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.