Marker-assisted reduction of redundancy in germplasm collections: genetic and economic aspects

Germplasm collections invariably contain duplicate accessions, both within and between genebanks. These redundancies are a burden for curators because they do not contribute to the diversity in the collection, but do require genebank budget for maintenance. Thus, both from a genetic and economic point of view, identification and elimination of redundancies should be an important genebank objective. Molecular analysis can complement traditional approaches towards identifying duplications. Interpretation of molecular data is, however, by no means straightforward because various genetic relationships among potential duplicates may occur. Since in all collections, even for self-fertilizing crops intra-accession variation is often observed, the question is not so much whether two accessions are identical, but rather whether they are sufficiently different to consider them distinct. To address this question, statistical methods can be applied to estimate and test molecular variance components. Genetic issues related to the answering of this question are illustrated by experimental data from redundancy studies carried out in various crop collections of the Centre for Genetic Resources, The Netherlands. In addition, economic aspects of rationalization studies are discussed. It is concluded that, considering the high costs of molecular analyses, the potential economic benefits of rationalization with the help of molecular technology should not be taken for granted and indeed strongly depend on the crop involved. In contrast, the added value obtained by molecular characterization in improving insight in the genetic composition of collections and the quality of genebank operations can be regarded considerable. Examples of spin-off from such studies are presented. INTRODUCTION Germplasm collections established and maintained by genebanks provide for the present and future utilization of crop genetic resources. In the initial phase of developing germplasm collections, the focus has been mainly on the acquisition of material due to the necessity of conservation. Many genebank collections have started as working collections for taxonomic studies and plant breeding activities. In many cases genebanks expanded their collections by including obsolete varieties and material obtained from expeditions to natural distribution areas of crop-related wild relatives. To extend the collection, it has also been common practice to request material from colleague genebanks. In many cases, this has resulted in collections of considerable size, rather unbalanced composition and unknown value. It has been estimated by the FAO that the number of genebank collections exceeds 1300, collectively containing more than six million accessions (FAO, 1996). As a result, genebanks are nowadays more concerned with gaining knowledge about their current collections and with the improvement of the efficiency of genetic resources management, rather than with the enlargement of their collections. Research aiming at the optimization of the composition of collections is therefore of particular interest, both from a genetic and economic point of view. Proc. XXVI IHC – Plant Genetic Resources Eds. P.L. Forsline et al. Acta Hort. 623, ISHS 2003 Publication supported by Can. Int. Dev. Agency (CIDA) 140 One of the possibilities to improve the composition of a collection is to identify and eliminate redundancies. Germplasm collections invariably contain duplicate accessions, both within and between genebanks. Duplicates may occur within collections for various reasons. For instance, transformation of information and common errors may give rise to the presence of identical material registered under different identifiers. Accessions originating from breeding activities may involve material derived from a common or identical genetic background. In the case of wild material, expeditions may have been organized to identical collection areas, or sampling may have been carried out without sufficient prior knowledge about the distribution of genetic variation across the natural areas. Duplication between genebanks, other than intended as safety backups, may have originated from the acquisition of material from common sources or from the exchange of material between genebanks. Therefore, international co-operation is indispensable to improve the efficiency of genetic resources management within the network of genebanks. The level of duplication encountered can be quite substantial. Based on passport data, a duplication study within and among four main lettuce collections revealed an average of 12% internal duplication, whereas the percentage of accessions unique to single collections ranged only from 33 to 54 (Hintum, 2000). Evidently, redundancies are a burden for curators because they do not contribute to the diversity conserved, but do consume genebank budget for maintenance. Thus, both for genetic and economic reasons, identification and elimination of redundancies are important options for improving genebank efficiency. Probable duplicates can be identified by comparison of passport data (Hintum and Knupffer, 1995; Hintum, 2000). These analyses may reveal accessions with identical or similar names, samples originating from identical collecting areas, or material with a common breeding history. Suspected redundancies can then be verified with additional information, such as data from morphological or evaluation studies. However, such studies may be hampered by a limited number of suitable characters that can be scored, the restricted level of variation that is often observed, and the sensitivity of many characters for environmental influences. Presently, molecular marker technologies can be applied as a useful tool in many aspects of plant genetic resources management (Bretting and Widrlechner, 1995; Brown and Kresovich, 1996). Therefore, redundancy studies are increasingly being carried out with the help of molecular characterization data (Waycott and Fort, 1994; Virk et al., 1995; Oliveira et al., 1997; Phippen et al., 1997; Cervera et al., 1998; Zeven et al., 1998; McGregor et al., 2002). The application of molecular marker analysis, however, introduced new issues related to redundancy studies. First, molecular marker technologies are used because of their higher resolving power, compared to traditional methods. As a result of the higher levels of variation that are usually detected, probable duplicates will rarely found to be completely identical. This may even be the case for self-fertilizing species for which intra-accession variation is often observed (Treuren and van Hintum, 2001). Therefore, verification of probable duplicates using molecular markers is not simply a matter of determining whether two accessions are identical or not, but rather whether they are sufficiently different in order to consider them distinct accessions. In that respect, the use of the term “duplicate” should preferably be avoided, and the term “redundancy” be used instead. The question, however, is how to decide whether populations are sufficiently different. This will require quantification of variation within and among samples. Statistical tests, such as AMOVA, may thereby be used to obtain necessary decision criteria (Excoffier et al., 1992; Phippen et al., 1997). Second, the variation that is measured by the majority of molecular markers will generally be neutral in nature, unless markers are used that are targeted to specific genes. Users of genetic resources will generally be interested in variation in a few specific characteristics. An important question in characterization studies therefore is to what extent molecular marker data are representative for functional diversity. This may vary with the kind of material analyzed, i.e. cultivars, landraces and wild material. For example, cultivars may appear redundant based on molecular data, but nevertheless differ in a single important selected character.