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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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 (2018). - ISSN 1751-7311 - p. 1 - 6.
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
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)5. - 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)77. - ISSN 1471-2229 - 19 p.
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 (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.
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