Optimization of the composition of crop collections for ex situ conservation

Abstract

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.

Germplasm Acquisition and Distribution by CGIAR Genebanks

“…First, so-called “diversity trees” have been constructed for 22 crops. The trees are developed using published literature and expert knowledge to categorize the diversity held in each crop gene pool into known variety or genotype groups or wild species, which allows the mapping of accessions into the groups and the quantitative representation (or not) of the gene pool by the collection [ 32 , 39 , 40 ]. Second, spatial analyses have been undertaken using a method to assess the ecogeographic gaps and coverage of current CGIAR crop collections.…”

Pearl millet

“…For collection management, NGS technologies could be useful to basically support all management areas (Van Treuren and Van Hintum, 2014). For example, DNA sequence data of genebank ac-cessions may be used to determine the genetic structure of collections and to improve the composition thereof by eliminating redundancies (Van Treuren et al, 2009). Ample sequence data of the existing collection allows genebank curators to take more informed decisions about acquisition by evaluating potentially interesting materials for their added value to the genetic diversity already present in the collection (Van Treuren et al, 2008).…”

“…Ample sequence data of the existing collection allows genebank curators to take more informed decisions about acquisition by evaluating potentially interesting materials for their added value to the genetic diversity already present in the collection (Van Treuren et al, 2008). One can consider removal of accessions that contribute least to the genetic diversity of the collection (Van Treuren et al, 2009). NGS data could also be used to monitor the regeneration of accessions in order to ensure the maintenance of genetic integrity thereof, for example, by comparing sequence data of samples before and after regeneration (Van Hintum et al, 2007).…”

A gap analysis modelling framework to prioritize collecting for ex situ conservation of crop landraces

“…Understanding the representation of crop diversity in ex situ repositories provides a foundation for conservation planning (Castañeda-Álvarez et al, 2016;García, Parra-Quijano, & Iriondo, 2017;van Treuren, Engels, Hoekstra, & Hintum, 2009). Methods to assess the current degree of representation, and to inform further collecting efforts, have increasingly been developed for over more than a decade [e.g.…”