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

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-012-1971-y) contains supplementary material, which is available to authorized users.

Peach palm core collection in Brazilian Amazonia

“…Minor changes in these strategies were justified for economic reasons, i.e., market demand, or to include material potentially important for understanding the origin and racial hierarchy of peach palm. Odong et al (2012) point out that these decisions should result in better uniformity of representation of the categories and that this better uniformity can be tested by comparing the Shannon diversity index of the full collection with that of the core collection.…”

“…The BAG has a Shannon diversity index of 0.67 due to the unevenness of landrace representation, while the Core has an index of 0.99 due to its greater evenness (Figure 2). Greater evenness is one indication that a Core represents its full collection (Odong et al 2012). …”

“…One way to increase the effectiveness of the available human and financial resources to ensure continuity and expand the usefulness of the BAG is to create a core collection within it, which will receive priority in future investments. A core collection consists of a limited set of accessions chosen to represent at least 70% of the genetic variation of the entire collection with minimal redundancy (Brown 1989, Brown and Spillane 1999, Odong et al 2012. Escribano et al (2008) e Odong et al (2012 review criteria for selecting and evaluating the accessions included in the core and the core's relationship with the total collection; some of these evaluation methods are used here.…”

“…Escribano et al (2008) e Odong et al (2012 review criteria for selecting and evaluating the accessions included in the core and the core's relationship with the total collection; some of these evaluation methods are used here. Several computer programs now exist to aid core collection design (see Escribano et al 2008, Odong et al 2012, but none handle disjointed data sets with dominant markers, like that of the Peach palm BAG. The aim of this study was to design and evaluate a core collection within the Peach palm BAG to support the better management of these genetic resources.…”

NGS-Based Genotyping, High-Throughput Phenotyping and Genome-Wide Association Studies Laid the Foundations for Next-Generation Breeding in Horticultural Crops

“…The method, which maximizes the possibility to capture specific adaptive traits by means of high-throughput geographic information system (GIS) technologies, has been mainly used to identify sources of resistance to abiotic and biotic stresses in cereals, but has not yet successfully applied in horticultural crops [26]. Despite the potentiality of CC, debate on their effectiveness and criteria of selection to adopt are still underway [27].…”