T.J.L. van Hintum

Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?

Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using real and simulated molecular marker data. Our study also compared the performance of traditional hierarchical clustering with model-based clustering (STRUCTURE). We showed that the cophenetic correlation coefficient is directly related to subgroup differentiation and can thus be used as an indicator of the presence of genetically distinct subgroups in germplasm collections. Whereas UPGMA performed well in preserving distances between accessions, Ward excelled in recovering groups. Our results also showed a close similarity between clusters obtained by Ward and by STRUCTURE. Traditional cluster analysis can provide an easy and effective way of determining structure in germplasm collections using molecular marker data, and, the output can be used for sampling core collections or for association studies.

Quality of core collections for effective utilisation of genetic resources review, discussion and interpretation

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.

Genetic and economic aspects of marker-assisted reduction of redundancy from a wild potato germplasm collection

The wild potato germplasm collection of the series Acaulia, maintained at the Centre for Genetic Resources, The Netherlands, consists of 314 accessions. In previous investigations, 15 potential duplication groups with a total of 36 accessions were identified based on AFLP analysis of a limited sample per accession. In the present study, the potential redundancies, plus one additional accession, were studied with increased sample sizes to examine intra- and inter-accession variation more accurately, with the aim to reduce the size of the collection. No variation was observed within two potential duplication groups, whereas only limited differentiation among accessions was detected within seven groups, resulting in a total of 15 redundant accessions (nearly 5% of the collection). A cluster analysis of all the accessions of the collection showed that these nine groups each had a distinct identity. It was decided to maintain the accessions of the remaining six groups as separate entries based on the large differentiation observed among accessions and the absence of a clear identity. An analysis of molecular variance in the set of 37 accessions showed that 91% of the observed variation could be found among accessions. This variance component appeared unaffected when the set was analysed without the 15 redundant accessions. The invested costs to identify redundancies in the series Acaulia by AFLP analysis are estimated at kε 57.3, whereas the savings achieved by reduction of the collection are estimated at kε 21.0 per generation. However, a cost-benefit analysis should not only focus on the short-term return of investments, but should also consider the value of newly obtained data and information. These include taxonomic information about accessions, optimised sampling strategies, optimised regeneration procedures, additional data for core collection formation and more efficient utilisation of germplasm.

Comparison of marker systems and construction of a core collection in a pedigree of European spring barley

Based on data in four publications describing European barley cultivars, similarities between pairs of cultivars were calculated using individual markers and combinations of markers. These markers included 19 isoenzyme patterns, Giemsa C-banding variants of each of the seven chromosomes, hordein polypeptide patterns, DDT susceptibility type, and three morphological descriptors. The rank correlation between the coefficients of parentage and marker-based similarities is low; the highest single marker correlation is with Est-1, 0.41, and the highest correlation with a combination of markers is 0.58. Giemsa C-banding patterns score rather high, as opposed to the three morphological characters that score very low. Selection of core collections using the effective-number-of-origin-lines theory is successful. The average number of types found in a core collection of cultivars of given size is always considerably larger than a random set of the same size. The core collection approaches the maximum possible number of types.

Diversity in ex situ genebank collections of barley

The genetic resources of a crop serve as the raw material for both plant breeding and scientific research. Therefore, genetic resources have to be available for present users, and have to be conserved for future utilization. Barley is relatively easy to conserve; the seeds store well, and regeneration is due to the selfing nature, easy. Nevertheless, care should be taken: the wild species need more attention, and even in the cultivated material studies have shown that the genetic integrity of barley genebank accessions is low. This can be due to incomplete selling but also to genetic drift, selection or contamination. The crop is well represented in genebanks; the number of accessions is very large. However—the secondary and tertiary genepools are hardly represented in ex situ collections; the ssp. spontaneum material, despite the relatively high number of accessions, can be shown to be derived from a limited number of populations; and the cultivated material is very heavily duplicated. Access to the information on material in genebanks is good and improving. The access tothe material in the genebanks is good, but under threat due to international developments.

Next-generation genebanking: plant genetic resources management and utilization in the sequencing era

Advances in sequencing technologies have made it possible to analyse large amounts of germplasm against low production costs, which has opened the door to screen genebank collections more efficiently for DNA sequence variation. The present study explores how these developments may affect the operations of genebanks and, consequently, how genebank agendas may change. It is argued that the new developments are more likely to have an impact on the user-oriented activities than the housekeeping operations of genebanks. To better facilitate the user community, genebanks may have to strengthen their core business, in particular, by improving quality management procedures and by providing access to a wider diversity of a crops gene pool. In addition, genebanks may have to provide novel services, such as the introduction of specific user-oriented collection types, including research populations and genetically purified lines, and the development of novel information services, including plant genetic resources portals that should guide users to the information and materials of specific interest. To improve their user-oriented services, genebanks need to increase their communication and collaboration with the user community and to develop strategic alliances with this sector.

Barley diversity - an introduction

Genetic diversity is one of the main resources sustaining human life on this planet. Genetic diversity also plays an important role in scientific research. To understand properly how plants grow and multiply, how populations develop, and how species evolve, one needs to improve his/her knowledge of distribution and function of genetic diversity. This chapter reviews the present state of knowledge on diversity in barley. Barley has a long history as a domesticated crop, as one of the first to be adopted for cultivation. Migration of people together with their seed crops led to a major diversification and adaptation to new areas, and the crop is now virtually found worldwide. The development of new technology and methods increased the genetic diversity even further and turned barley into the universal, highly diverse crop it is today. Barley has the advantage, apart from being an important agricultural crop for food and feed, that it has also been used virtually worldwide as a model species for biological research.

Marker-assisted reduction of redundancy in a genebank collection of cultivated lettuce

To reduce the level of redundancy in a collection of cultivated lettuce, data from 160 amplified fragment length polymorphism (AFLP) fragments and 10 polymorphic microsatellites were used in combination with passport data and morphological data, the latter obtained from an experimental field trial performed for verification purposes. Based on the observed distribution of the number of marker differences between and within accessions, a minimum of three AFLP differences and two microsatellite differences were regarded as levels warranting distinction between accessions in the redundancy analysis. The strategy followed in the redundancy analysis was mainly based on the confirmation of duplication by each of two independently generated data sources. The molecular data were used for the validation as well as the identification of potential duplicates, revealing a total number of 198 redundancies, corresponding to 12.9% of the total collection. Trueness to type, number of characterization and evaluation data, and collection management considerations, such as available seed quantities and germination percentages, were used as primary, secondary and tertiary criteria to decide which accession from duplication groups to maintain in the collection. Removal of accessions showed negligible effects on total collection diversity, as quantified for AFLPs and microsatellites, characterization and evaluation traits and resistance profiles against downy mildew pathotypes, indicating that the applied strategy was effective.

Data resolution : a jackknife procedure for determining the consistency of molecular marker datasets

The results of genetic diversity studies using molecular markers not only depend on the biology of the studied objects but also on the quality of the marker data. Poor data quality may hamper the correct answering of biological questions. A new statistic is proposed to estimate the quality of a marker data set with regard to its ability to describe the structure of the biological material under study. This statistic is called data resolution (DR). It is calculated by splitting a marker data set at random into two sets each with half the number of markers. In each set, similarities between all pairs of objects are calculated. Subsequently, the similarities obtained for the two sets are correlated. This process is repeated a large number of times. The average of the correlation coefficients obtained in this way is the DR of the dataset. In the present paper, the DR statistic is applied to four studies involving amplified fragment length polymorphism as well as micro-satellite markers. In addition, some properties and possible applications of DR are discussed, including the prediction of the added value of scoring additional markers, and the determination of which similarity measure is, apart from genetical considerations, most appropriate for analyzing the data.

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.