Optimization of the composition of crop collections for ex situ conservation

Many crop genetic resources collections have been established without a clearly defined conservation goal or mandate, which has resulted in collections of considerable size, unbalanced composition and high levels of duplication. Attempts to improve the composition of collections are hampered by the fact that conceptual views to optimize collection composition are very rare. An optimization strategy is proposed herein, which largely builds on the concepts of core collection and core selection. The proposed strategy relies on hierarchically structuring the crop gene pool and assigning a relative importance to each of its different components. Comparison of the resulting optimized distribution of the number of accessions with the actual distribution allows identification of under- and over-representation within a collection. Application of this strategy is illustrated by an example using potato. The proposed optimization strategy is applicable not only to individual genebanks, but also to consortia of cooperating genebanks, which makes it relevant for ongoing activities within projects that aim at sharing responsibilities among institutions on the basis of rational conservation, such as a European genebank integrated system and the global cacao genetic resources network CacaoNet

Genetic resources collections of leafy vegetables (lettuce, spinach, chicory, artichoke, asparagus, lamb’s lettuce, rhubarb and rocket salad): composition and gaps

Lettuce, spinach and chicory are generally considered the main leafy vegetables, while a fourth group denoted by ‘minor leafy vegetables’ includes, amongst others, rocket salad, lamb’s lettuce, asparagus, artichoke and rhubarb. Except in the case of lettuce, central crop databases of leafy vegetables were lacking until recently. Here we report on the update of the international Lactuca database and the development of three new central crop databases for each of the other leafy vegetable crop groups. Requests for passport data of accessions available to the user community were addressed to all known European collection holders and to the main collection holders located outside Europe. Altogether, passport data of 17,530 accessions from a total of 129 collections were collected. The four separate databases were made available on line via a common entry page accessible at http://documents.plant.wur.nl/cgn/pgr/LVintro/. Based on a literature study, an analysis of the gene pool structure of the crops was performed and an inventory was made of the distribution areas of the species involved. The results of these surveys were related to the contents of the newly established databases in order to identify the main collection gaps. Priorities are presented for future germplasm acquisition aimed at improving the coverage of the crop gene pools in ex situ collections

Application of Molecular Markers in Genetic Resources Management of Perennial Ryegrass

Key points Molecular markers are effective tools to support traditional approaches in plant genetic resources management. Genetic diversity assessed for perennial ryegrass by AFLP analysis revealed differentiation of populations occurring in traditional Dutch grasslands from commercial varieties, but not from populations occurring in Dutch nature reserves. No specific conservation measures were recommended to maintain the genetic diversity of perennial ryegrass occurring in traditional Dutch grasslands. Pollination rates estimated by microsatellite analysis for a rejuvenated population of a perennial ryegrass genebank accession were very well described by an inverse quadratic function of inter-plant distance between potential mating pairs, while recorded flowering characteristics contributed only to a minor extent. Compared to variation in pollination rates, the genetic integrity of the rejuvenated perennial ryegrass accession was found to be more threatened by contamination, which indicated the need for improved regeneration protocols to prevent gene flow from other germplasm

Marker-assisted optimization of an expert-based strategy for the acquisition of modern lettuce varieties to improve a genebank collection

To regularly improve the composition of the lettuce collection of the Centre for Genetic Resources, the Netherlands (CGN) with modern varieties, feedback from crop experts is used to select approximately 10% of the new material for incorporation in the collection. In the present study, assessments of six experts were compared to microsatellite data of 414 new varieties and 1408 existing accessions. Based on the microsatellite data, the extent to which the genetic diversity of the collection would be enriched (added value) was calculated for specific sets of new varieties. When individual assessments of experts were evaluated, the total added value of expert-based selections was not significantly higher compared to randomly chosen groups, except for a single expert. Unfamiliarity with new varieties was shown to be a crucial factor in the assessment of crop experts. According to the current acquisition protocol that seeks for consensus among experts, varieties are selected based on recommendations from at least three experts. This protocol also did not perform better than randomly chosen groups of new varieties. However, significantly better results were obtained with alternative protocols. It was concluded that breeding value was a more decisive criterion in the current acquisition protocol than maximal extension of the genetic diversity within the collection. A modified protocol addressing both commercial and diversity aspects was suggested in order to meet the demands of plant breeders as well as conservationist

Microsatellite genotyping of apple (Malus × domestica Borkh.) genetic resources in the Netherlands: application in collection management and variety identification

A highly informative set of 16 microsatellite markers was used to fingerprint 695 apple accessions from eight Dutch collections. Among the total sample, 475 different genotypes were distinguished based on multi-locus microsatellite variation, revealing a potential redundancy within the total sample of 32%. The majority of redundancies were found between collections, rather than within collections. No single collection covered the total observed diversity well, as each collection consisted of about 50% of unique accessions. These findings reflected the fact that most collection holders focus on common Dutch varieties, as well as on region-specific diversity. Based on the diversity patterns observed, maintenance of genetic resources by a network of co-operating collection holders, rather than by collecting the total diversity in a single collection appears to be an efficient approach. Comparison of microsatellite and passport data showed that for many accessions the marker data did not provide support for the registered variety names. Verification of accessions showed that discrepancies between passport and molecular data were largely due to documentation and phenotypic determination errors. With the help of the marker data the varietal names of 45 accessions could be corrected. Microsatellite genotyping of apple appears to be an efficient tool in the management of collections and in variety identification. The development of a marker database was considered relevant as a reference instrument in variety identification and as a source of information about thus far unexplored diversity that could be of interest in the development of new apple varietie

Traditional grasslands : Conservation measures needed?

A number of temperate grasses and legumes, important for animal feeding, have their centre of diversity in the North-West European region, including perennial ryegrass (Lolium perenne L.; Engels raaigras), white clover (Trifolium repens L.; witte klaver) and Kentucky bluegrass (Poa pratensis L.; veldbeemdgras). These species traditionally occur in Dutch grasslands where they can be considered as typical. Undisturbed grasslands that are still in agricultural use have severely become reduced in number in the Netherlands. To investigate the need for conservation policies for such grasslands, diversity was assessed in perennial ryegrass, white clover and Kentucky bluegrass collected from traditional grasslands. This diversity was then compared with the diversity in commercial reference cultivars and in grasslands from nature reserves. Diversity estimation included morphological analyses and molecular characterization. The analyses indicated no substantial distinction between the gene pools of the three investigated groups for any of the three investigated species. In particular, comparison of traditional grasslands with grasslands from nature reserves indicated that basically these two groups covered the same range of genetic variation. It was therefore concluded that no specific in situ conservation measures are currently needed to maintain the genetic diversity of perennial ryegrass, white clover and Kentucky bluegrass occurring in traditional grasslands, considering that nature reserves are already under protective measures. Because perennial ryegrass, white clover and Kentucky bluegrass can be regarded key species of grasslands, the obtained results may be indicative of other species with similar life-history characteristics. Therefore, the need for specific conservation measures for traditional grasslands cannot be warranted

Genetic erosion in crops: concept, research results and challenges

The loss of variation in crops clue to the modernization of agriculture has been described as genetic erosion The current paper discusses the different views that exist on the concept of genetic erosion in crops Genetic erosion of cultivated diversity is reflected in a modernization bottleneck in the diversity levels that occurred during the history of the crop Two stages in this bottleneck are recognized the initial replacement of landraces by modern cultivars, and further trends in diversity as a consequence of modern breeding practices Genetic erosion may occur at three levels of integration crop, variety and allele The different approaches in the recent literature to measure genetic erosion in crops are reviewed. Genetic erosion as reflected in a reduction of allelic evenness and richness appears to be the most useful definition, but has to be viewed in conjunction with events at variety level According to the reviewed literature, the most likely scenario of diversity trends during modernization is the following a reduction in diversity clue to the replacement of landraces by modern cultivars, but no further reduction after this replacement has been complete

Distribution of genetic diversity in wild European populations of prickly lettuce (Lactuca serriola): implications for plant genetic resources management

Genetic variation in Lactuca serriola, the closest wild relative of cultivated lettuce, was studied across Europe from the Czech Republic to the United Kingdom, using three molecular marker systems, simple sequence repeat (SSR, microsatellites), AFLP and nucleotide-binding site (NBS) profiling. The ‘functional’ marker system NBS profiling, targeting disease resistance genes of the NBS/LRR family, did not show marked differences in genetic diversity parameters to the other systems. The autogamy of the species resulted in low observed heterozygosity and high population differentiation. Intra-population variation ranged from complete homogeneity to nearly complete heterogeneity. The highest genetic diversity was found in central Europe. The SSR results were compared to SSR variation screened earlier in the lettuce collection of the Centre for Genetic Resources, the Netherlands (CGN). In the UK, practically only a single SSR genotype was found. This genotype together with a few other common SSR genotypes comprised a large part of the plants sampled on the continent. Among the ten most frequent SSR genotypes observed, eight were already present in the CGN collection. Overall, the CGN collection appears to already have a fair representation of genetic variation from NW Europe. The results are discussed in relation to sampling strategies for improving genebank collections of crop wild relatives