were novel. The predicted QTL genotypes show that some QTL were segregating in all families while other QTL were segregating in a subset of the families. The progeny varied for breeding value, with some progeny having higher breeding values than their parents. The results illustrate the use of multiple pedigree-linked families for integrated QTL mapping in an outbred crop to discover novel QTL and predict QTL genotypes and breeding values.
    Epigenetic changes and transposon reactivation in Thai rice hybrids. Molecular Breeding
    Kantama, L. ; Junbuathong, S. ; Sakulkoo, J. ; Jong, J.H.S.G.M. de; Apisitwanich, S. - \ 2013
    Molecular Breeding 31 (2013)4. - ISSN 1380-3743 - p. 815 - 827.
    cytosine methylation - dna methylation - elements mites - genome - retrotransposons - hybridization - markers - inheritance - activation - expression
    Inter- or intraspecific hybridization is the first step in transferring exogenous traits to the germplasm of a recipient crop. One of the complicating factors is the occurrence of epigenetic modifications of the hybrids, which in turn can change their gene expression and phenotype. In this study we present an analysis of epigenome changes in rice hybrids that were obtained by crossing rice cultivars, most of them of indica type and Thai origin. Comparing amplified fragment length polymorphism (AFLP) fingerprints of twenty-four cultivars, we calculated Nei’s indexes for measuring genetic relationships. Epigenetic changes in their hybrids were established using methylation-sensitive AFLP fingerprinting and transposon display of the rice transposable elements (TEs) Stowaway Os-1 and Mashu, leading to the question whether the relationship between parental genomes is a predictor of epigenome changes, TE reactivation and changes in TE methylation. Our study now reveals that the genetic relationship between the parents and DNA methylation changes in their hybrids is not significantly correlated. Moreover, genetic distance correlates only weakly with Mashu reactivation, whereas it does not correlate with Stowaway Os-1 reactivation. Our observations also suggest that epigenome changes in the hybrids are localized events affecting specific chromosomal regions and transposons rather than affecting the genomic methylation landscape as a whole. The weak correlation between genetic distance and Mashu methylation and reactivation points at only limited influence of genetic background on the epigenetic status of the transposon. Our study further demonstrates that hybridizations between and among specific japonica and indica cultivars induce both genomic DNA methylation and reactivation/methylation change in the Stowaway Os-1 and Mashu transposons. The observed epigenetic changes seem to affect the transposons in a clear manner, partly driven by stochastic processes, which may account for a broader phenotypic plasticity of the hybrids. A better understanding of the epigenome changes leading to such transposon activation can lead to the development of novel tools for more variability in future rice breeding
    Linkage mapping in the oilseed crop Jatropha curcas L. reveals a locus controlling the biosynthesis of phorbol esters which cause seed toxicity
    King, A.J. ; Montes, L.R. ; Clarke, J.G. ; Affleck, J. ; Li, Y. ; Witsenboer, H. ; Vossen, E. van der; Linde, P. van der; Tripathi, Y. ; Tavares, E. ; Shukla, P. ; Rajasekaran, T. ; Loo, E.N. van; Graham, I.A. - \ 2013
    Plant Biotechnology Journal 11 (2013)8. - ISSN 1467-7644 - p. 986 - 996.
    transcriptome analysis - genetic diversity - biofuel plant - genome - oil - markers - qtl - construction - sequence - maps
    Current efforts to grow the tropical oilseed crop Jatropha curcas L. economically are hampered by the lack of cultivars and the presence of toxic phorbol esters (PE) within the seeds of most provenances. These PE restrict the conversion of seed cake into animal feed, although naturally occurring ‘nontoxic’ provenances exist which produce seed lacking PE. As an important step towards the development of genetically improved varieties of J. curcas, we constructed a linkage map from four F2 mapping populations. The consensus linkage map contains 502 codominant markers, distributed over 11 linkage groups, with a mean marker density of 1.8 cM per unique locus. Analysis of the inheritance of PE biosynthesis indicated that this is a maternally controlled dominant monogenic trait. This maternal control is due to biosynthesis of the PE occurring only within maternal tissues. The trait segregated 3 : 1 within seeds collected from F2 plants, and QTL analysis revealed that a locus on linkage group 8 was responsible for phorbol ester biosynthesis. By taking advantage of the draft genome assemblies of J. curcas and Ricinus communis (castor), a comparative mapping approach was used to develop additional markers to fine map this mutation within 2.3 cM. The linkage map provides a framework for the dissection of agronomic traits in J. curcas, and the development of improved varieties by marker-assisted breeding. The identification of the locus responsible for PE biosynthesis means that it is now possible to rapidly breed new nontoxic varieties.
    Assessment of inflammatory resilience in healthy subjects using dietary lipid and glucose challenges
    Wopereis, S. ; Wolvers, D. ; Erk, M. van; Gribnau, M. ; Kremer, B. ; Dorsten, F.A. van; Boelsma, E. ; Garczarek, U. ; Cnubben, N. ; Frenken, L. ; Logt, P. van der; Hendriks, H.F.J. ; Albers, R. ; Duynhoven, J.P.M. van; Ommen, B. van; Jacobs, D.M. - \ 2013
    BMC Medical Genomics 6 (2013). - ISSN 1755-8794 - 16 p.
    type-2 diabetic-patients - necrosis-factor-alpha - oxidative stress - endothelial dysfunction - cytokine concentrations - postprandial variations - fatty-acids - obese men - fish-oil - markers
    Background Resilience or the ability of our body to cope with daily-life challenges has been proposed as a new definition of health, with restoration of homeostasis as target resultant of various physiological stress responses. Challenge models may thus be a sensitive measure to study the body’s health. The objective of this study was to select a dietary challenge model for the assessment of inflammatory resilience. Meals are a challenge to metabolic homeostasis and are suggested to affect inflammatory pathways, yet data in literature are limited and inconsistent. Method The kinetic responses of three different dietary challenges and a water control challenge were assessed on various metabolic and inflammatory markers in 14 healthy males and females using a full cross-over study design. The dietary challenges included glucose (75 g glucose in 300 ml water), lipids (200 ml whipping cream) and a mix of glucose and lipids (same amounts as above), respectively. Blood samples were collected at baseline and at 0.5, 1, 2, 4, 6, 8 and 10 h after consumption of the treatment products. Inflammation (IFN¿, IL-1ß, IL-6, IL-8, IL-10, IL-12p70, TNF-a CRP, ICAM-1, VCAM-1, SAA, E-selectin, P-selectin, thrombomodulin, leukocytes, neutrophils, lymphocytes) and clinical (e.g. glucose, insulin, triglycerides) markers as well as gene expression in blood cells and plasma oxylipin profiles were measured. Results All three dietary challenges induced changes related to metabolic control such as increases in glucose and insulin after the glucose challenge and increases in triglycerides after the lipid challenge. In addition, differences between the challenges were observed for precursor oxylipins and some downstream metabolites including DiHETrE’s and HODE’s. However, none of the dietary challenges induced an acute inflammatory response, except for a modest increase in circulating leukocyte numbers after the glucose and mix challenges. Furthermore, subtle, yet statistically significant increases in vascular inflammatory markers (sICAM-1 and sVCAM-1) were found after the mix challenge, when compared to the water control challenge. Conclusions This study shows that dietary glucose and lipid challenges did not induce a strong acute inflammatory response in healthy subjects, as quantified by an accurate and broad panel of parameters.
    Genetic diversity and differentiation in roses: A gardenrose perspective
    Vukosavljev, M. ; Zhang, J. ; Esselink, G. ; Westende, W.P.C. van 't; Cox, P. ; Visser, R.G.F. ; Arens, P. ; Smulders, M.J.M. - \ 2013
    Scientia Horticulturae 162 (2013). - ISSN 0304-4238 - p. 320 - 332.
    population-structure - markers - identification - varieties - assignment
    tFor the first time genetic diversity among modern garden rose cultivars has been evaluated using a setof 24 microsatellite markers covering most chromosomes. A total of 518 different alleles were obtainedin the set of 138 rose cultivars and this led to the conclusion that in terms of genetic diversity cut rosescan be considered as a subgroup of the garden roses.Genetic differentiation among types of garden roses (Fst= 0.022) was four times that among cut roses,and similar in magnitude to the differentiation among breeders, due to the fact that horticultural groupsand breeders overlap largely in classification. Winter hardy Svejda’s cultivars (Canadian Explorer roses)showed the least similarities to European roses, and introgression from wild species for winter hardinesswas clearly visible. Roses of Harkness and Olesen shared a similar genepool. Comparison of the differen-tiation among linkage groups indicated that linkage group 5 is potentially a region containing importantQTLs for winter hardiness. Linkage group 6 contains the largest amount of genetic diversity, while linkagegroup 2 is the most differentiated among types of garden roses.
    Authentication of geographical origin of palm oil by chromatographic fingerprinting of triacylglycerols an partial least square-discriminant analysis
    Ruiz-Samblas, C. ; Arrebola-Pascual, C. ; Tres, A. ; Ruth, S.M. van; Cuadros-Rodriquez, L. - \ 2013
    Talanta 116 (2013). - ISSN 0039-9140 - p. 788 - 793.
    charged aerosol detection - gas-chromatography - vegetable-oils - universal response - fatty-acids - olive oil - chemometrics - detector - markers
    Main goals of the present work were to develop authentication models based on liquid and gas chromatographic fingerprinting of triacylglycerols (TAGs) from palm oil of different geographical origins in order to compare them. For this purpose, a set of palm oil samples were collected from different continents: South eastern Asia, Africa and South America. For the analysis of the information in these fingerprint profiles, a pattern recognition technique such as partial least square discriminant analysis (PLS-DA) was applied to discriminate the geographical origin of these oils, at continent level. The liquid chromatography, coupled to a charged aerosol detector, (HPLC–CAD) TAGs separation was optimized in terms of mobile phase composition and by means of a solid silica core column. The gas chromatographic method with a mass spectrometer was applied under high temperature (HTGC–MS) in order to analyze the intact TAGs. Satisfactory chromatographic resolution within a short total analysis time was achieved with both chromatographic approaches and without any prior sample treatment. The rates of successful in prediction of the geographical origin of the 85 samples varied between 70% and 100%.
    Biomerkers voor de selectie van robuuste tomatenonderstammen
    Scholten, O.E. ; Lammerts Van Bueren, E. - \ 2013
    merkers - plantenveredeling - biologische plantenveredeling - onderstammen - tomaten - glasgroenten - selectiemethoden - markers - plant breeding - organic plant breeding - rootstocks - tomatoes - greenhouse vegetables - selection methods
    Brochure met onderzoeksinformatie. Het doel van het onderzoek is het ontwikkelen van een snelle en effectieve methode die veredelaars in staat stelt onderstammen te selecteren die ook bij wisselende teeltcondities een goede groeikracht en opbrengst garanderen. Dergelijke robuuste onderstammen moeten het mogelijk maken om het nutriëntgebruik van zowel de gangbare als biologische tomatenteelt efficiënter te maken.
    Multiple inflammatory biomarker detection in a prospective cohort study: a cross-validation between well-established single-biomarker techniques and electrochemiluminescense-based multi-array platform
    Bussel, B.C.T. van; Ferreira, I. ; Waarenburg, M.P.H. ; Greevenbroek, M.M.J. van; Kallen, C.J.H. van der; Henry, R.M.A. ; Feskens, E.J.M. ; Stehouwer, C.D.A. ; Schalkwijk, C.G. - \ 2013
    PLoS ONE 8 (2013)3. - ISSN 1932-6203 - 11 p.
    coronary-artery-disease - public-health practice - low-grade inflammation - cardiovascular-disease - deming regression - atherosclerosis - risk - cytokines - markers - association
    Background - In terms of time, effort and quality, multiplex technology is an attractive alternative for well-established single-biomarker measurements in clinical studies. However, limited data comparing these methods are available. Methods - We measured, in a large ongoing cohort study (n = 574), by means of both a 4-plex multi-array biomarker assay developed by MesoScaleDiscovery (MSD) and single-biomarker techniques (ELISA or immunoturbidimetric assay), the following biomarkers of low-grade inflammation: C-reactive protein (CRP), serum amyloid A (SAA), soluble intercellular adhesion molecule 1 (sICAM-1) and soluble vascular cell adhesion molecule 1 (sVCAM-1). These measures were realigned by weighted Deming regression and compared across a wide spectrum of subjects’ cardiovascular risk factors by ANOVA. Results - Despite that both methods ranked individuals’ levels of biomarkers very similarly (Pearson’s r all=0.755) absolute concentrations of all biomarkers differed significantly between methods. Equations retrieved by the Deming regression enabled proper realignment of the data to overcome these differences, such that intra-class correlation coefficients were then 0.996 (CRP), 0.711 (SAA), 0.895 (sICAM-1) and 0.858 (sVCAM-1). Additionally, individual biomarkers differed across categories of glucose metabolism, weight, metabolic syndrome and smoking status to a similar extent by either method. Conclusions - Multiple low-grade inflammatory biomarker data obtained by the 4-plex multi-array platform of MSD or by well-established single-biomarker methods are comparable after proper realignment of differences in absolute concentrations, and are equally associated with cardiovascular risk factors, regardless of such differences. Given its greater efficiency, the MSD platform is a potential tool for the quantification of multiple biomarkers of low-grade inflammation in large ongoing and future clinical studies.
    Relative validity of the food frequency questionnaire used to assess dietary intake in the Leiden Longevity Study
    Streppel, M.T. ; Vries, J.H.M. de; Meyboom, S. ; Beekman, M. ; Craen, A.J.M. ; Slagboom, P.E. ; Feskens, E.J.M. - \ 2013
    Nutrition Journal 12 (2013). - ISSN 1475-2891 - 8 p.
    basal metabolic-rate - energy-intake - goldberg cutoff - limitations - validation - markers - design
    Background - Invalid information on dietary intake may lead to false diet-disease associations. This study was conducted to examine the relative validity of the food frequency questionnaire (FFQ) used to assess dietary intake in the Leiden Longevity Study. Methods - A total of 128 men and women participating in the Leiden Longevity Study were included in the present validation study. The performance of the FFQ was evaluated using the mean of three 24-hour recalls as the reference method. Evaluation in estimating dietary intake at the group level was done by paired t-tests. The relative validity of the individual energy adjusted level of intake was assessed with correlation analyses (Pearson’s), with correction for measurement error. Results - On group level, the FFQ overestimated as well as underestimated absolute intake of various nutrients and foods. The Bland and Altman plot for total energy intake showed that the agreement between the FFQ and the 24-hour recalls was dependent of intake level. Pearson correlation coefficients ranged from 0.21 (alpha linolenic acid) to 0.78 (ethanol) for nutrients and from -0.02 (legumes, non-significant) to 0.78 (alcoholic beverages) for foods. Adjustment for energy intake slightly lowered the correlation coefficients for nutrients (mean coefficient: 0.48 versus 0.50), while adjustment for within-subject variation in the 24-h recalls resulted in higher correlation coefficients for both nutrients and foods (mean coefficient: 0.69 for nutrients and 0.65 for foods). Conclusions - For most nutrients and foods, the ability of the FFQ to rank subjects was acceptable to good.
    Nutrition of grazing cattle in the Mid Rift Valley of Ethiopia: use of an improved n-alkane method to estimate nutrient intake
    Derseh, M.B. - \ 2013
    Wageningen University. Promotor(en): Wouter Hendriks, co-promotor(en): Wilbert Pellikaan; A. Tolera. - S.l. : s.n. - ISBN 9789461734686 - 160
    rundvee - begrazing - weiden - merkers - voedingsstoffenopname (mens en dier) - voedselsamenstelling - voedingswaarde - verteerbaarheid - ruwvoer (roughage) - diervoeding - ethiopië - cattle - grazing - pastures - markers - nutrient intake - food composition - nutritive value - digestibility - roughage - animal nutrition - ethiopia

    Nutrient intake is an important factor that determines the performance of production animals. In free ranging animals, direct measurement of nutrient intake is difficult to conduct, and it is frequently estimated indirectly by the aid of markers. The aim of this thesis was to investigate the potential of using cuticular n-alkanes and their carbon isotope enrichments (δ13C) as markers to study the nutritional ecology of grazing animals under tropical conditions. In addition, this improved method was used to determine the seasonal patterns of nutrient intake and diet composition of grazing cattle in the Mid Rift Valley grasslands of Ethiopia. The first focus of the thesis was to quantify the interspecies variability in the n-alkane profile and δ13C values of alkanes among commonly available pasture species in the Mid Rift Valley of Ethiopia. The analysis showed that the variability is sufficiently large to allow n-alkane and their δ13C values to be used as diet composition markers, with a combined use of the two increasing the discriminatory power. Faecal recovery of dosed and natural alkanes in cattle consuming low-quality tropical roughages was investigated in an indoor balance study. The recovery of synthetic alkanes dosed in the form of molasses boluses was considerably higher than adjacent natural odd-chain alkanes, and correction appears necessary when intake is estimated with the double n-alkane method. The next focus of the thesis was to generate information on the nutritive value of pasture species and nutritional status of grazing cattle in the region. Large variability was observed in the nutritive value and methane production potential of pasture species as evaluated in vitro, with scope for selection of genotypes with high nutritive value and low methane production potential for a sustainable pastureland management. The nutritional status of grazing cattle measured using a combination of n-alkanes, their δ13C values and visual observations showed that diet composition and nutrient intake of the animals is highly dependent on rainfall patterns, with a cyclic positive (wet period) and negative (dry period) energy and nutrient balance observed over the grazing seasons. Energy intake was more limiting than crude protein for body weight gain in most of the grazing seasons. While mature and non-producing animals appeared to tolerate nutritional restriction in the dry period and regain lost body condition in the following wet periods, young animals before the age of puberty may need supplementary feeding. Furthermore, concentrate supplementation of finishing animals needs to coincide with the onset of the wet season to take advantage of compensatory growth. In conclusion, the n-alkanes method coupled with isotope enrichment in n-alkanes and visual observations as used in the present study can provide realistic nutritional data for free-ranging cattle which correlates well with changes in body conditions.

    Genome-wide association study of osteochondrosis in the tarsocrural joint of Dutch Warmblood horses identifies susceptibility loci on chromosomes 3 and 10
    Orr, N. ; Hill, E.W. ; Gu, G. ; Govindarajan, P. ; Conroy, J. ; Grevenhof, E.M. van; Ducro, B.J. ; Arendonk, J.A.M. van; Knaap, J.H. ; Weeren, P.R. van; Machugh, D.E. ; Ennis, S. ; Brama, P.A. - \ 2013
    Animal Genetics 44 (2013)4. - ISSN 0268-9146 - p. 408 - 412.
    german coldblood horses - manifestations - prevalence - dissecans - markers - fetlock
    Equine osteochondrosis is a developmental joint disease that is a significant source of morbidity affecting multiple breeds of horse. The genetic variants underlying osteochondrosis susceptibility have not been established. Here, we describe the results of a genome-wide association study of osteochondrosis using 90 cases and 111 controls from a population of Dutch Warmblood horses. We report putative associations between osteochondrosis and loci on chromosome 3 (BIEC2-808543; P = 5.03 × 10-7) and chromosome 10 (BIEC2-121323; P = 2.62 × 10-7).
    Unhealthy dietary patterns associated with inflammation and endothelial dysfunction in type 1 diabetes: The EURODIAB study
    Bussel, B.C.T. van; Soedamah-Muthu, S.S. ; Henry, R.M.A. ; Schalkwijk, C.G. ; Ferreira, I. ; Chaturvedi, N. ; Toeller, M. ; Fuller, J.H. ; Stehouwer, C.D.A. - \ 2013
    Nutrition, Metabolism & Cardiovascular Diseases 23 (2013)8. - ISSN 0939-4753 - p. 758 - 764.
    iddm complications - microvascular complications - metabolic syndrome - risk-factors - life-style - determinants - markers - mortality - disease - protein
    Background and aims - A healthy diet has been inversely associated with endothelial dysfunction (ED) and low-grade inflammation (LGI). We investigated the association between nutrient consumption and biomarkers of ED and LGI in type 1 diabetes. Methods and results - We investigated 491 individuals. Nutrient consumption and lifestyle risk factors were measured in 1989 and 1997. Biomarkers of ED (von Willebrand factor, soluble vascular cell adhesion molecule-1 and soluble endothelial selectin) and LGI (C-reactive protein, interleukin 6 and tumour necrosis factor a) were measured in 1997 and averaged into Z-scores. The nutrient residual method was used to adjust individual nutrient intake for energy intake. Data were analysed with generalised estimation equations. We report increments/decrements in nutrient consumption, averaged over time, per +1 standard deviation (SD) of 1997 ED or LGI Z-scores, after adjustment for sex, age, duration of diabetes, investigation centre, body mass index, energy intake, smoking behaviour, alcohol consumption, and each of the other nutrients. One SD elevation in ED Z-score was associated with a diet lower in fibre [ß(95%CI);-0.09(-0.18;-0.004)], polyunsaturated fat [-0.18(-0.31;-0.05)] and vegetable protein [-0.10(-0.20;-0.001)]. For the LGI Z-score results showed associations with fibre [-0.09(-0.17;-0.01)], polyunsaturated fat [-0.14(-0.24;-0.03)] and cholesterol [0.10(0.01; 0.18)]. Conclusion - In type 1 diabetes, consumption of less fibre, polyunsaturated fat and vegetable protein, and more cholesterol over the study period was associated with more ED and LGI. Following dietary guidelines in type 1 diabetes may reduce cardiovascular disease risk by favourably affecting ED and LGI.
    Population structure of Phytophthora infestans in China – geographic clusters and presence of the EU genotype Blue_13
    Li, Y. ; Lee, T.A.J. van der; Zhu, J.H. ; Jin, G.H. ; Lan, C.Z. ; Zhu, S.X. ; Zhang, R.F. ; Liu, B.W. ; Zhao, Z.J. ; Kessel, G.J.T. ; Huang, S.W. ; Jacobsen, E. - \ 2013
    Plant Pathology 62 (2013)4. - ISSN 0032-0862 - p. 932 - 942.
    potato - diversity - haplotypes - virulence - markers - tomato - dna
    The population structure of Phytophthora infestans in China was studied and three mitochondrial haplotypes (Ia, IIa, IIb) were observed. Genetic analysis with 10 highly informative SSR markers identified 68 different genotypes, including three dominant clonal lineages. In the Chinese P. infestans population, the genotypes were strongly clustered according to their geographic origin. One of dominant clonal lineages was genetically similar to Blue_13, a dominant clonal lineage found in Europe since 2004. This is the first report of Blue_13 outside Europe. Only one mating type (A1) was found in the northern and southeastern provinces, but in southern and northwestern China both mating types were observed. The mating type ratio and SSR allele frequencies indicate that in China the sexual cycle of P. infestans is rare. These results emphasize that the migration of asexual propagules and the generation of subclonal variation are the dominant driving factors of the population structure of P. infestans in China. They may also have implications for the role of monitoring P. infestans populations in potato late blight management strategies in China
    Genome-wide SNP analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations
    Goedbloed, D.J. ; Megens, H.J.W.C. ; Hooft, W.F. van; Herrero-Medrano, J. ; Lutz, W. ; Alexandri, P. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. ; Wieren, S.E. van; Ydenberg, R.C. ; Prins, H.H.T. - \ 2013
    Molecular Ecology 22 (2013)3. - ISSN 0962-1083 - p. 856 - 866.
    sus-scrofa - snp discovery - dna - association - diversity - program - ecology - density - markers - set
    Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far-reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genome-wide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele frequency spectrum analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to first-generation hybrids until fifth-generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced-generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome-wide SNP analysis is a promising tool to quantify recent hybridization in free-living populations.
    Quality of core collections for effective utilisation of genetic resources review, discussion and interpretation
    Odong, T.L. ; Jansen, J. ; Eeuwijk, F.A. van; Hintum, T.J.L. van - \ 2013
    Theoretical and Applied Genetics 126 (2013)2. - ISSN 0040-5752 - p. 289 - 305.
    morphological descriptors - germplasm collection - sampling strategies - diversity - algorithm - establishment - accessions - selection - markers - sorghum
    Definition of clear criteria for evaluation of the quality of core collections is a prerequisite for selecting high-quality cores. However, a critical examination of the different methods used in literature, for evaluating the quality of core collections, shows that there are no clear guidelines on the choices of quality evaluation criteria and as a result, inappropriate analyses are sometimes made leading to false conclusions being drawn regarding the quality of core collections and the methods to select such core collections. The choice of criteria for evaluating core collections appears to be based mainly on the fact that those criteria have been used in earlier publications rather than on the actual objectives of the core collection. In this study, we provide insight into different criteria used for evaluating core collections. We also discussed different types of core collections and related each type of core collection to their respective evaluation criteria. Two new criteria based on genetic distance are introduced. The consequences of the different evaluation criteria are illustrated using simulated and experimental data. We strongly recommend the use of the distance-based criteria since they not only allow the simultaneous evaluation of all variables describing the accessions, but they also provide intuitive and interpretable criteria, as compared with the univariate criteria generally used for the evaluation of core collections. Our findings will provide genebank curators and researchers with possibilities to make informed choices when creating, comparing and using core collections
    Analysis of average standardized SSR allele size supports domestication of soybean along the Yellow River
    Li, Y.H. ; Zhang, C. ; Smulders, M.J.M. ; Li, W. ; Ma, Y.S. ; Xu, Qu ; Chang, R.Z. ; Qiu, Li-Juan - \ 2013
    Genetic Resources and Crop Evolution 60 (2013)2. - ISSN 0925-9864 - p. 763 - 776.
    genetic diversity - microsatellite evolution - directional evolution - glycine-max - landraces - markers - origin - maize - wild - length
    Soybean (Glycine max) was domesticated in China from its wild progenitor G. soja. The geographic region of domestication is, however, not exactly known. Here we employed the directional evolution of SSR (microsatellite) repeats (which mutate preferentially into longer alleles) to analyze the domestication process and to infer the most ancestral soybean landraces. In this study, the average standardized SSR allele sizes across 42 SSR loci in 62 accessions of G. soja were determined, and compared with those in 1504 landraces of G. max, collected from all over China and representing the diversity in the gene bank. The standardized SSR allele size in the landraces (0.009) was significantly (P = 8.63 × 10-58) larger than those in G. soja (-0.406). Pairwise comparisons between inferred clusters and sub-clusters of Chinese landraces indicated that the average standardized SSR allele size also increased with the further differentiation of landraces populations. Spring-sowed types had the shortest size, followed by summer-sown types, while the sub-cluster of autumn-sown type had the largest length. The spring-sowed landraces located near the middle region along the Yellow River had the smallest allele sizes, indicating that this is the most ancestral population of cultivated soybean. We concluded that soybean was most likely domesticated in the middle region of the Yellow River in central China, initially as a spring-sown type.
    Discrimination of hybrid classes using cross-species amplification of microsatellite loci: methodological challenges and solutions in Daphnia
    Thielsch, A. ; Volker, E. ; Kraus, R.H.S. ; Schwenk, K. - \ 2012
    Molecular Ecology Resources 12 (2012)4. - ISSN 1755-098X - p. 697 - 705.
    interspecific hybridization - population-structure - longispina complex - genotyping errors - european daphnia - clonal structure - evolution - markers - individuals - cucullata
    Microsatellite markers are important tools in population, conservation and forensic studies and are frequently used for species delineation, the detection of hybridization and introgression. Therefore, marker sets that amplify variable DNA regions in two species are required; however, cross-species amplification is often difficult, as genotyping errors such as null alleles may occur. To estimate the level of potential misidentifications based on genotyping errors, we compared the occurrence of parental alleles in laboratory and natural Daphnia hybrids (Daphnia longispina group). We tested a set of 12 microsatellite loci with regard to their suitability for unambiguous species and hybrid class identification using F1 hybrids bred in the laboratory. Further, a large set of 44 natural populations of D. cucullata, D. galeata and D. longispina (1715 individuals) as well as their interspecific hybrids were genotyped to validate the discriminatory power of different marker combinations. Species delineation using microsatellite multilocus genotypes produced reliable results for all three studied species using assignment tests. Daphnia galeata × cucullata hybrid detection was limited due to three loci exhibiting D. cucullata-specific null alleles, which most likely are caused by differences in primer-binding sites of parental species. Overall, discriminatory power in hybrid detection was improved when a subset of markers was identified that amplifies equally well in both species.
    Genomic Selection for Fruit Quality Traits in Apple (Malus x domestica Borkh.)
    Kumar, S. ; Chagné, D. ; Bink, M.C.A.M. ; Volz, R.K. ; Whitworth, C. ; Carlisle, C. - \ 2012
    PLoS ONE 7 (2012)5. - ISSN 1932-6203
    genetic-relationship information - estimated breeding value - linkage disequilibrium - status number - accuracy - values - prediction - markers - cattle - parameters
    The genome sequence of apple (Malus×domestica Borkh.) was published more than a year ago, which helped develop an 8K SNP chip to assist in implementing genomic selection (GS). In apple breeding programmes, GS can be used to obtain genomic breeding values (GEBV) for choosing next-generation parents or selections for further testing as potential commercial cultivars at a very early stage. Thus GS has the potential to accelerate breeding efficiency significantly because of decreased generation interval or increased selection intensity. We evaluated the accuracy of GS in a population of 1120 seedlings generated from a factorial mating design of four females and two male parents. All seedlings were genotyped using an Illumina Infinium chip comprising 8,000 single nucleotide polymorphisms (SNPs), and were phenotyped for various fruit quality traits. Random-regression best liner unbiased prediction (RR-BLUP) and the Bayesian LASSO method were used to obtain GEBV, and compared using a cross-validation approach for their accuracy to predict unobserved BLUP-BV. Accuracies were very similar for both methods, varying from 0.70 to 0.90 for various fruit quality traits. The selection response per unit time using GS compared with the traditional BLUP-based selection were very high (>100%) especially for low-heritability traits. Genome-wide average estimated linkage disequilibrium (LD) between adjacent SNPs was 0.32, with a relatively slow decay of LD in the long range (r2 = 0.33 and 0.19 at 100 kb and 1,000 kb respectively), contributing to the higher accuracy of GS. Distribution of estimated SNP effects revealed involvement of large effect genes with likely pleiotropic effects. These results demonstrated that genomic selection is a credible alternative to conventional selection for fruit quality traits.
    Estimation of feed intake and digestibility in cattle consuming quality tropical roughage diets using molasses-based n-alkane boluses
    Derseh, M.B. ; Pellikaan, W.F. ; Tolera, A. ; Hendriks, W.H. - \ 2012
    Animal Feed Science and Technology 177 (2012)3-4. - ISSN 0377-8401 - p. 161 - 171.
    dry-matter intake - herbage intake - vegetation communities - detergent fiber - sheep - markers - accuracy - pasture - validation - nutrition
    A feeding experiment was conducted to measure the faecal recovery rates of n-alkanes and to evaluate molasses-based alkane boluses for feed intake and digestibility estimations in cattle consuming low-quality tropical roughages. The experiment was performed in a cross-over design with four experimental diets, four 21-day feeding runs and eight bulls. The animals received a measured amount of the experimental diets that resulted in little refusal throughout the experiment. After seven days of adaptation, the animals were dosed with molasses-based alkane boluses (each containing 200 g C32 and 150 g C36) twice daily at 07:00 and 18:00 h. Concurrent with the alkane dosing, faecal spot samples were taken twice daily until the end of each run. In addition, total faecal collections were performed over the last 5 days of each run. The mean faecal recovery rate of both natural and dosed n-alkanes ranged between 0.61 and 0.86, with the recovery showing an upward trend with increasing carbon-chain length. The recovery rate of dosed alkanes was considerably higher than that of adjacent odd-chain alkanes. Whilst diets did not differ (P=0.23) in the recovery of even-chain n-alkanes, an effect of diet (P=0.01) was observed in the recovery of odd-chain n-alkanes. The faecal concentration of dosed alkanes reached equilibrium 3.30 days into the alkane dosing. On the assumption of similar faecal recovery of adjacent n-alkanes, intake was underestimated by 12% (P
    Nutrients, technological properties and genetic relationships among twenty cowpea landraces cultivated in West Africa
    Madode, Y.E.E. ; Linnemann, A.R. ; Nout, M.J.R. ; Vosman, B.J. ; Hounhouigan, D.J. ; Boekel, T. van - \ 2012
    International Journal of Food Science and Technology 47 (2012)12. - ISSN 0950-5423 - p. 2636 - 2647.
    unguiculata l. walp. - chickpea cicer-arietinum - vigna-unguiculata - aflp analysis - diversity - functionality - markers - protein - dna - variability
    The genetic relationships among twenty phenotypically different cowpea landraces were unravelled regarding their suitability for preparing West African dishes. Amplified fragment length polymorphism classified unpigmented landraces (UPs) as highly similar (65%, one cluster), contrary to pigmented landraces (PLs, three clusters). UPs contained, in g kg-1 d.w., less fibre (24) and phenolics (3) than PLs (56 and 8, respectively) but had bigger seeds (200 g d.w. for 1000 seeds) and lower water absorption capacity at 30 °C (1049 g kg-1) than PLs (139 and 1184, respectively). In g kg-1 d.w., protein (255), ash (39), calcium (0.95), phytate (9.3), iron (0.07) and zinc (0.04) contents were similar. UPs genetic similarities corroborated with their chemical composition and functionality clustered by principal component analysis. Therefore, UPs are well interchangeable regarding chemical composition and suitability for boiled and fried cowpea dishes in contrast to PLs. PLs have potential for innovative product design owing to their functional properties.
    The Development of a Genome Wide SNP Set for the Barnacle Goose Branta leucopsis
    Jonker, R.M. ; Zhang, Q. ; Hooft, W.F. van; Loonen, M.J.J.E. ; Jeugd, H.P. van der; Crooijmans, R.P.M.A. ; Groenen, M.A.M. ; Prins, H.H.T. ; Kraus, Robert - \ 2012
    PLoS ONE 7 (2012)7. - ISSN 1932-6203
    breeding range expansion - migratory connectivity - bird migration - geese - markers - conservation - relatedness - populations - divergence - evolution
    Migratory birds are of particular interest for population genetics because of the high connectivity between habitats and populations. A high degree of connectivity requires using many genetic markers to achieve the required statistical power, and a genome wide SNP set can fit this purpose. Here we present the development of a genome wide SNP set for the Barnacle Goose Branta leucopsis, a model species for the study of bird migration. We used the genome of a different waterfowl species, Mallard Anas platyrhynchos, as a reference to align Barnacle Goose second generation sequence reads from an RRL library and detected 2188 SNPs genome wide. Furthermore, we used chimeric flanking sequences, merged from both Mallard and Barnacle Goose DNA sequence information, to create primers for validation by genotyping. Validation with a 384 SNP genotyping set resulted in 374 (97%) successfully typed SNPs in the assay, of which 358 (96%) were polymorphic. Additionally, we validated our SNPs on relatively old (30 years) museum samples, which resulted in a success rate of at least 80%. This shows that museum samples could be used in standard SNP genotyping assays. Our study also shows that the genome of a related species can be used as reference to detect genome wide SNPs in birds, because genomes of birds are highly conserved. This is illustrated by the use of chimeric flanking sequences, which showed that the incorporation of flanking nucleotides from Mallard into Barnacle Goose sequences lead to equal genotyping performance when compared to flanking sequences solely composed of Barnacle Goose sequence
    Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple
    Chagné, D. ; Crowhurst, R.N. ; Troggio, M. ; Davey, M.W. ; Gilmore, B. ; Lawley, C. ; Vanderzande, S. ; Hellens, R.P. ; Kumar, S. ; Cestaro, A. ; Velasco, R. ; Main, D. ; Rees, J.D. ; Iezzoni, A.F. ; Mockler, T. ; Wilhelm, L. ; Weg, W.E. van de; Gardiner, S.E. ; Bassil, N. ; Peace, C. - \ 2012
    PLoS ONE 7 (2012)2. - ISSN 1932-6203
    x-domestica borkh. - single-nucleotide polymorphisms - transcription factor - malus-domestica - genus vitis - shelf-life - fruit - markers - diversity - discovery
    As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of ‘Golden Delicious’, SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple
    Genetic characterization of a reciprocal translocation present in a widely grown barley variety
    Farré, A. ; Cuadrado, A. ; Lacasa-Benito, I. ; Cistué, L. ; Schubert, I. ; Comadran, J. ; Jansen, J. ; Romagosa, I. - \ 2012
    Molecular Breeding 30 (2012)2. - ISSN 1380-3743 - p. 1109 - 1119.
    in-situ hybridization - nonhomologous chromosomes - genome duplication - hordeum-vulgare - breakpoints - map - localization - interchange - reduction - markers
    Artificially induced translocation stocks have been used to physically map the barley genome; however, natural translocations are extremely uncommon in cultivated genotypes. Albacete is a barley variety widely grown in recent decades in Spain and carrying a reciprocal translocation which obviously does not affect its agronomical fitness. This translocation has been characterized by a combination of cytological and molecular genetic approaches. Firstly, recombination frequencies between markers on chromosomes 1H and 3H were estimated to determine the boundaries of the reciprocal interchange. Secondly, 1H-3H wheat barley telosome addition lines were used to assign selected markers to chromosome arms. Thirdly, fluorescence in situ hybridization (FISH) with rDNA probes (5S and 18S-5.8S-26S) and microsatellite probes [(ACT)5, (AAG)5 and (CAG)5] was used to determine the locations of the translocation breakpoints more precisely. Fourthly, fine-mapping of the regions around the translocation breakpoints was used to increase the marker density for comparative genomics. The results obtained in this study indicate that the translocation is quite large with breakpoints located on the long arms of chromosomes 1H and 3H, between the pericentromeric (AAG)5 bands and above the (ACT)5 interstitial distal bands, resulting in the reciprocal translocation 1HS.1HL-3HL and 3HS.3HL-1HL. The gene content around the translocation breakpoints could be inferred from syntenic relationships observed among different species from the grass family Poaceae (rice, Sorghum and Brachypodium) and was estimated at approximately 1,100 and 710 gene models for 1H and 3H, respectively. Duplicated segments between chromosomes Os01 and Os05 in rice derived from ancestral duplications within the grass family overlap with the translocation breakpoints on chromosomes 1H and 3H in the barley variety Albacete.
    Protein supplementation lowers blood pressure in overweight adults: effect of dietary proteins on blood pressure (PROPRES), a randomized trail
    Teunissen-Beekman, K.F.M. ; Dopheide, J. ; Geleijnse, J.M. ; Bakker, S.J.L. ; Brink, E.J. ; Leeuw, P.W. de; Baak, M.A. van - \ 2012
    American Journal of Clinical Nutrition 95 (2012)4. - ISSN 0002-9165 - p. 966 - 971.
    carbohydrate intake - hypertension - excretion - markers - women - fat
    Background: Dietary protein intake may help to manage blood pressure (BP) and prevent complications associated with elevated BP. Objective: The objective of this study was to determine whether 4 wk of increased protein intake (~25% compared with ~15% of energy intake that isoenergetically replaces carbohydrate intake) lowers office and daytime BP compared with increased carbohydrate intake. Design: A randomized, double-blind, parallel study compared consumption of 3 × 20 g protein/d (20% pea, 20% soy, 30% egg, and 30% milk-protein isolate) with 3 × 20 g maltodextrin/d. Protein or maltodextrin were isoenergetically substituted for a sugar-sweetened drink. Primary outcomes were office and daytime BP. A total of 99 men and women [age range: 20–70 y; BMI (in kg/m2): 25–35] with untreated elevated BP (BP =130/85 and
    Review and simulation of homoplasy and collision in AFLP
    Gort, G. ; Eeuwijk, F.A. van - \ 2012
    Euphytica 183 (2012)3. - ISSN 0014-2336 - p. 389 - 400.
    fragment length distributions - in-silico - markers - bands - probabilities - homology - size
    In this paper we give a short review of the problems of homoplasy and collision in AFLP, and describe a software tool that we developed to illustrate these problems. AFLP is a DNA fingerprinting technique, producing profiles of bands, the result of the separation of DNA fragments by length on a gel or microcapillary system. The profiles are usually interpreted as binary band absence/presence patterns. We focus on two major problems: (1) Within a profile two or more fragments of the same length but of different genomic origin may have been selected, colliding into a single band. This collision problem, akin to the birthday problem, may be surprisingly large. (2) In a pair of profiles two equally long fragments of different genomic origin may have been selected, appearing as identical bands in the two profiles. This is called homoplasy. Both problems are quantified by modeling AFLP as a random sampling technique of fragment lengths. AFLP may be used in phylogenetic studies to estimate the pairwise genetic similarity of individuals. Similarity coefficients like Dice and Jaccard coefficients overestimate the true genetic similarity because of homoplasy, with increasing bias for higher numbers of bands per profile. Corrected estimators are described, which do not suffer from bias. The ideas are illustrated using a new software tool. Data from studies on Arabidopsis and tomato serve as examples. Finally, we make some recommendations with respect to the use of AFLP.
    Dynamics of senescence-related QTLs in potato
    Hurtado Lopez, P.X. ; Schnabel, S.K. ; Zaban, A. ; Vetelainen, M. ; Virtanen, E. ; Eilers, P. ; Eeuwijk, F.A. van; Visser, R.G.F. ; Maliepaard, C.A. - \ 2012
    Euphytica 183 (2012)3. - ISSN 0014-2336 - p. 289 - 302.
    solanum-tuberosum - model - growth - temperature - resistance - gene - chromosome-4 - markers - aflp
    The study of quantitative trait’s expression over time helps to understand developmental processes which occur in the course of the growing season. Temperature and other environmental factors play an important role. The dynamics of haulm senescence was observed in a diploid potato mapping population in two consecutive years (2004 and 2005) under field conditions in Finland. The available time series data were used in a smoothed generalized linear model to characterize curves describing the senescence development in terms of its onset, mean and maximum progression rate and inflection point. These characteristics together with the individual time points were used in a Quantitative trait loci (QTL) analysis. Although QTLs occurring early in the senescence process coincided with QTLs for onset of senescence, the analysis of the time points made it difficult to study senescence as a continuous trait. Characteristics estimated from the senescence curve allowed us to study it as a developmental process and provide a meaningful biological interpretation to the results. Stable QTLs in the two experimental years were identified for progression rate and year-specific QTLs were detected for onset of senescence and inflection point. Specific interactions between loci controlling senescence development were also found. Epistatic interaction between QTLs on chromosomes 4, 5 and 7 were detected in 2004 and pleiotopic effects of QTLs on chromosomes 3 and 4 were observed in 2005.
    Botanical DNA evidence in criminal cases: Knotgrass (Polygonum aviculare L.) as a model species
    Koopman, W.J.M. ; Kuiper, I. ; Klein Geltink, D.J.A. ; Sabatino, G.J.H. ; Smulders, M.J.M. - \ 2012
    Forensic Science International Genetics 6 (2012)3. - ISSN 1872-4973 - p. 366 - 374.
    populus-nigra l. - cannabis-sativa - phenotypic plasticity - self-incompatibility - genetic diversity - mating systems - markers - plants - aflp - identification
    The possibilities and strategies for using DNA characteristics to link a botanical sample to a specific source plant or location vary with its breeding system. For inbreeding species, which often form small patches of identical genotypes, knotgrass (Polygonum aviculare L.) is a suitable model species because of its (1) occurrence in a wide range of natural environments, (2) abundant presence in pieces of evidence, and (3) ease in molecular processing. The value of knotgrass for forensic casework was demonstrated using data from a homicide case. Using the DNA fingerprinting technique AFLP® we were able to identify the knotgrass population at the crime site as the most likely origin of the botanical evidence. We expect that the development of tailored marker systems for knotgrass and other frequently occurring (model) species will considerably accelerate the use of botanical DNA evidence in criminal cases
    Construction of an integrated microsatellite and key morphological characteristic database of potato varieties on the EU common catalogue
    Reid, A. ; Hof, L. ; Felix, G. ; Rucker, B. ; Tams, S. ; Milczynska, E. ; Esselink, G. ; Uenk-Stunnenberg, G.E. ; Vosman, B. ; Weitz, A. - \ 2011
    Euphytica 182 (2011)2. - ISSN 0014-2336 - p. 239 - 249.
    identification - markers - tomato - plants
    The European Union Common Catalogue (EUCC) for potato contains over 1000 varieties. Each year member states add varieties to the list after they have undergone Distinctness, Uniformity and Stability (DUS) testing according to international guidelines. A rapid and robust method for variety identification to aid the management and maintenance of existing variety collections and for the screening of new candidate varieties would therefore be a highly useful tool for DUS testing stations. A database containing key morphological characteristics and microsatellite data was constructed for varieties on the 2006 list of the EUCC for potato. Rules for scoring SSR markers in different laboratories were established to allow a harmonized scoring of markers. Almost all varieties (99.5%) were shown to have unique molecular profiles and in pair wise comparisons 99.99% of all variety pairs could be distinguished. This clearly shows the versatility of the markers and database for identifying potato samples.
    Fish consumption in healthy adults is associated with decreased circulating biomarkers of endothelial dysfunction and inflammation during a 6-year follow-up
    Bussel, B.C.T. van; Henry, R.M.A. ; Schalkwijk, C.G. ; Ferreira, I. ; Feskens, E.J.M. ; Streppel, M.T. ; Smulders, Y.M. ; Twisk, J.W.R. ; Stehouwer, C.D.A. - \ 2011
    The Journal of Nutrition 141 (2011)9. - ISSN 0022-3166 - p. 1719 - 1725.
    c-reactive protein - von-willebrand-factor - dietary history interview - coronary-heart-disease - amsterdam growth - cardiovascular-disease - plasma-concentrations - markers - patterns - mortality
    A healthy diet rich in fish, fruit, and vegetables, moderate in alcoholic beverages, and low in dairy products has been associated with lower circulating concentrations of biomarkers of endothelial dysfunction (ED) and low-grade inflammation (LGI). It is, however, unknown how consumption of these food groups affects ED and/or LGI over time. We measured diet by the computer-assisted crosscheck dietary history method at 36 ± 0.63 y of age (n = 301, women = 161). At 36 and 42 y of age, we measured von Willebrand factor, soluble intercellular adhesion molecule 1 (sICAM-1), soluble endothelial selectin, soluble vascular cell adhesion molecule 1 and soluble thrombomodulin (circulating biomarkers of ED); and C-reactive protein, serum amyloid A, IL-6, IL-8, TNFa, and sICAM-1 (circulating biomarkers of LGI). We investigated the associations between food groups and changes in combined biomarker Z-scores of ED and LGI [higher scores associated with greater risk of (incident) cardiovascular disease]. After adjustment for sex, energy intake, BMI, physical activity, alcohol consumption, smoking behavior, and other food groups, consumption of fish (per 100 g/wk), but none of the other food groups, was inversely associated with changes in ED [ß (95%CI) = -0.06 (-0.10; -0.02); P = 0.003] and LGI [-0.05 (-0.09; -0.003); P = 0.036]. Additionally, EPA+DHA intake was inversely associated with changes in ED [ß (95%CI) = -0.13 (-0.19; -0.07); P = 0.001] and LGI [-0.09 (-0.16; -0.02); P = 0.013] and explained 83 and 40% of the association between fish and changes in ED and LGI. In conclusion, fish consumption, but not fruit, vegetable, alcoholic beverage, or dairy product consumption, was associated with decreased ED and LGI in healthy adults.
    Identification of high utility SNPs for population assignment and traceability purposes in the pig using high-throughput sequencing
    Ramos, A.M. ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Schook, L.B. ; Groenen, M.A.M. - \ 2011
    Animal Genetics 42 (2011)6. - ISSN 0268-9146 - p. 613 - 620.
    nucleotide polymorphism discovery - multilocus genotype data - reduced representation - breed assignment - markers - genome - cattle - technology - inference - assay
    The objectives of this study were to develop breed-specific single nucleotide polymorphisms (SNPs) in five pig breeds sequenced with Illumina's Genome Analyzer and to investigate their usefulness for breed assignment purposes. DNA pools were prepared for Duroc, Landrace, Large White, Pietrain and Wild Boar. The total number of animals used for sequencing was 153. SNP discovery was performed by aligning the filtered reads against Build 7 of the pig genome. A total of 313,964 high confidence SNPs were identified and analysed for the presence of breed-specific SNPs (defined in this context as SNPs for which one of the alleles was detected in only one breed). There were 29,146 putative breed-specific SNPs identified, of which 4441 were included in the PorcineSNP60 beadchip. Upon re-examining the genotypes obtained using the beadchip, 193 SNPs were confirmed as being breed specific. These 193 SNPs were subsequently used to assign an additional 490 individuals from the same breeds, using the sequenced individuals as reference populations. In total, four breed assignment tests were performed. Results showed that for all methods tested 99% of the animals were correctly assigned, with an average probability of assignment of at least 99.2%, indicating the high utility of breed-specific markers for breed assignment and traceability. This study provides a blueprint for the way next-generation sequencing technologies can be used for the identification of breed-specific SNPs, as well as evidence that these SNPs may be a powerful tool for breed assignment and traceability of animal products to their breeds of origin.
    Towards F1 Hybrid Seed Potato Breeding
    Lindhout, P. ; Meijer, D.A. ; Schotte, T. ; Hutten, R.C.B. ; Visser, R.G.F. ; Eck, H.J. van - \ 2011
    Potato Research 54 (2011)4. - ISSN 0014-3065 - p. 301 - 312.
    plantenveredeling - plantenveredelingsmethoden - hybridisatie - hybriden - diploïdie - zelfincompatibiliteit - aardappelen - plant breeding - plant breeding methods - hybridization - hybrids - diploidy - self incompatibility - potatoes - species solanum-chacoense - inhibitor sli gene - self-compatibility - quantitative trait - diploid potatoes - yield - heterosis - sequence - markers - tomato
    Compared to other major food crops, progress in potato yield as the result of breeding efforts is very slow. Genetic gains cannot be fixed in potato due to obligatory out-breeding. Overcoming inbreeding depression using diploid self-compatible clones should enable to replace the current method of out-breeding and clonal propagation into an F1 hybrid system with true seeds. This idea is not new, but has long been considered unrealistic. Severe inbreeding depression and self-incompatibility in diploid germplasm have hitherto blocked the development of inbred lines. Back-crossing with a homozygous progenitor with the Sli gene which inhibits gametophytic self-incompatibility gave self-compatible offspring from elite material from our diploid breeding programme. We demonstrate that homozygous fixation of donor alleles is possible, with simultaneous improvement of tuber shape and tuber size grading of the recipient inbred line. These results provide proof of principle for F1 hybrid potato breeding. The technical and economic perspectives are unprecedented as these will enable the development of new products with combinations of useful traits for all stakeholders in the potato chain. In addition, the hybrid’s seeds are produced by crossings, rendering the production and voluminous transport of potato seed tubers redundant as it can be replaced by direct sowing or the use of healthy mini-tubers, raised in greenhouses.
    No evident spatial genetic structuring in the rapidly declining Black-tailed Godwit Limosa limosa in the Netherlands
    Trimbos, K.B. ; Kentie, R. ; Verkuil, Y. ; Musters, C.J.M. ; Piersma, Th. ; Snoo, G.R. de - \ 2011
    Conservation Genetics 12 (2011)3. - ISSN 1566-0621 - p. 629 - 636.
    population-genetics - software - markers - microsatellites - management - regression - diversity - program - tests - dna
    With 40% of the European Black-tailed Godwit population breeding in The Netherlands, this country harbours internationally significant numbers of this species. However, ongoing agricultural intensification has resulted in the fragmentation of the population and drastic population declines since 1967. By establishing genetic diversity, genetic differentiation and gene flow on the basis of 12 microsatellites, we investigated whether the population genetic structure of the Dutch Black-tailed Godwit bears the marks of these changes. Genetic diversity appeared to be moderate, and Bayesian model-based analysis of individual genotypes revealed no clustering in the Dutch populations. This was supported by pairwise FST values and AMOVA, which indicated no differentiation among the nine breeding areas. Gene flow estimates were larger than “one migrant per generation” between sample locations, and no isolation by distance was demonstrated. Our results indicate the maintenance of moderate levels of genetic diversity and genetic connectivity between breeding sites throughout the Dutch Black-tailed Godwit breeding population. We suggest that the Dutch Black-tailed Godwit breeding areas should be managed as a single panmictic unit, much as it is presently done
    Detection of Mycosphaerella graminicola in Wheat Leaves by a Microsatellite Dinucleotide Specific-Primer
    Abd-Elsalam, K. ; Bahkali, A.H. ; Moslem, M. ; Wit, P.J.G.M. de; Verreet, J.A. - \ 2011
    International Journal of Molecular Sciences 12 (2011)1. - ISSN 1661-6596 - p. 682 - 693.
    real-time pcr - septoria-tritici - stagonospora-nodorum - plant-pathogens - rapid detection - markers - assay - diagnostics - resistance - diseases
    Early detection of infection is very important for efficient management of Mycosphaerella graminicola leaf blotch. To monitor and quantify the occurrence of this fungus during the growing season, a diagnostic method based on real-time PCR was developed. Standard and real-time PCR assays were developed using SYBR Green chemistry to quantify M. graminicola in vitro or in wheat samples. Microsatellite dinucleotide specific-primers were designed based on microsatellite repeats of sequences present in the genome of M. graminicola. Specificity was checked by analyzing DNA of 55 M. graminicola isolates obtained from different geographical origins. The method appears to be highly specific for detecting M. graminicola; no fluorescent signals were observed from 14 other closely related taxa. Primer (CT) 7 G amplified a specific amplicon of 570 bp from all M. graminicola isolates. The primers did not amplify DNA extracted from 14 other fungal species. The approximate melting temperature (Tm) of the (CT) 7 G primer was 84.2 °C. The detection limit of the real-time PCR assay with the primer sets (CT) 7 G is 10 fg/25 µL, as compared to 10 pg/25 µL using conventional PCR technology. From symptomless leaves, a PCR fragment could be generated two days after inoculation. Both conventional and real-time PCR could successfully detect the fungus from artificially inoculated wheat leaves. However, real-time PCR appeared much more sensitive than conventional PCR. The developed quantitative real-time PCR method proved to be rapid, sensitive, speci¿c, cost-effective and reliable for the identi¿cation and quanti¿cation of M. graminicola in wheat
    A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome
    Boer, J.M. de; Borm, T.J.A. ; Jesse, T. ; Brugmans, B.W. ; Tang, X. ; Bryan, G.J. ; Bakker, J. ; Eck, H.J. van; Visser, R.G.F. - \ 2011
    BMC Genomics 12 (2011). - ISSN 1471-2164 - 60 p.
    quantitative trait loci - candidate genes - disease resistance - linkage map - tomato - aflp - solanum - markers - dna - construction
    Background Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH). Results First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP) BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map. Conclusions The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches.
    Mitochondrial DNA signature for range-wide populations of Bicyclus anynana suggests a rapid expansion from recent refugia
    Jong, M.A. de; Wahlberg, N. ; Eijk, M. van; Brakefield, P.M. ; Zwaan, B.J. - \ 2011
    PLoS ONE 6 (2011)6. - ISSN 1932-6203 - 5 p.
    lepidoptera - butterflies - plasticity - biology - systematics - haplotypes - neutrality - evolution - selection - markers
    This study investigates the genetic diversity, population structure and demographic history of the afrotropical butterfly Bicyclus anynana using mitochondrial DNA (mtDNA). Samples from six wild populations covering most of the species range from Uganda to South Africa were compared for the cytochrome c oxidase subunit gene (COI). Molecular diversity indices show overall high mtDNA diversity for the populations, but low nucleotide divergence between haplotypes. Our results indicate relatively little geographic population structure among the southern populations, especially given the extensive distributional range and an expectation of limited gene flow between populations. We implemented neutrality tests to assess signatures of recent historical demographic events. Tajima's D test and Fu's FS test both suggested recent population growth for the populations. The results were only significant for the southernmost populations when applying Tajima's D, but Fu's FS indicated significant deviations from neutrality for all populations except the one closest to the equator. Based on our own findings and those from pollen and vegetation studies, we hypothesize that the species range of B. anynana was reduced to equatorial refugia during the last glacial period, and that the species expanded southwards during the past 10.000 years. These results provide crucial background information for studies of phenotypic and molecular adaptation in wild populations of B. anynana
    Belowground DNA-based techniques: untangling the network of plant root interactions
    Mommer, L. ; Dumbrell, A.J. ; Wagemaker, C.A.M. ; Ouborg, N.J. - \ 2011
    Plant and Soil 348 (2011)1-2. - ISSN 0032-079X - p. 115 - 121.
    molecular-identification - niche differentiation - species composition - soil - biodiversity - diversity - markers - distributions - competition - depth
    Pea powdery mildew er1 resistance is associated to loss-of-function mutations at a MLO homologous locus
    Pavan, S.N.C. ; Schiavulli, A. ; Appiano, M. ; Visser, R.G.F. ; Bai, Y. - \ 2011
    Theoretical and Applied Genetics 123 (2011)8. - ISSN 0040-5752 - p. 1425 - 1431.
    pisum-sativum l. - gene - markers - er-1 - ol-2 - rapd
    The powdery mildew disease affects several crop species and is also one of the major threats for pea (Pisum sativum L.) cultivation all over the world. The recessive gene er1, first described over 60 years ago, is well known in pea breeding, as it still maintains its efficiency as a powdery mildew resistance source. Genetic and phytopathological features of er1 resistance are similar to those of barley, Arabidopsis, and tomato mlo powdery mildew resistance, which is caused by the loss of function of specific members of the MLO gene family. Here, we describe the obtainment of a novel er1 resistant line by experimental mutagenesis with the alkylating agent diethyl sulfate. This line was found to carry a single nucleotide polymorphism in the PsMLO1 gene sequence, predicted to result in premature termination of translation and a non-functional protein. A cleaved amplified polymorphic sequence (CAPS) marker was developed on the mutation site and shown to be fully co-segregating with resistance in F2 individuals. Sequencing of PsMLO1 from three powdery mildew resistant cultivars also revealed the presence of loss-of-function mutations. Taken together, results reported in this study strongly indicate the identity between er1 and mlo resistances and are expected to be of great breeding importance for the development of resistant cultivars via marker-assisted selection.
    Identification of Mendelian inconsistencies between SNP and pedigree Information of Sibs
    Calus, M.P.L. ; Mulder, H.A. ; Bastiaansen, J.W.M. - \ 2011
    Genetics, Selection, Evolution 43 (2011)1. - ISSN 0999-193X
    dairy-cattle - genomic evaluation - breeding value - technical-note - selection - misidentification - population - assignment - markers - impact
    Background Using SNP genotypes to apply genomic selection in breeding programs is becoming common practice. Tools to edit and check the quality of genotype data are required. Checking for Mendelian inconsistencies makes it possible to identify animals for which pedigree information and genotype information are not in agreement. Methods Straightforward tests to detect Mendelian inconsistencies exist that count the number of opposing homozygous marker (e.g. SNP) genotypes between parent and offspring (PAR-OFF). Here, we develop two tests to identify Mendelian inconsistencies between sibs. The first test counts SNP with opposing homozygous genotypes between sib pairs (SIBCOUNT). The second test compares pedigree and SNP-based relationships (SIBREL). All tests iteratively remove animals based on decreasing numbers of inconsistent parents and offspring or sibs. The PAR-OFF test, followed by either SIB test, was applied to a dataset comprising 2,078 genotyped cows and 211 genotyped sires. Theoretical expectations for distributions of test statistics of all three tests were calculated and compared to empirically derived values. Type I and II error rates were calculated after applying the tests to the edited data, while Mendelian inconsistencies were introduced by permuting pedigree against genotype data for various proportions of animals. Results Both SIB tests identified animal pairs for which pedigree and genomic relationships could be considered as inconsistent by visual inspection of a scatter plot of pairwise pedigree and SNP-based relationships. After removal of 235 animals with the PAR-OFF test, SIBCOUNT (SIBREL) identified 18 (22) additional inconsistent animals. Seventeen animals were identified by both methods. The numbers of incorrectly deleted animals (Type I error), were equally low for both methods, while the numbers of incorrectly non-deleted animals (Type II error), were considerably higher for SIBREL compared to SIBCOUNT. Conclusions Tests to remove Mendelian inconsistencies between sibs should be preceded by a test for parent-offspring inconsistencies. This parent-offspring test should not only consider parent-offspring pairs based on pedigree data, but also those based on SNP information. Both SIB tests could identify pairs of sibs with Mendelian inconsistencies. Based on type I and II error rates, counting opposing homozygotes between sibs (SIBCOUNT) appears slightly more precise than comparing genomic and pedigree relationships (SIBREL) to detect Mendelian inconsistencies between sibs
    Gene and QTL detection in a three-way barley cross under selection by a mixed model with kinship information using SNPs
    Malosetti, M. ; Eeuwijk, F.A. van; Boer, M. ; Casas, A. ; Elia, M. ; Bhat, P. ; Ramsay, L. ; Molina-Cano, J.L. - \ 2011
    Theoretical and Applied Genetics 122 (2011)8. - ISSN 0040-5752 - p. 1605 - 1616.
    quantitative trait loci - major genes - environmental covariables - flowering time - dwarfing gene - heading date - line crosses - inbred lines - markers - maize
    Quantitative trait locus (QTL) detection is commonly performed by analysis of designed segregating populations derived from two inbred parental lines, where absence of selection, mutation and genetic drift is assumed. Even for designed populations, selection cannot always be avoided, with as consequence varying correlation between genotypes instead of uniform correlation. Akin to linkage disequilibrium mapping, ignoring this type of genetic relatedness will increase the rate of false-positives. In this paper, we advocate using mixed models including genetic relatedness, or kinship information for QTL detection in populations where selection forces operated. We demonstrate our case with a three-way barley cross, designed to segregate for dwarfing, vernalization and spike morphology genes, in which selection occurred. The population of 161 inbred lines was screened with 1,536 single nucleotide polymorphisms (SNPs), and used for gene and QTL detection. The coefficient of coancestry matrix was estimated based on the SNPs and imposed to structure the distribution of random genotypic effects. The model incorporating kinship, coancestry, information was consistently superior to the one without kinship (according to the Akaike information criterion). We show, for three traits, that ignoring the coancestry information results in an unrealistically high number of markertrait associations, without providing clear conclusions about QTL locations. We used a number of widely recognized dwarfing and vernalization genes known to segregate in the studied population as landmarks or references to assess the agreement of the mapping results with a priori candidate gene expectations. Additional QTLs to the major genes were detected for all traits as well. Electronic supplementary material
    Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos)
    Kraus, R.H.S. ; Kersten, H.H.D. ; Hooft, W.F. van; Crooijmans, R.P.M.A. ; Poel, J.J. van der; Elmberg, J. ; Vignal, A. ; Huang, Y. ; Li, N. ; Prins, H.H.T. ; Groenen, M.A.M. - \ 2011
    BMC Genomics 12 (2011). - ISSN 1471-2164 - 11 p.
    pathogenic avian influenza - conservation - divergence - markers - virus - birds - power - base - map
    Background - Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard DNA and compared our data with ongoing genome and EST sequencing of domesticated conspecifics. This is the first study of its kind for waterfowl. Results - More than one billion base pairs of sequence information were generated resulting in a 16× coverage of a reduced representation library of the mallard genome. Sequence reads were aligned to a draft domesticated duck reference genome and allowed for the detection of over 122,000 SNPs within our mallard sequence dataset. In addition, almost 62,000 nucleotide positions on the domesticated duck reference showed a different nucleotide compared to wild mallard. Approximately 20,000 SNPs identified within our data were shared with SNPs identified in the sequenced domestic duck or in EST sequencing projects. The shared SNPs were considered to be highly reliable and were used to benchmark non-shared SNPs for quality. Genotyping of a representative sample of 364 SNPs resulted in a SNP conversion rate of 99.7%. The correlation of the minor allele count and observed minor allele frequency in the SNP discovery pool was 0.72. Conclusion We identified almost 150,000 SNPs in wild mallards that will likely yield good results in genotyping. Of these, ~101,000 SNPs were detected within our wild mallard sequences and ~49,000 were detected between wild and domesticated duck data. In the ~101,000 SNPs we found a subset of ~20,000 SNPs shared between wild mallards and the sequenced domesticated duck suggesting a low genetic divergence. Comparison of quality metrics between the total SNP set (122,000 + 62,000 = 184,000 SNPs) and the validated subset shows similar characteristics for both sets. This indicates that we have detected a large amount (~150,000) of accurately inferred mallard SNPs, which will benefit bird evolutionary studies, ecological studies (e.g. disentangling migratory connectivity) and industrial breeding programs.
    Toetsen op agressief snot in bloembollen
    Doorn, J. van; Martin, W.S. ; Vreeburg, P.J.M. ; Korsuize, C.A. ; Dees, R.H.L. - \ 2011
    bloembollen - plantenziekten - erwinia - pectobacterium carotovorum subsp. carotovorum - dna - merkers - verspreiding - onderzoek - ornamental bulbs - plant diseases - erwinia - pectobacterium carotovorum subsp. carotovorum - dna - markers - dispersal - research
    Presentatie over toetsen op agressief snot in bloembollen. Het doel is het snel en gevoelig kunnen toetsen van bolmateriaal, vooral op Dickeya (kwaliteitsverbetering) en het vinden van isolaat_specifieke DNA merkers voor verspreidingsonderzoek (waar komt agressief snot nu vandaan)
    Genetic mapping in Lilium: mapping of major genes and quantitative trait loci for several ornamental traits and disease resistances
    Shahin, A. ; Arens, P.F.P. ; Heusden, S. van; Linden, C.G. van der; Kaauwen, M.P.W. van; Nadeem Khan, M. ; Schouten, H.J. ; Weg, W.E. van de; Visser, R.G.F. ; Tuyl, J.M. van - \ 2011
    Plant Breeding 130 (2011)3. - ISSN 0179-9541 - p. 372 - 382.
    diversity arrays technology - linkage map - zea-mays - segregation distortion - wild relatives - durum-wheat - markers - dart - construction - pollination
    Construction of genetic linkage maps for lily was achieved using two populations, LA and AA that share one parent ‘Connecticut King’. Three different molecular marker systems (AFLP™, DArT and NBS profiling) were used in generating linkage maps for ‘Connecticut King’. The LA and the AA populations consist of 20 and 21 linkage groups (LGs), respectively. Average density between markers was 3.9 cM for the LA and 5 cM for the AA population. Several horticultural traits were mapped for the first time in Lilium and showed to be single gene based. We propose to name these genes as LFCc for flower colour, lfs for flower spots, LSC for stem colour, lal for antherless phenotype and lfd for flower direction whereby upper and lower case names refer to dominant and recessive genes, respectively. Additionally, resistance to Lily mottle virus (LMoV) was mapped as a locus on LG AA10. For Fusarium resistance, the Kruskal–Wallis test identified six putative quantitative trait loci (QTL) in the AA population of which one QTL (explaining 25% of the variation in resistance) could be confirmed by interval mapping
    A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei)
    Ciobanu, D.C. ; Bastiaansen, J.W.M. ; Magrin, J. ; Rocha, J.L. ; Jiang, D.H. ; Yu, N. ; Geiger, B. ; Deeb, N. ; Rocha, D. ; Gong, H. ; Kinghorn, B.P. ; Plastow, G.S. ; Steen, H.A.M. van der; Mileham, A.J. - \ 2010
    Animal Genetics 41 (2010)1. - ISSN 0268-9146 - p. 39 - 47.
    taura-syndrome virus - pig skeletal-muscle - linkage map - glycogen-content - penaeus - markers - mutation - resistance - discovery - growth
    Bioinformatics and re-sequencing approaches were used for the discovery of sequence polymorphisms in Litopenaeus vannamei. A total of 1221 putative single nucleotide polymorphisms (SNPs) were identified in a pool of individuals from various commercial populations. A set of 211 SNPs were selected for further molecular validation and 88% showed variation in 637 samples representing three commercial breeding lines. An association analysis was performed between these markers and several traits of economic importance for shrimp producers including resistance to three major viral diseases. A small number of SNPs showed associations with test weekly gain, grow-out survival and resistance to Taura Syndrome Virus. Very low levels of linkage disequilibrium were revealed between most SNP pairs, with only 11% of SNPs showing an r2-value above 0.10 with at least one other SNP. Comparison of allele frequencies showed small changes over three generations of the breeding programme in one of the commercial breeding populations. This unique SNP resource has the potential to catalyse future studies of genetic dissection of complex traits, tracing relationships in breeding programmes, and monitoring genetic diversity in commercial and wild populations of L. vannamei
    Population genetic analysis of Fusarium asiaticum populations from barley suggest a recent shift favoring 3ADON producers in southern Chin
    Zhang, H. ; Zhang, Z. ; Lee, T.A.J. van der; Xu, J. ; Xu, J.S. ; Yang, L. ; Yu, D. ; Waalwijk, C. ; Feng, J. - \ 2010
    Phytopathology 100 (2010)4. - ISSN 0031-949X - p. 328 - 336.
    head blight pathogen - gibberella-zeae - graminearum clade - united-states - wheat scab - chemotypes - diversity - deoxynivalenol - culmorum - markers
    Fusarium asiaticum is the predominant causal agent of Fusarium head blight (FHB) in southern China. The genetic diversity was assessed by analyzing 448 single-spore F. asiaticum isolates from 18 sampling sites that were 10 to 2,000 km apart, using seven highly informative variable number of tandem repeat (VNTR) markers. This analysis showed a significant degree of population subdivision (P <0.001) among populations from upper, middle, and lower valleys of the Yangtze River, with little gene flow (Nm = 1.210). We observed a strong association between this genetic population subdivision and the mycotoxin produced. Our results show that the dramatic cline in trichothecene chemotypes may be explained by a recent and significant invasion of 3-acetyldeoxynivalenol (3ADON) producers in FHB pathogen composition in the middle valley. Using Bayesian statistics, we found a biased gene flow from 3ADON to nivalenol (NIV) populations. In addition, we observed significant genetic differentiation and linkage disequilibrium between NIV- and 3ADON-producing isolates at the same sampling sites. The impact of the changed agronomy and trade of cereal commodities on the spread of the new Fusarium population and the consequent increase of FHB observed in southern China are discussed.
    A SNP based linkage map of the turkey genome reveals multiple intrachromosomal rearrangements between the Turkey and Chicken genomes
    Aslam, M.L. ; Bastiaansen, J.W.M. ; Crooijmans, R.P.M.A. ; Vereijken, A. ; Groenen, M.A.M. ; Megens, H.J.W.C. - \ 2010
    BMC Genomics 11 (2010). - ISSN 1471-2164
    gene density - avian genome - evolution - microchromosomes - recombination - conservation - galliformes - pattern - markers - gallus
    Background The turkey (Meleagris gallopavo) is an important agricultural species that is the second largest contributor to the world's poultry meat production. The genomic resources of turkey provide turkey breeders with tools needed for the genetic improvement of commercial breeds of turkey for economically important traits. A linkage map of turkey is essential not only for the mapping of quantitative trait loci, but also as a framework to enable the assignment of sequence contigs to specific chromosomes. Comparative genomics with chicken provides insight into mechanisms of genome evolution and helps in identifying rare genomic events such as genomic rearrangements and duplications/deletions. Results Eighteen full sib families, comprising 1008 (35 F1 and 973 F2) birds, were genotyped for 775 single nucleotide polymorphisms (SNPs). Of the 775 SNPs, 570 were informative and used to construct a linkage map in turkey. The final map contains 531 markers in 28 linkage groups. The total genetic distance covered by these linkage groups is 2,324 centimorgans (cM) with the largest linkage group (81 loci) measuring 326 cM. Average marker interval for all markers across the 28 linkage groups is 4.6 cM. Comparative mapping of turkey and chicken revealed two inter-, and 57 intrachromosomal rearrangements between these two species. Conclusion Our turkey genetic map of 531 markers reveals a genome length of 2,324 cM. Our linkage map provides an improvement of previously published maps because of the more even distribution of the markers and because the map is completely based on SNP markers enabling easier and faster genotyping assays than the microsatellitemarkers used in previous linkage maps. Turkey and chicken are shown to have a highly conserved genomic structure with a relatively low number of inter-, and intrachromosomal rearrangements.
    Adipose tissue dysfunction signals progression of hepatic steatosis towards nonalcoholic steatohepatitis in C57BL/6 mice
    Duval, C.N.C. ; Thissen, U. ; Keshtkar, S. ; Accart, B. ; Stienstra, R. ; Boekschoten, M.V. ; Roskams, T. ; Kersten, A.H. ; Müller, M.R. - \ 2010
    Diabetes 59 (2010)12. - ISSN 0012-1797 - p. 3181 - 3191.
    fatty liver-disease - insulin-resistance - copy number - obesity - leptin - inflammation - fibrosis - nash - adiponectin - markers
    Objective: Nonalcoholic fatty liver disease (NAFLD) is linked to obesity and diabetes, suggesting an important role of adipose tissue in the pathogenesis of NAFLD. Here we aim to investigate the interaction between adipose tissue and liver in NAFLD, and identify potential early plasma markers that predict NASH. Research Design and Methods: C57Bl/6 mice were chronically fed a high fat diet to induce NAFLD and compared with mice fed low fat diet. Extensive histological and phenotypical analyses coupled with a time-course study of plasma proteins using multiplex assay was performed. Results: Mice exhibited pronounced heterogeneity in liver histological scoring, leading to classification into 4 subgroups: LF-low (LFL) responders displaying normal liver morphology, LF-high (LFH) responders showing benign hepatic steatosis, HF-low (HFL) responders displaying pre-NASH with macrovesicular lipid droplets, and HF-high (HFH) responders exhibiting overt NASH characterized by ballooning of hepatocytes, presence of Mallory bodies, and activated inflammatory cells. Compared to HFL responders, HFH mice gained weight more rapidly and exhibited adipose tissue dysfunction characterized by decreased final fat mass, enhanced macrophage infiltration and inflammation, and adipose tissue remodelling. Plasma haptoglobin, IL-1ß, TIMP-1, adiponectin and leptin were significantly changed in HFH mice. Multivariate analysis indicated that in addition to leptin, plasma CRP, haptoglobin, eotaxin and MIP-1a early in the intervention were positively associated with liver triglycerides. Intermediate prognostic markers of liver triglycerides included IL-18, IL-1ß, MIP-1¿ and MIP-2, whereas insulin, TIMP-1, GCP-2 and MPO emerged as late markers. Conclusions: Our data support the existence of a tight relationship between adipose tissue dysfunction and NASH pathogenesis and point to several novel potential predictive biomarkers for NASH
    Regional differences in recombination hotspots between two chicken populations
    Elferink, M.G. ; As, P. van; Veenendaal, A. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. - \ 2010
    BMC Genetics 11 (2010). - ISSN 1471-2156
    ascites-related traits - whole genome scan - linkage map - physical map - broilers - markers
    Background Although several genetic linkage maps of the chicken genome have been published, the resolution of these maps is limited and does not allow the precise identification of recombination hotspots. The availability of more than 3.2 million SNPs in the chicken genome and the recent advances in high throughput genotyping techniques enabled us to increase marker density for the construction of a high-resolution linkage map of the chicken genome. This high-resolution linkage map allowed us to study recombination hotspots across the genome between two chicken populations: a purebred broiler line and a broiler × broiler cross. In total, 1,619 animals from the two different broiler populations were genotyped with 17,790 SNPs. Results The resulting linkage map comprises 13,340 SNPs. Although 360 polymorphic SNPs that had not been assigned to a known chromosome on chicken genome build WASHUC2 were included in this study, no new linkage groups were found. The resulting linkage map is composed of 31 linkage groups, with a total length of 3,054 cM for the sex-average map of the combined population. The sex-average linkage map of the purebred broiler line is 686 cM smaller than the linkage map of the broiler × broiler cross. Conclusions In this study, we present a linkage map of the chicken genome at a substantially higher resolution than previously published linkage maps. Regional differences in recombination hotspots between the two mapping populations were observed in several chromosomes near the telomere of the p arm; the sex-specific analysis revealed that these regional differences were mainly caused by female-specific recombination hotspots in the broiler × broiler cross.
    Including copy number variation in association studies to predict genotypic values
    Calus, M.P.L. ; Koning, de, D.J. ; Haley, C.S. - \ 2010
    Genetics Research 92 (2010)2. - ISSN 0016-6723 - p. 115 - 125.
    wide linkage disequilibrium - human genome - mutation-rates - genetic risk - disease - polymorphism - markers - cattle - snps - microsatellite
    The objective of this study was to investigate, both empirically and deterministically, the ability to explain genetic variation resulting from a copy number polymorphism (CNP) by including the CNP, either by its genotype or by a continuous derivation thereof, alone or together with a nearby single nucleotide polymorphism (SNP) in the model. This continuous measure of a CNP genotype could be a raw hybridization measurement, or a predicted CNP genotype. Results from simulations showed that the linkage disequilibrium (LD) between an SNP and CNP was lower than LD between two SNPs, due to the higher mutation rate at the CNP loci. The model R2 values from analysing the simulated data were very similar to the R2 values predicted with the deterministic formulae. Under the assumption that x copies at a CNP locus lead to the effect of x times the effect of 1 copy, including a continuous measure of a CNP locus in the model together with the genotype of a nearby SNP increased power to explain variation at the CNP locus, even when the continuous measure explained only 15% of the variation at the CNP locus.
    Identity-by-Descent Matrix Decomposition Using Latent Ancestral Allele Models
    Braak, C.J.F. ter; Boer, M.P. ; Totir, L. ; Winkler, C.R. ; Smith, O.S. ; Bink, M.C.A.M. - \ 2010
    Genetics 185 (2010)3. - ISSN 0016-6731 - p. 1045 - 1057.
    quantitative trait loci - population-structure - plant-populations - genotype data - association - stratification - prediction - regression - selection - markers
    Genetic linkage and association studies are empowered by proper modeling of relatedness among individuals. Such relatedness can be inferred from marker and/or pedigree information. In this study, the genetic relatedness among n inbred individuals at a particular locus is expressed as an n x n square matrix Q. The elements of Q are identity-by-descent probabilities, that is, probabilities that two individuals share an allele descended from a common ancestor. In this representation the definition of the ancestral alleles and their number remains implicit. For human inspection and further analysis, an explicit representation in terms of the ancestral allele origin and the number of alleles is desirable. To this purpose, we decompose the matrix Q by a latent class model with K classes (latent ancestral alleles). Let P be an n x K matrix with assignment probabilities of n individuals to K classes constrained such that every element is nonnegative and each row sums to 1. The problem then amounts to approximating Q by PPT, while disregarding the diagonal elements. This is not an eigenvalue problem because of the constraints on P. An efficient algorithm for calculating P is provided. We indicate the potential utility of the latent ancestral allele model. For representative locus-specific Q matrices constructed for a set of maize inbreds, the proposed model recovered the known ancestry.
    Codominant scoring of AFLP in association panels
    Gort, G. ; Eeuwijk, F.A. van - \ 2010
    Theoretical and Applied Genetics 121 (2010)2. - ISSN 0040-5752 - p. 337 - 351.
    likelihood ratio test - normal mixture - collision probabilities - em approach - markers - model - information
    A study on the codominant scoring of AFLP markers in association panels without prior knowledge on genotype probabilities is described. Bands are scored codominantly by fitting normal mixture models to band intensities, illustrating and optimizing existing methodology, which employs the EM-algorithm. We study features that improve the performance of the algorithm, and the unmixing in general, like parameter initialization, restrictions on parameters, data transformation, and outlier removal. Parameter restrictions include equal component variances, equal or nearly equal distances between component means, and mixing probabilities according to Hardy–Weinberg Equilibrium. Histogram visualization of band intensities with superimposed normal densities, and optional classification scores and other grouping information, assists further in the codominant scoring. We find empirical evidence favoring the square root transformation of the band intensity, as was found in segregating populations. Our approach provides posterior genotype probabilities for marker loci. These probabilities can form the basis for association mapping and are more useful than the standard scoring categories A, H, B, C, D. They can also be used to calculate predictors for additive and dominance effects. Diagnostics for data quality of AFLP markers are described: preference for three-component mixture model, good separation between component means, and lack of singletons for the component with highest mean. Software has been developed in R, containing the models for normal mixtures with facilitating features, and visualizations. The methods are applied to an association panel in tomato, comprising 1,175 polymorphic markers on 94 tomato hybrids, as part of a larger study within the Dutch Centre for BioSystems Genomics.
    Genetic diversity and genetic similarities between Iranian rose species
    Samiei, L. ; Naderi, R. ; Khalighi, A. ; Shahnejat-Bushehri, A.A. ; Mozaffarian, V. ; Esselink, G.D. ; Kazempour Osaloo, S. ; Smulders, M.J.M. - \ 2010
    Journal of Horticultural Science and Biotechnology 85 (2010)3. - ISSN 1462-0316 - p. 231 - 237.
    damascena mill. accessions - microsatellite analysis - phylogenetic-relationships - genus rosa - markers - aflp - ssr - identification - differentiation - varieties
    Wild rose species were collected from different regions of Iran for a rose breeding programme. They included accessions from Rosa persica, R. foetida, R. pimpinellifolia, R. hemisphaerica, R. canina, R. iberica, R. damascena, R. beggeriana, and R. orientalis. Ten microsatellite (simple sequence repeat; SSR) markers were used to analyse the genetic variation among these rose species. The SSR markers amplified alleles in all species, even if they were from different sections within the genus. An unweighted pair group method cluster analysis (UPGMA) based on similarity values revealed five main Groups. The data showed no support for any distinction between R. canina and R. iberica, as all the accessions were placed in one Group, and accessions of these two species were more closely-related to each other within a Province than to accessions of the same species in other Provinces. Accessions of sect. Pimpinellifoliae were combined with plants from sect. Rosa and Cinnamomeae in two different Groups. Genetically, R. persica clustered distinctly from all others, with few alleles shared with the other taxa. We discuss the use of SSR markers for phylogenetic analysis when these markers are amplified in all species of a genus
    Tobacco blue mould disease caused by Peronospora hyoscyami f. sp. tabacina
    Borrás-Hidalgo, O. ; Thomma, B.P.H.J. ; Silva, Y. ; Chacón, O. ; Pujol, M. - \ 2010
    Molecular Plant Pathology 11 (2010)1. - ISSN 1464-6722 - p. 13 - 18.
    systemic acquired-resistance - nicotiana-tabacum - fungal spores - mosaic-virus - markers - gene - identification - beta-1,3-glucanase - pathogens - transport
    Blue mould [Peronospora hyoscyami f. sp. tabacina (Adam) Skalicky 1964] is one of the most important foliar diseases of tobacco that causes significant losses in the Americas, south-eastern Europe and the Middle East. This review summarizes the current knowledge of the mechanisms employed by this oomycete pathogen to colonize its host, with emphasis on molecular aspects of pathogenicity. In addition, key biochemical and molecular mechanisms involved in tobacco resistance to blue mould are discussed. Taxonomy: Kingdom: Chromista (Straminipila); Phylum: Heterokontophyta; Class: Oomycete; Order: Peronosporales; Family: Peronosporaceae; Genus: Peronospora; Species: Peronospora hyoscyami f. sp. tabacina. Disease symptoms: The pathogen typically causes localized lesions on tobacco leaves that appear as single, or groups of, yellow spots that often coalesce to form light-brown necrotic areas. Some of the leaves exhibit grey to bluish downy mould on their lower surfaces. Diseased leaves can become twisted, such that the lower surfaces turn upwards. In such cases, the bluish colour of the diseased plants becomes quite conspicuous, especially under moist conditions when sporulation is abundant. Hence the name of the disease: tobacco blue mould. Infection process: The pathogen develops haustoria within plant cells that are thought to establish the transfer of nutrients from the host cell, and may also act in the delivery of effector proteins during infection. Resistance: Several defence responses have been reported to occur in the Nicotiana tabacum-P. hyoscyami f. sp. tabacina interaction. These include the induction of pathogenesis-related genes, and a correlated increase in the activities of typical pathogenesis-related proteins, such as peroxidases, chitinases, ß-1,3-glucanases and lipoxygenases. Systemic acquired resistance is one of the best characterized tobacco defence responses activated on pathogen infection
    A pipeline for high throughput detection and mapping of SNPs from EST databases
    Anithakumari, A.M. ; Tang, Jifeng ; Eck, H.J. van; Visser, R.G.F. ; Leunissen, J.A.M. ; Vosman, B. ; Linden, C.G. van der - \ 2010
    Molecular Breeding 26 (2010)1. - ISSN 1380-3743 - p. 65 - 75.
    single-nucleotide polymorphisms - map-based cloning - linkage maps - genome - markers - potato - discovery - construction - varieties - haplotype
    Single nucleotide polymorphisms (SNPs) represent the most abundant type of genetic variation that can be used as molecular markers. The SNPs that are hidden in sequence databases can be unlocked using bioinformatic tools. For efficient application of these SNPs, the sequence set should be error-free as much as possible, targeting single loci and suitable for the SNP scoring platform of choice. We have developed a pipeline to effectively mine SNPs from public EST databases with or without quality information using QualitySNP software, select reliable SNP and prepare the loci for analysis on the Illumina GoldenGate genotyping platform. The applicability of the pipeline was demonstrated using publicly available potato EST data, genotyping individuals from two diploid mapping populations and subsequently mapping the SNP markers (putative genes) in both populations. Over 7000 reliable SNPs were identified that met the criteria for genotyping on the GoldenGate platform. Of the 384 SNPs on the SNP array approximately 12% dropped out. For the two potato mapping populations 165 and 185 SNPs segregating SNP loci could be mapped on the respective genetic maps, illustrating the effectiveness of our pipeline for SNP selection and validation. Electronic supplementary material The online version of this article (doi:10.1007/s11032-009-9377-5) contains supplementary material, which is available to authorized users
    Isolation and characterization of six microsatellite loci in the larch budmoth Zeiraphera diniana (Lepidoptera: Tortricidae)
    Delamaire, S. ; Esselink, G.D. ; Samiei, L. ; Courtin, C.M. ; Magnoux, E. ; Rousselet, J. ; Smulders, M.J.M. - \ 2010
    European Journal of Entomology 107 (2010)2. - ISSN 1210-5759 - p. 267 - 269.
    host races - markers - dna - l.
    Six microsatellite markers were developed for the larch budmoth Zeiraphera diniana Guénée 1845, using two enrichment protocols. The number of alleles ranged from 3 to 15 per locus and observed heterozygosities ranged from 0.09 to 0.98 for the 69 individuals genotyped. Using these markers significant genetic differentiation between one population from Poland and samples from Alpine populations in France and Switzerland (overall FST = 0.0298) was detected. However, the two Alpine samples did not differ significantly. These microsatellite markers are valuable tools for studying the population genetics of Zeiraphera diniana.
    Genetic composition of cultured and wild mussels Mytilus from The Netherlands and transfers from Ireland and Great Britain
    Kijewski, T. ; Wijsman, J.W.M. ; Hummel, H. ; Wenne, R. - \ 2009
    Aquaculture 287 (2009)3-4. - ISSN 0044-8486 - p. 292 - 296.
    galloprovincialis - populations - edulis - trossulus - coast - selection - markers - protein - hybrids - zone
    The genetic composition of wild and cultured mussel populations from the Oosterschelde, The Netherlands, is compared to representative samples of mussel shipments from culture sites in Ireland and Great Britain. A total of 2272 mussels from 27 samples were assayed for the nuclear DNA markers Me 15116, EFbis and M7. The three markers showed similar patterns of taxonomic consistency across the mussel samples. However, some variation between markers was observed. While, all samples were almost "pure" Mytilus edulis, nevertheless Dutch wild populations Were more admixed with M. galloprovincialis and M. trossulus alleles than those from eastern Ireland, Wales and southern England. The mixed allele genotypes (hybrids) indicate the pre-existing occurrence of non-indigenous Mytilus taxa or natural introgression into Oosterschelde. Our results demonstrated that at the genetic level. there is no immediate threat from the introduction of nonindigenous Mytilus taxa through import from the studied sites in Ireland and Great Britain into the Oosterschelde. However, it is possible that with the import of mussels, M. galloprovincialis will be translocated, especially in the face of expected climate changes in the future.
    Association of 1-y changes in diet pattern with cardiovascular disease risk factors and adipokines: results from the 1-y randomized Oslo Diet and Exercise Study
    Jacobs, D.R. ; Sluik, D. ; Rokling-Andersen, M.H. ; Anderssen, S.A. ; Drevon, C.A. - \ 2009
    American Journal of Clinical Nutrition 89 (2009)2. - ISSN 0002-9165 - p. 509 - 517.
    insulin-resistance - atherosclerosis mesa - adipose-tissue - inflammation - markers - food - intervention - carbohydrate - obesity - women
    Background: We hypothesized that favorable changes in dietary patterns would lead to a reduction in body size and an improvement in metabolic status. Objective: The objective was to study changes in diet patterns relative to changes in body size, blood pressure, and circulating concentrations of lipids, glucose, insulin, adiponectin, and other cytokines in the context of a 1-y randomized intervention study. Design: For 1 y, 187 men aged 45 +/- 2 y, approximate to 50% of whom met the criteria of the metabolic syndrome, were randomly assigned to a diet protocol (n = 45), an exercise protocol (n = 48), a protocol of diet plus exercise (n = 58), or a control protocol (n = 36). A previously defined a priori diet score was created by summing tertile rankings of 35 food group variables; a higher score generally reflected recommended dietary changes in the trial (mean +/- SD at baseline: 31 +/- 6.5; range: 15-47). Results: Over the study year, the diet score increased by approximate to 2 +/- 5.5 in both diet groups, with a decrease of an equivalent amount in the exercise and control groups. The weight change was 23.5 +/- 0.6 kg/10-point change in diet score (P <0.0001), similarly within each intervention group, independently of the change in energy intake or baseline age and smoking status. Weight change was attenuated but remained significant after adjustment for intervention group and percentage body fat. Subjects with an increased diet score had more favorable changes in other body size variables, systolic blood pressure, and blood lipid, glucose, insulin, and adiponectin concentrations. Change in diet score was unrelated to resistin and several cytokines. Conclusion: The change toward a more favorable diet pattern was associated with improved body size and metabolic profile. Am J Clin Nutr 2009; 89: 509-17.
    Development and use of a monoclonal antibody to detect semi-digested proteins of the English grain aphid, Sitobion avenae, in the guts of ladybird beetle predators
    Gao, S.J. ; Zhou, X.R. ; Pang, B.P. ; Loon, J.J.A. van; Zhao, G.Q. - \ 2009
    Entomologia Experimentalis et Applicata 133 (2009)2. - ISSN 0013-8703 - p. 193 - 198.
    bemisia-tabaci - elisa - markers - prey - pcr
    A monoclonal antibody (McAb), EGA-4A9, was developed to detect the semi-digested proteins of the English grain aphid, Sitobion avenae (Fabricius) (Hemiptera: Aphididae), in predatory ladybird beetles (species of the genera Adonia, Coccinella, Hippodamia, and Propylea) using the gut homogenate of Adonia variegata (Goeze) (Coleoptera: Coccinellidae) adults which had fed on S. avenae as immunogen. The McAb was selected by screening hybridoma lines for antibodies that bound with the semi-digested aphid proteins in ladybirds. A double antibody sandwich enzyme-linked immuno-sorbent assay (ELISA) using ClonotypingTM System/HRP showed that it belonged to the IgG2a isotype. It did not cross-react with any of the 21 arthropod species tested besides the ladybird beetles fed on S. avenae with an indirect ELISA. It could still detect the semi-digested proteins in the gut of a ladybird adult, kept at 25 °C, that had ingested one aphid 6 days before. The extended antigen detection period and the high specificity of the antibody indicated that EGA-4A9 could be used to study interactions between English grain aphids and their ladybird predators in the field. Between 28 and 72% of coccinellids collected from the field were positive for English grain aphid protein by ELISA. The percentage of McAb-positive predatory ladybird beetles was positively correlated with the density of S. avenae in wheat fields
    Reliability of Genomic Predictions Across Multiple Populations
    Roos, S. de; Hayes, B.J. ; Goddard, M.E. - \ 2009
    Genetics 183 (2009). - ISSN 0016-6731 - p. 1545 - 1553.
    linkage disequilibrium - genetic risk - wide association - selection - accuracy - cattle - disease - information - markers - traits
    Genomic prediction of future phenotypes or genetic merit using dense SNP genotypes can be used for prediction of disease risk, forensics, and genomic selection of livestock and domesticated plant species. The reliability of genomic predictions is their squared correlation with the true genetic merit and indicates the proportion of the genetic variance that is explained. As reliability relies heavily on the number of phenotypes, combining data sets from multiple populations may be attractive as a way to increase reliabilities, particularly when phenotypes are scarce. However, this strategy may also decrease reliabilities if the marker effects are very different between the populations. The effect of combining multiple populations on the reliability of genomic predictions was assessed for two simulated cattle populations, A and B, that had diverged for T = 6, 30, or 300 generations. The training set comprised phenotypes of 1000 individuals from population A and 0, 300, 600, or 1000 individuals from population B, while marker density and trait heritability were varied. Adding individuals from population B to the training set increased the reliability in population A by up to 0.12 when the marker density was high and T = 6, whereas it decreased the reliability in population A by up to 0.07 when the marker density was low and T = 300. Without individuals from population B in the training set, the reliability in population B was up to 0.77 lower than in population A, especially for large T. Adding individuals from population B to the training set increased the reliability in population B to close to the same level as in population A when the marker density was sufficiently high for the marker–QTL linkage disequilibrium to persist across populations. Our results suggest that the most accurate genomic predictions are achieved when phenotypes from all populations are combined in one training set, while for more diverged populations a higher marker density is required.
    Eukaryotic transcriptomics in silico: Optimizing cDNA-AFLP efficiency
    Stölting, K.N. ; Gort, G. ; Wüst, C. ; Wilson, A.B. - \ 2009
    BMC Genomics 10 (2009). - ISSN 1471-2164 - 15 p.
    full-length cdnas - differential gene-expression - identification - distributions - resistance - sequences - resources - markers - library - plant
    Background - Complementary-DNA based amplified fragment length polymorphism (cDNA-AFLP) is a commonly used tool for assessing the genetic regulation of traits through the correlation of trait expression with cDNA expression profiles. In spite of the frequent application of this method, studies on the optimization of the cDNA-AFLP assay design are rare and have typically been taxonomically restricted. Here, we model cDNA-AFLPs on all 92 eukaryotic species for which cDNA pools are currently available, using all combinations of eight restriction enzymes standard in cDNA-AFLP screens. Results - In silco simulations reveal that cDNA pool coverage is largely determined by the choice of individual restriction enzymes and that, through the choice of optimal enzyme combinations, coverage can be increased from
    Zoeken naar genen voor melkvetsamenstelling : milk genomics-onderzoek vindt twee genen die een grote rol spelen in de genetische verschillen in melkvetsamenstelling
    Schennink, A. ; Visker, M.H.P.W. ; Arendonk, J.A.M. van - \ 2009
    Veeteelt 26 (2009)7. - ISSN 0168-7565 - p. 10 - 12.
    melkveehouderij - melkkoeien - melkvet - samenstelling - melksamenstelling - heritability - dierveredeling - merkers - dairy farming - dairy cows - milk fat - composition - milk composition - heritability - animal breeding - markers
    Verschillen in de samenstelling van het melkvet zijn voor een groot deel erfelijk bepaald. Twee genen spelen een grote rol in deze verschillen. Merkerinformatie kan in de toekomst gebruikt worden om te selecteren op een verbeterde samenstelling van het melkvet
    Homoplasy corrected estimation of genetic similarity from AFLP bands, and the effect of the number of bands on the precision of estimation
    Gort, G. ; Hintum, T.J.L. van; Eeuwijk, F.A. van - \ 2009
    Theoretical and Applied Genetics 119 (2009)3. - ISSN 0040-5752 - p. 397 - 416.
    fragment length distributions - collision probabilities - species relationships - size homoplasy - diversity - markers - homology - lettuce - genome - barley
    AFLP is a DNA fingerprinting technique, resulting in binary band presence–absence patterns, called profiles, with known or unknown band positions. We model AFLP as a sampling procedure of fragments, with lengths sampled from a distribution. Bands represent fragments of specific lengths. We focus on estimation of pairwise genetic similarity, defined as average fraction of common fragments, by AFLP. Usual estimators are Dice (D) or Jaccard coefficients. D overestimates genetic similarity, since identical bands in profile pairs may correspond to different fragments (homoplasy). Another complicating factor is the occurrence of different fragments of equal length within a profile, appearing as a single band, which we call collision. The bias of D increases with larger numbers of bands, and lower genetic similarity. We propose two homoplasy- and collision-corrected estimators of genetic similarity. The first is a modification of D, replacing band counts by estimated fragment counts. The second is a maximum likelihood estimator, only applicable if band positions are available. Properties of the estimators are studied by simulation. Standard errors and confidence intervals for the first are obtained by bootstrapping, and for the second by likelihood theory. The estimators are nearly unbiased, and have for most practical cases smaller standard error than D. The likelihood-based estimator generally gives the highest precision. The relationship between fragment counts and precision is studied using simulation. The usual range of band counts (50–100) appears nearly optimal. The methodology is illustrated using data from a phylogenetic study on lettuce
    A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate
    Groenen, M.A.M. ; Wahlberg, O. ; Foglio, M. ; Cheng, H.H. ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Besnier, F. ; Lathrop, A. ; Muir, W.M. ; Wong, G.K. ; Gut, I. ; Andersson, L. - \ 2009
    Genome Research 19 (2009). - ISSN 1088-9051 - p. 510 - 519.
    genetic maps - physical map - sex - chromosome - evolution - polymorphisms - frequencies - difference - inversion - markers
    The resolution of the chicken consensus linkage map has been dramatically improved in this study by genotyping 12,945 single nucleotide polymorphisms (SNPs) on three existing mapping populations in chicken: the Wageningen (WU), East Lansing (EL), and Uppsala (UPP) mapping populations. As many as 8599 SNPs could be included, bringing the total number of markers in the current consensus linkage map to 9268. The total length of the sex average map is 3228 cM, considerably smaller than previous estimates using the WU and EL populations, reflecting the higher quality of the new map. The current map consists of 34 linkage groups and covers at least 29 of the 38 autosomes. Sex-specific analysis and comparisons of the maps based on the three individual populations showed prominent heterogeneity in recombination rates between populations, but no significant heterogeneity between sexes. The recombination rates in the F1 Red Jungle fowl/White Leghorn males and females were significantly lower compared with those in the WU broiler population, consistent with a higher recombination rate in purebred domestic animals under strong artificial selection. The recombination rate varied considerably among chromosomes as well as along individual chromosomes. An analysis of the sequence composition at recombination hot and cold spots revealed a strong positive correlation between GC-rich sequences and high recombination rates. The GC-rich cohesin binding sites in particular stood out from other GC-rich sequences with a 3.4-fold higher density at recombination hot spots versus cold spots, suggesting a functional relationship between recombination frequency and cohesin binding
    Iridoid and caffeoyl phenylethanoid glycosides of the endangered carnivorous plant Pinguicula lusitanica L. (Lentibulariaceae)
    Grevenstuk, T. ; Hooft, J.J.J. van der; Vervoort, J.J.M. ; Waard, P. de; Romano, A. - \ 2009
    Biochemical Systematics and Ecology 37 (2009)4. - ISSN 0305-1978 - p. 285 - 289.
    spe-nmr - markers - chemotaxonomy - glucosides - hyphenation - vulgaris - veronica - families
    This work reports for the first time the identification of the major compounds of Pinguicula lusitanica, an endangered carnivorous plant species, using minimal amounts of plant material. A methanol extract was prepared from in vitro cultured plantlets and analyzed by HPLC–SPE–NMR/HPLC–MS. Three iridoid and five caffeoyl phenylethanoid glycosides were identified. These groups of natural compounds were previously reported in the Lentibulariaceae family and have been used as chemotaxonomic markers in related families.
    Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) landraces from the East African highlands
    Asfaw, A. ; Blair, M.W. ; Almekinders, C.J.M. - \ 2009
    Theoretical and Applied Genetics 120 (2009)1. - ISSN 0040-5752 - p. 1 - 12.
    iberian peninsula - markers - variability - origin - fabaceae - allozyme - centers - races - pool - rapd
    The East African highlands are a region of important common bean production and high varietal diversity for the crop. The objective of this study was to uncover the diversity and population structure of 192 landraces from Ethiopia and Kenya together with four genepool control genotypes using morphological phenotyping and microsatellite marker genotyping. The germplasm represented different common bean production ecologies and seed types common in these countries. The landraces showed considerable diversity that corresponded well to the two recognized genepools (Andean and Mesoamerican) with little introgression between these groups. Mesoamerican genotypes were predominant in Ethiopia while Andean genotypes were predominant in Kenya. Within each country, landraces from different collection sites were clustered together indicating potential gene flow between regions within Kenya or within Ethiopia. Across countries, landraces from the same country of origin tended to cluster together indicating distinct germplasm at the national level and limited gene flow between the two countries highlighting divided social networks within the regions and a weak trans-national bean seed exchange especially for landrace varieties. One exception to this may be the case of small red-seeded beans where informal cross-border grain trade occurs. We also observed that genetic divergence was slightly higher for the Ethiopian landraces compared to Kenyan landraces and that Mesoamerican genotypes were more diverse than the Andean genotypes. Common beans in eastern Africa are often cultivated in marginal, risk-prone farming systems and the observed landrace diversity should provide valuable alleles for adaptation to stressful environments in future breeding programs in the region
    Differential recognition of Phytophthora infestans races in potato R4 breeding lines
    Poppel, P.M.J.A. van; Huigen, D.J. ; Govers, F. - \ 2009
    Phytopathology 99 (2009)10. - ISSN 0031-949X - p. 1150 - 1155.
    blight resistance - disease resistance - avirulence genes - downy mildew - virulence - effector - inheritance - markers - locus - specificities
    Introgression breeding has resulted in several potato lines that are resistant to late blight, a devastating plant disease caused by the oomycete Phytophthora infestans. The traditional differential set consists of potato lines with 11 late blight resistance specificities, referred to as R1 to R11. With the exception of the R4 locus, all the resistance loci in these lines have been genetically mapped or positioned in resistance (R) gene clusters. In this study, we show that potato lines that are defined to carry R4 do not necessarily recognize the same P. infestans strains. Field isolates appeared to be avirulent on either the R4 differential developed by Mastenbroek or the one developed by Black but not on both. Previously, we identified the avirulence gene PiAvr4, which is a member of the RXLR effector family. In planta expression of PiAvr4 revealed that recognition of PiAvr4 is strictly confined to the Mastenbroek R4 differential. Segregation of the trait in two independent F1 progenies showed that late blight resistance in this differential is determined by a single dominant gene, now referred to as R4Ma.
    Hoornloze koeien in aantocht
    Windig, J.J. - \ 2009
    V-focus 2003 (2009)6. - ISSN 1574-1575 - p. 26 - 27.
    melkveehouderij - melkkoeien - zwartbont - hoornloosheid - dierveredeling - merkers - selectief fokken - dairy farming - dairy cows - holstein-friesian - polled condition - animal breeding - markers - selective breeding
    Hoornloosheid komt bij enkele koeienrassen voor. Om het in de huidige melkkoe in te fokken, zou een fokprogramma hulp kunnen bieden. De veehouderij vindt gebruik van zo'n programma prima, de gemiddelde burger is daar wat terughoudender in en ook meer verdeeld.
    Autosomal and sex-linked microsatellite loci in the green oak leaf roller Tortrix viridana L.
    Schroeder, H.C. ; Arens, P.F.P. ; Smulders, M.J.M. - \ 2009
    Molecular Ecology Resources 9 (2009)3. - ISSN 1755-098X - p. 809 - 811.
    identification - markers
    Eight microsatellite markers were developed for the lepidopteran species Tortrix viridana using an enrichment protocol. The loci were highly variable with number of alleles ranging from four to 38. Six of the eight loci were in Hardy¿Weinberg equilibrium. The other two were linked to the Z-chromosome. Values of observed heterozygosity ranged for the autosomal loci from 0.510 to 0.957. All loci will be useful to study dispersal and the autosomal loci, as well for phylogeographical studies.
    Genetic variability in yam cultivars from Guinea-Sudan of Benin assessed by random amplified polymorphic DNA
    Zannou, A. ; Agbicodo, E. ; Zoundjihékpon, J. ; Struik, P.C. ; Ahanchédé, A. ; Kossou, D.K. ; Sanni, A. - \ 2009
    African journal of biotechnology 8 (2009)1. - ISSN 1684-5315 - p. 26 - 36.
    cayenensis/dioscorea-rotundata complex - diversity - markers - rapd - populations - allozyme - model - aflp
    Yam (Dioscorea spp.) is an important food and cash crop in the Guinea-Sudan zone of Benin. The genetic diversity of about 70 cultivars of Dioscorea cayenensis/Dioscorea rotundata (Guinea yam) and about 20 cultivars of Dioscorea alata (water yam) was analysed using random amplified polymorphic DNA (RAPD). The amplified bands revealed high polymorphism. These polymorphic DNA fragments were used to construct dendrograms, clustering all accessions into 18 groups: 12 for D. cayenensis/D. rotundata and six for D. alata. The analysis of molecular variance revealed highly significant variation among species, among groups within species, and among cultivars within groups. The study showed that the genetic diversity changed along a spatial gradient. In general, there was a tendency that most of the varieties from the north-east and north-west of the zone investigated appeared to be distinctive from the ones of the centre. However, few varieties were distributed randomly and did not reflect any specific relation to their zone of collection. The current study suggests that the Guinea-Sudan zone of Benin has a large gene pool of yam varieties. Yam farmers may have played a significant role in the enrichment and the maintenance of the genetic diversity of yam.
    Broeigegevens t.b.v. onderzoek naar merkers rooirijpheid
    Dam, M.F.N. van - \ 2008
    Lisse : Praktijkonderzoek Plant & Omgeving, Business Unit Bloembollen, Boomkwekerij & Fruit - 12
    merkers - tulpen - forceren van planten - bloembollen - landbouwkundig onderzoek - markers - tulips - forcing - ornamental bulbs - agricultural research
    In het rooiseizoen van 2007 werden door 6 bedrijven, monsters gerooid van 2 cultivars op 4 verschillende tijdstippen.Er werd gerooid uit het partijdeel van plantmaat 9 (opgeplant herfst 2006). Deze monsters werden gebruikt voor merkeranalyse (door Genetwister) en voor afbroei (door PPO). Per bedrijf werd in de tweede week van juni bepaald wat de te verwachten rooidatum was. Daarna werd bemonsterd op 4 tijdstippen, namelijk: - 14 dagen voor de verwachte rooidatum: T-14 - 7 dagen voor de verwachte rooidatum: T-7 - Op de verwachte rooidatum: T0 - 7 dagen na de verwachte rooidatum: T+7 De monsters waren steeds 2 x 50 bollen groot. Deze werden op de dag van rooien verzameld op een centraal adres en de volgende morgen opgehaald en naar PPO in Lisse gebracht. Daar werden de bollen geschoond en gesorteerd. Van de maat die het meest voorkwam in het monsterdeel werden 10 bollen genomen. Hiervan werden per bol 5 ponsjes van 6-7 mm doorsnede uit de buitenste rok ingevroren. Deze ponsjes werden door Genetwister gebruikt om merkeranalyses uit te voeren en zo het optimale rooimoment vast te stellen. De overige bollen werden behandeld voor afbroei, waarbij de monsters niet alleen per rooidatum maat maar ook per maat apart werden afgebroeid. Door deze werkwijze kwam het nog wel eens voor, dat er van sommigen rooidatum-bolmaat combinatie weinig of geen bollen waren om af te broeien. Dit had invloed op de beoordeelbaarheid van de monsters. De beoordeling van de broeikwaliteit bestond uit een vergelijking op het gewicht, de lengte en het gewicht per centimeter. Hierbij werd in principe steeds bollen met dezelfde maat met elkaar vergeleken. Per bedrijf- cultivar combinatie werd als eindoordeel bepaald welke rooidatum de beste kwaliteit bloemen gaf. De resultaten zijn overgedragen aan Genetwister. Hier werd het eindoordeel van de afbroei vergeleken met de resultaten van de merkeranalyse.
    Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology
    Botton, A. ; Galla, G. ; Conesa, A. ; Bachem, C.W.B. ; Ramina, A. ; Barcaccia, G. - \ 2008
    BMC Genomics 9 (2008). - ISSN 1471-2164 - 19 p.
    genome-wide expression - pseudo-testcross strategy - poa-pratensis l - cdna-aflp - candidate genes - seed-germination - cell-division - linkage map - identification - markers
    Background: After 10-year-use of AFLP (Amplified Fragment Length Polymorphism) technology for DNA fingerprinting and mRNA profiling, large repertories of genome- and transcriptome-derived sequences are available in public databases for model, crop and tree species. AFLP marker systems have been and are being extensively exploited for genome scanning and gene mapping, as well as cDNA-AFLP for transcriptome profiling and differentially expressed gene cloning. The evaluation, annotation and classification of genomic markers and expressed transcripts would be of great utility for both functional genomics and systems biology research in plants. This may be achieved by means of the Gene Ontology (GO), consisting in three structured vocabularies (i.e. ontologies) describing genes, transcripts and proteins of any organism in terms of their associated cellular component, biological process and molecular function in a species-independent manner. In this paper, the functional annotation of about 8,000 AFLP-derived ESTs retrieved in the NCBI databases was carried out by using GO terminology. Results: Descriptive statistics on the type, size and nature of gene sequences obtained by means of AFLP technology were calculated. The gene products associated with mRNA transcripts were then classified according to the three main GO vocabularies. A comparison of the functional content of cDNA-AFLP records was also performed by splitting the sequence dataset into monocots and dicots and by comparing them to all annotated ESTs of Arabidopsis and rice, respectively. On the whole, the statistical parameters adopted for the in silico AFLP-derived transcriptome-anchored sequence analysis proved to be critical for obtaining reliable GO results. Such an exhaustive annotation may offer a suitable platform for functional genomics, particularly useful in non-model species. Conclusion: Reliable GO annotations of AFLP-derived sequences can be gathered through the optimization of the experimental steps and the statistical parameters adopted. The Blast2GO software was shown to represent a comprehensive bioinformatics solution for an annotation-based functional analysis. According to the whole set of GO annotations, the AFLP technology generates thorough information for angiosperm gene products and shares common features across angiosperm species and families. The utility of this technology for structural and functional genomics in plants can be implemented by serial annotation analyses of genome- anchored fragments and organ/tissue-specific repertories of transcriptome-derived fragments.
    Genetic diversity and population structure of locally adapted South African chicken lines: Implications for conservation.
    Marle-Koster, E. van; Hefer, C.A. ; Nel, L.H. ; Groenen, M.A.M. - \ 2008
    South African Journal of Animal Science = Suid-Afrikaanse Tydskrif Vir Veekun 38 (2008)4. - ISSN 0375-1589 - p. 271 - 281.
    kippen - inheems vee - rassen (dieren) - differentiatie - genetische variatie - genetische diversiteit - microsatellieten - merkers - bevolkingsstructuur - conservering - zuid-afrika - fowls - native livestock - breeds - differentiation - genetic variation - genetic diversity - microsatellites - markers - population structure - conservation - south africa - domestic-animal diversity - microsatellite markers - linkage map - naked neck - polymorphisms - biodiversity - genome
    In this study microsatellite markers were applied to investigate the genetic diversity and population structure of the six local chicken lines kept in the “Fowls for Africa” program, for better clarification of parameters for breed differentiation and genetic conservation of this valuable resource. The lines included the Black Australorp, Potchefstroom Koekoek, New Hampshire, Ovambo, Lebova- Venda and a Naked Neck line. Unbiased estimates for heterozygosity ranged from 50% in the Potchefstroom Koekoek to as high as 65% in the Naked Neck chickens. FIS values varied from as low as 0.16 for the Black Australorp line to as high as 0.35 for the Ovambo chickens. The FST values indicated moderate to high genetic differentiation between the Naked Neck and New Hampshire (0.11); Ovambo and Naked Neck lines (0.12), and Naked Neck and Lebowa- Venda (0.14). A total of 13% of the total genetic variation observed was between the chicken lines and 87% within the lines, supporting moderate genetic differentiation. Population structure was assessed using STRUCTURE where the Black Australorp was genetically best defined. Although six clusters for the different populations could be distinguished, the other lines were not as clearly defined, with individual birds tending to share more than one cluster. Results support a broad classification of these lines and further investigation of unique alleles is recommended for conservation of the lines within the program.
    Selecteren op DNA-niveau: genomic selection zorgt voor revolutie in fokkerij
    Calus, M.P.L. ; Bastiaansen, J.W.M. ; Meuwissen, T.H.E. ; Veerkamp, R.F. - \ 2008
    Veeteelt 25 (2008)18. - ISSN 0168-7565 - p. 12 - 15.
    melkveehouderij - dierveredeling - selectief fokken - genomen - dna - merkers - dairy farming - animal breeding - selective breeding - genomes - dna - markers
    10 jaar geleden waren het nog futuristische ideeën, nu is genomic selection in de fokkerijwereld het gesprek van de dag. Maar wat houdt het precies in? ASG-onderzoekers schetsen de achtergrond van de nieuwe techniek
    Genomic Selection
    Calus, Mario - \ 2008
    animal breeding - genomes - selective breeding - inbreeding - dna - markers
    Genome wide diversity: variation over a genome
    Engelsma, Krista - \ 2008
    genetic diversity - genomes - heterozygosity - markers - animal breeding - haplotypes
    Genetic variability of cultivated cowpea in Benin assessed by random amplified polymorphic DNA
    Zannou, A. ; Kossou, D.K. ; Ahanchédé, A. ; Zoundjihékpon, J. ; Agbicodo, E. ; Struik, P.C. ; Sanni, A. - \ 2008
    African journal of biotechnology 7 (2008)24. - ISSN 1684-5315 - p. 4407 - 4414.
    linkage map - diversity - aflp - markers - populations - model - wild
    Characterization of genetic diversity among cultivated cowpea [Vigna unguiculata (L.) Walp.] varieties is important to optimize the use of available genetic resources by farmers, local communities, researchers and breeders. Random amplified polymorphic DNA (RAPD) markers were used to evaluate the genetic diversity in 70 cowpea accessions collected throughout Benin. Nine random primers were screened on 24 accessions to assess their ability to reveal polymorphisms in cowpea and four of them were selected for use in characterizing the total sample. A total of 32 amplified bands were generated by the four primers. The number of loci detected varied from 5 to 11. RAPD profiles were analysed and amplified polymorphic DNA fragments were used to construct a dendrogram, clustering the accessions into nine groups at a similarity index of 71% based on the Unweighted Pair-Group Method using Arithmetic Averages. The genetic diversity among the cowpea cultivars investigated was large and the RAPD proved to be a useful technique to characterise it. Based on the molecular variance, the fixation index suggests a large differentiation of cowpea cultivars in Benin.
    Collision probabilities for AFLP bands, with an application to simple measures of genetic similarity
    Gort, G. ; Koopman, W.J.M. ; Stein, A. ; Eeuwijk, F.A. van - \ 2008
    Journal of Agricultural, Biological, and Environmental Statistics 13 (2008)2. - ISSN 1085-7117 - p. 177 - 198.
    fragment length distributions - size homoplasy - markers - lettuce
    AFLP is a frequently used DNA fingerprinting technique that is popular in the plant sciences. A problem encountered in the interpretation and comparison of individual plant profiles, consisting of band presence-absence patterns, is that multiple DNA fragments of the same length can be generated that eventually show up as single bands on a gel. The phenomenon of two or more fragments coinciding in a band within an individual profile is a type of homoplasy, that we call collision. Homoplasy biases estimates of genetic similarity. In this study, we show how to calculate collision probabilities for bands as a function of band length, given the fragment count, the band count, or band lengths. We also determine probabilities of higher order collisions, and estimate the total number of collisions for a profile. Since short fragments occur more often, short bands are more likely to contain collisions. For a typical plant genome and AFLP procedure, the collision probability for the shortest band is 25 times larger than for the longest. In a profile with 100 bands a quarter of the bands may contain collisions, concentrated at the shorter band lengths. All calculations require a careful estimate of the monotonically decreasing fragment length distribution. Modifications of Dice and Jaccard coefficients are proposed. The principles are illustrated on data from a phylogenetic study in lettuce
    Genome-wide scan for short and medium chain milk fatty acids
    Stoop, W.M. ; Schennink, A. ; Visker, M.H.P.W. ; Mullaart, E. ; Arendonk, J.A.M. van; Bovenhuis, H. - \ 2008
    melkvee - zwartbont - melkvet - vetzuren met een lange keten - loci voor kwantitatief kenmerk - merkers - genotyping - genexpressieanalyse - dairy cattle - holstein-friesian - milk fat - long chain fatty acids - quantitative trait loci - markers - genotyping - genomics
    Aim of this research was to identify Quantitative Trait Loci (QTL) for long chain milk fatty acids. Therefore 1905 Dutch Holstein Friesian heifers were phenotyped. One of the conclusions was that the identification of QTL for long chain fatty acids, and in particular for C18:1trans fatty acids, strongly supports the hypothesis of a genetic component for these fatty acids
    Comparison of information content for microsatellites and SNPs in poultry and cattle
    Schopen, G.C.B. ; Bovenhuis, H. ; Visker, M.H.P.W. ; Arendonk, J.A.M. van - \ 2008
    Animal Genetics 39 (2008)4. - ISSN 0268-9146 - p. 451 - 453.
    quantitative trait loci - linkage map - genetic-map - markers - genome - population - chicken
    Data were available for 12 poultry microsatellites and 29 poultry single nucleotide polymorphisms (SNPs), and for 34 cattle microsatellites and 36 cattle SNPs. Stochastic permutation was used to determine the number of SNPs needed to obtain the same average information content as a given number of microsatellites. For poultry, the information content averaged 0.71 for the 12 microsatellites compared to 0.72 for the 29 SNPs. For cattle, the information content averaged 0.92 for the 34 microsatellites compared with 0.79 for the 36 SNPs. This study shows that, for each microsatellite, three SNPs are needed to obtain the same average information content.
    Persistentie van KVP-virus in gevaccineerde dieren: een risico? = Persistence of classical swine fever virus in vaccinated animals: a risk?
    Loeffen, W.L.A. - \ 2008
    Tijdschrift voor Diergeneeskunde 133 (2008)11. - ISSN 0040-7453 - p. 482 - 484.
    landbouwbeleid - classical swine fever virus - varkenspest - varkenshouderij - ziektedistributie - verplichte vaccinatie - merkergenen - merkers - klassieke varkenspest - maatregelen - dierziektepreventie - agricultural policy - classical swine fever virus - swine fever - pig farming - disease distribution - mandatory vaccination - marker genes - markers - classical swine fever - measures - animal disease prevention
    Het is dit jaar geleden dat in Nederland het geval van klassieke varkenspest werd gedetecteerd. Het was het laatste geval in een epidemie die ruim een jaar had geduurd. Op dat moment waren we 429 besmette bedrijven verder, waren 12 miljoen varkens vernietigd en was de schade opgelopen tot meer dan 2 miljard euro. Om nog maar te zwijgen over de emotionele en psychotische schade bij vele betrokkenen. Sindsdien zit de angst voor een nieuwe uitbraak er goed in en zijn er veel maatregelen genomen om een herhaling te voorkomen. Een van die maatregelen is het aanpassen van het beleidsdraaiboek en het daarin opnemen van de optie om tijdens een volgende uitbraak eventueel te gaan vaccineren met een markergen. Het CV1 heeft veel onderzoek gedaan naar effectiviteit en veiligheid van een vaccinatiestrategie met markervaccins. Onder andere werd onderzocht wat de kans is dat gevaccineerde dieren na infectie een chronische infectie ontwikkelen en vervolgens langdurig infectieus zijn
    Development of a high-throughput microsatellite typing approach for forensic and population genetic analysis of wild and domestic African Bovini
    Greyling, B.J. ; Kryger, P. ; Plessis, S. du; Hooft, W.F. van; Helden, P. van; Getz, W.M. ; Bastos, A.D.S. - \ 2008
    African journal of biotechnology 7 (2008)5. - ISSN 1684-5315 - p. 655 - 660.
    syncerus caffer - polymorphic bovine - southern africa - linkage map - buffalo - markers - identification - cattle
    Conservation management and forensic traceability of African buffalo and cattle rely on the timely provision of unbiased and accurate genetic information. An approach in which 17 cattle microsatellite markers are co-electrophoresed, following amplification in three core multiplex reactions was established for this purpose. Mean allelic richness per locus was 8.24 and 6.47, for buffalo and Bonsmara cattle, respectively, whilst an unbiased match probability of 6.5x×10-17 and 1.03 × 10-16 was obtained for each. These results confirm the usefulness of this rapid, cost-effective typing approach for forensic, paternity and fine-scale genetic analyses of wild and domestic African Bovini tribe members
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