Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions

Abstract

Genebanks are valuable resources for crop improvement through the acquisition, ex-situ conservation and sharing of unique germplasm among plant breeders and geneticists. With over seven million existing accessions and increasing storage demands and costs, genebanks need efficient characterization and curation to make them more accessible and usable and to reduce operating costs, so that the crop improvement community can most effectively leverage this vast resource of untapped novel genetic diversity. However, the sharing and inconsistent documentation of germplasm often results in unintentionally duplicated collections with poor characterization and many identical accessions that can be hard or impossible to identify without passport information and unmatched accession identifiers. Here we demonstrate the use of genotypic information from these accessions using a cost-effective next generation sequencing platform to find and remove duplications. We identify and characterize over 50% duplicated accessions both within and across genebank collections of Aegilops tauschii, an important wild relative of wheat and source of genetic diversity for wheat improvement. We present a pipeline to identify and remove identical accessions within and among genebanks and curate globally unique accessions. We also show how this approach can also be applied to future collection efforts to avoid the accumulation of identical material. When coordinated across global genebanks, this approach will ultimately allow for cost effective and efficient management of germplasm and better stewarding of these valuable resources.

Molecular Genetic Diversity and Population Structure of Ginseng Germplasm in RDA-Genebank: Implications for Breeding and Conservation

“…Among 1109 ginseng accessions, 167 (15.1%) (12 accessions in CN, five accessions in CB, and 133 accessions in NIHHS) might be duplicated ( Table 2). It is important to identify these duplicated accessions, due to the limitation of funding and resources in genebanks [45]. Although not all duplicate accessions are worthless, identifying unique accessions within and across the genebanks will facilitate the better use of plant germplasms [45,46].…”

“…It is important to identify these duplicated accessions, due to the limitation of funding and resources in genebanks [45]. Although not all duplicate accessions are worthless, identifying unique accessions within and across the genebanks will facilitate the better use of plant germplasms [45,46]. In this study, 167 ginseng accessions identified will also require the management of duplicate accessions using various additional methods such as evaluation of morphological and/or biochemical traits.…”

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

“…These landraces constitute reservoirs of genetic diversity that can be directly cross‐bred into modern cultivars. There are thousands of these landrace accessions available; however, many of them are heterogeneous, often duplicated seed stocks (Singh et al ., ), which remain confined to germplasm repositories. Of special note is the Watkins landrace collection (Wingen et al ., ) encompassing over 1000 landraces collected in the 1920s and 1930s from a wide geographic distribution.…”

Bioinformatic Extraction of Functional Genetic Diversity from Heterogeneous Germplasm Collections for Crop Improvement

“…Collections are sometimes large: 21,393 accessions of Hordeum vulgare at the Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), 53,777 accessions of Sorghum bicolor in the US National Plant Germplasm System (NPGS), 124,378 accessions of Oryza sativa at the International Rice Research Institute (IRRI). Within a species, genetic diversity is unevenly partitioned across accessions, with ample evidence of redundancy [38,39]. Phenotypic characterization may also be uneven ( Figure 5).…”