Center for Genetic Resources

Lelystad, Netherlands

Center for Genetic Resources

Lelystad, Netherlands

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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.


Eilmann B.,Wageningen University | Sterck F.,Wageningen University | Wegner L.,Wageningen University | De Vries S.M.G.,Center for Genetic Resources | And 4 more authors.
Tree Physiology | Year: 2014

Planting provenances originating from southern to northern locations has been discussed as a strategy to speed up species migration and mitigate negative effects of climate change on forest stability and productivity. Especially for droughtsusceptible species such as European beech (Fagus sylvatica L.), the introduction of drought-tolerant provenances from the south could be an option. Yet, beech has been found to respond plastically to environmental conditions, suggesting that the climate on the plantation site might be more important for tree growth than the genetic predisposition of potentially drought-adapted provenances. In this study, we compared the radial growth, wood-anatomical traits and leaf phenology of four beech provenances originating from southern (Bulgaria, France) and northern locations (Sweden, the Netherlands) and planted in a provenance trial in the Netherlands. The distribution of precipitation largely differs between the sites of origin. The northern provenances experience a maximum and the southern provenances experience a minimum of rainfall in summer. We compared tree productivity and the anatomy of the water-conducting system for the period from 2000 to 2010, including the drought year 2003. In addition, tree mortality and the timing of leaf unfolding in spring were analysed for the years 2001, 2007 and 2012. Comparison of these traits in the four beech provenances indicates the influence of genetic predisposition and local environmental factors on the performance of these provenances under moderate site conditions. Variation in radial growth was controlled by environment, although the growth level slightly differed due to genetic background. The Bulgarian provenance had an efficient water-conducting system which was moreover unaffected by the drought in 2003, pointing to a high ability of this provenance to cope well with dry conditions. In addition, the Bulgarian provenance showed up as most productive in terms of height and radial growth. Altogether, we conclude that the similarity in ring-width variation among provenances points to environmental control of this trait, whereas the differences encountered in wood-anatomical traits between the well-performing Bulgarian provenance and the other three provenances, as well as the consistent differences in flushing pattern over 3 years under various environmental conditions, support the hypothesis of genetic control of these features. © The Author 2014. Published by Oxford University Press. All rights reserved.


PubMed | Wageningen University, Center for Genetic Resources and Swiss Federal Institute of forest
Type: Comparative Study | Journal: Tree physiology | Year: 2014

Planting provenances originating from southern to northern locations has been discussed as a strategy to speed up species migration and mitigate negative effects of climate change on forest stability and productivity. Especially for drought-susceptible species such as European beech (Fagus sylvatica L.), the introduction of drought-tolerant provenances from the south could be an option. Yet, beech has been found to respond plastically to environmental conditions, suggesting that the climate on the plantation site might be more important for tree growth than the genetic predisposition of potentially drought-adapted provenances. In this study, we compared the radial growth, wood-anatomical traits and leaf phenology of four beech provenances originating from southern (Bulgaria, France) and northern locations (Sweden, the Netherlands) and planted in a provenance trial in the Netherlands. The distribution of precipitation largely differs between the sites of origin. The northern provenances experience a maximum and the southern provenances experience a minimum of rainfall in summer. We compared tree productivity and the anatomy of the water-conducting system for the period from 2000 to 2010, including the drought year 2003. In addition, tree mortality and the timing of leaf unfolding in spring were analysed for the years 2001, 2007 and 2012. Comparison of these traits in the four beech provenances indicates the influence of genetic predisposition and local environmental factors on the performance of these provenances under moderate site conditions. Variation in radial growth was controlled by environment, although the growth level slightly differed due to genetic background. The Bulgarian provenance had an efficient water-conducting system which was moreover unaffected by the drought in 2003, pointing to a high ability of this provenance to cope well with dry conditions. In addition, the Bulgarian provenance showed up as most productive in terms of height and radial growth. Altogether, we conclude that the similarity in ring-width variation among provenances points to environmental control of this trait, whereas the differences encountered in wood-anatomical traits between the well-performing Bulgarian provenance and the other three provenances, as well as the consistent differences in flushing pattern over 3years under various environmental conditions, support the hypothesis of genetic control of these features.


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.


Chakanda R.,Center for Genetic Resources | Chakanda R.,Wageningen University | van Treuren R.,Center for Genetic Resources | van Treuren R.,Wageningen University | And 3 more authors.
Genetic Resources and Crop Evolution | Year: 2013

The objective of the current research was to investigate the status of rice genetic resources in post-war Sierra Leone using both morphological and amplified fragment length polymorphism (AFLP) data. Specifically, we aimed at investigating farmers' rice genetic resources for homogeneity and differentiation, and at examining the genetic identity of similarly named varieties, including varieties within Sierra Leone, and between Sierra Leone and Guinea. This research was also motivated by the assumption that genetic erosion might have occurred as a result of the civil war. To determine the level of diversity and genetic relationships among farmers' varieties of rice recently collected in Sierra Leone, two methods were used using subsets of the collected samples: (1) Using morphological data, 74 samples of 29 different varieties were analysed to investigate the relationship between (a) varieties grown in two districts in Sierra Leone, and (b) the two main cultivated species, Oryza sativa and Oryza glaberrima. A dendrogram largely clustered the varieties according to region and to the species to which the varieties belonged. (2) Using AFLP data, three separate investigations were conducted: (a) 33 samples of 10 varieties were investigated to evaluate diversity within and between varieties. The results indicated that the rice varieties possess different levels of intra-variety variation, whereas inter-variety diversity was high enough to distinguish one variety from the other. In particular, an AMOVA analysis revealed that 38 % of the total variation occurred within varieties, and 62 % between varieties. (b) 37 samples of 18 different varieties were investigated to determine the consistency of naming of varieties by farmers. The results showed that there was consistency in the naming by farmers of traditional varieties, but inconsistency in the naming of newly acquired varieties and cultivars. (c) 12 samples were investigated to check the identity of varieties carrying identical names collected in two separate regions, Sierra Leone and the neighbouring country of Guinea. The results indicated no close genetic relationships between the varieties found in Sierra Leone and Guinea despite similarities in the names given to these varieties by farmers, indicating the influence of different cultivation practices in the two countries. © 2012 Springer Science+Business Media Dordrecht.


van Treuren R.,Center for Genetic Resources | van Treuren R.,Wageningen University | de Groot E.C.,Center for Genetic Resources | de Groot E.C.,Wageningen University | And 2 more authors.
Genetic Resources and Crop Evolution | Year: 2013

Maintaining sufficient viability is critical to the sustainability of ex situ conserved seed collections. For this reason, accessions are regenerated when viability falls below a predefined threshold. Viability is monitored by determining the germination ability of accessions at predefined time intervals. Optimizing the frequency of these germination tests, in order to avoid waste of resources, is hampered by the scarce availability of data about seed longevity, particularly for material maintained under genebank conditions. Here we report on the analysis of nearly 40,000 germination test results collected for a wide range of crop species over a 25-years period by the centre for genetic resources, the Netherlands (CGN), where seeds of genebank accessions are dried to 3-7 % moisture content and stored for the long term under near-vacuum in aluminium foil bags at -20 °C. The results indicate that seed viability is well maintained for the large majority of seed lots during the first 25 years after regeneration as only 3. 3 % of the monitoring tests revealed below-threshold germination values. It is argued that the majority of these sub-standard seed lots are due to other causes than seed ageing, including dormancy problems and estimation error in germination testing. For material, maintained under the seed management procedures and storage conditions practiced by CGN, it is therefore recommended to delay the first germination monitoring tests to 25 years after regeneration. © 2012 Springer Science+Business Media Dordrecht.


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.


Odong T.L.,Wageningen University | Jansen J.,Wageningen University | van Eeuwijk F.A.,Wageningen University | van Hintum T.J.L.,Center for Genetic Resources
Theoretical and Applied Genetics | Year: 2013

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. © 2012 The Author(s).

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