Engelsma K.A.,Wageningen UR Livestock Research |
Engelsma K.A.,Center for Genetic Resources |
Veerkamp R.F.,Wageningen UR Livestock Research |
Calus M.P.L.,Wageningen UR Livestock Research |
And 3 more authors.
Journal of Animal Breeding and Genetics | Year: 2012
Genetic diversity is often evaluated using pedigree information. Currently, diversity can be evaluated in more detail over the genome based on large numbers of SNP markers. Pedigree- and SNP-based diversity were compared for two small related groups of Holstein animals genotyped with the 50k SNP chip, genome-wide, per chromosome and for part of the genome examined. Diversity was estimated with coefficient of kinship (pedigree) and expected heterozygosity (SNP). SNP-based diversity at chromosome regions was determined using 5-Mb sliding windows, and significance of difference between groups was determined by bootstrapping. Both pedigree- and SNP-based diversity indicated more diversity in one of the groups; 26 of the 30 chromosomes showed significantly more diversity for the same group, as did 25.9% of the chromosome regions. Even in small populations that are genetically close, differences in diversity can be detected. Pedigree- and SNP-based diversity give comparable differences, but SNP-based diversity shows on which chromosome regions these differences are based. For maintaining diversity in a gene bank, SNP-based diversity gives a more detailed picture than pedigree-based diversity. © 2012 Blackwell Verlag GmbH.
Maurice-Van Eijndhoven M.H.T.,Wageningen UR Livestock Research |
Maurice-Van Eijndhoven M.H.T.,Wageningen University |
Hiemstra S.J.,Wageningen UR Livestock Research |
Hiemstra S.J.,Center for Genetic Resources |
Calus M.P.L.,Wageningen UR Livestock Research
Journal of Dairy Science | Year: 2011
Milk fatty acid (FA) composition was compared among 4 cattle breeds in the Netherlands: Dutch Friesian (DF; 47 animals/3 farms), Meuse-Rhine-Yssel (MRY; 52/3), Groningen White Headed (GWH; 45/3), and Jersey (JER; 46/3). Each cow was sampled once between December 2008 and March 2009 during the indoor housing season, and samples were analyzed using gas chromatography. Significant breed differences were found for all traits including fat and protein contents, 13 major individual FA, 9 groups of FA, and 5 indices. The saturated fatty acid proportion, which is supposed to be unfavorable for human health, was smaller for GWH (68.9%) compared with DF (74.1%), MRY (72.3%), and JER (74.3%) breeds. The proportion of conjugated linoleic acid and the unsaturation index, which are associated positively with human health, were both highest for GWH. Differences in milk fat composition can be used in strategies to breed for milk with a FA profile more favorable for human health. Our results support the relevance of safeguarding the local Dutch breeds. © 2011 American Dairy Science Association.
Eilmann B.,Wageningen University |
de Vries S.M.G.,Center for Genetic Resources |
den Ouden J.,Wageningen University |
Mohren G.M.J.,Wageningen University |
And 2 more authors.
Forest Ecology and Management | Year: 2013
Forests of the future should be resistant to exacerbating climatic conditions, especially to increasing drought, but at the same time provide a sufficient amount and quality of timber. In this context coastal Douglas-fir (Pseudotsuga menziesii (Mirb.)) is a promising species since it remains productive even under chronic drought. By choosing suitable provenances within the range of Douglas-fir (P. menziesii (Mirb.)) for a given site we can further optimise tree fitness under dry conditions or even increase timber yield.Eighteen coastal Douglas-fir (Pseudotsuga menziesii (Mirb.) var. menziesii) provenances were tested for seedling survival, yield, wood quality, and drought tolerance by taking advantage of a Dutch provenance trial, established in 1971 within the framework of the 1966/1967 IUFRO seed collection program. The site of the Dutch trial is representative for many sites in Central Europe and is characterised by a moderate precipitation and temperature regime. Measurements on height and diameter growth were combined with a dendrochronological study on growth response to drought years.We found a clear latitudinal trend indicating that Douglas-fir provenances from the northern part of the species-distribution range are generally more productive than provenances from the south. In contrast, drought tolerance increased towards the south. This suggests that it is impossible to identify provenances combining maximum productivity with lowest susceptibility towards drought. However, based on the results from the trial we can give recommendations on suitable provenances that are expected to perform best under future conditions in Central Europe. On sites where severe drought events are unlikely to occur in future, fast growing provenances from the north, like Nimkish, should be planted. These provenances respond plastically to drought years, but the strong reduction of tree growth in the drought year itself indicates that these provenances will be harmed by an increasing frequency of drought events. However, on sites where water availability is likely to decrease, provenances from the Olympic Peninsula like Forks and Matlock are very promising since they showed still relatively high yield in combination with a high potential to cope with drought.If summer drought increases in frequency and severity as expected, the latewood/earlywood ratio will be drastically reduced with negative consequences for wood quality and cavitation resistance. However, some provenances, like Marblemount or Matlock, might compensate for the negative effect of summer drought on latewood/earlywood ratio by the contribution of photosynthesis in winter to whole-year carbon stock. © 2013 Elsevier B.V.
Odong T.L.,Wageningen University |
van Heerwaarden J.,University of California at Davis |
Jansen J.,Wageningen University |
van Hintum T.J.L.,Center for Genetic Resources |
van Eeuwijk F.A.,Wageningen University
Crop Science | Year: 2011
Exploitation of the available genetic resources around the world requires information about the relationships and genetic diversity present among genebank collections. These relations can be established by defining for each crop a small but informative set of accessions, together with a small set of reliable molecular markers, that can be used as reference material. In this study, various strategies to arrive at small but informative reference sets are discussed. For selection of accessions, we proposed genetic distance optimization (GDOpt) method, which selects a subset of accessions that optimally represent the accessions not included in the core collection. The performance of GDOpt was compared with Core Hunter, an advanced stochastic local search algorithm for selecting core subsets. For the selection of molecular markers, we evaluated (i) the backward elimination (BE) method and (ii) methods based on principal component analysis (PCA). We examined the performance of the proposed methodologies using five real datasets. Relative to average distance between an accession and the nearest selected accession (representativeness), GDOpt outperformed Core Hunter. However, Core Hunter outperformed GDOpt with respect to allelic richness. The BE performed much better than other methods in selecting subsets of markers. Methods based on PCA showed that, for practical purposes, the inclusion of the first few (two or three) principal components (PCs) was often sufficient. To obtain robust and highquality reference sets of accessions and markers we advise a combination of GDOpt (for accessions) and BE or methods based on PCA using a few PCs (for subsets of markers). © Crop Science Society of America.
Odong T.L.,Wageningen University |
van Heerwaarden J.,Wageningen University |
van Hintum T.J.L.,Center for Genetic Resources |
van Eeuwijk F.A.,Wageningen University |
Jansen J.,Wageningen University
Crop Science | Year: 2013
Understanding the genetic structure of germplasm collections is a prerequisite for effective and efficient use of crop genetic resources in genebanks. Currently, hierarchical clustering techniques are most popular for describing genetic structure in germplasm collections. Traditionally performed using dissimilarities based on raw genotypic data, recent studies have shown that cluster analysis can be improved by first condensing the genotypic data using principal component analysis (PCA). Although the two-step approach (PCA followed by cluster analysis) is gaining popularity, no systematic study into its benefits over traditional clustering methods has been performed. In particular, the relationship between the number of principal components (PCs) to be retained and the performance of cluster analysis have not been established. It is also not clear whether genetic data should be scaled before performing PCA. Here we present a detailed study comparing cluster analysis using distances based on condensed data using significant PCs and clustering based on the full dataset. We also studied the effect of data scaling on PCA-based clustering. Using simulations, we show that in discretely subdivided populations, maximum clustering performance is attained by using a subset of PCs that relate to differentiation between subpopulations and that scaling of the data is key to achieving improvement in PCA-based clustering. For scaled data, we report consistently higher clustering success for PCA, particularly at lower levels of population differentiation, while gains for unscaled data are minor. This is confirmed by real data, where PCA-based clustering of scaled genotypic data leads to visible improvements in resolving finer patterns of geographic subdivision. Our results show clearly that proper scaling and reduction of genotypic data is key to improving clustering performance. © Crop Science Society of America.