Sequencing germplasm collections: challenges and opportunities

The application of next generation sequencing (NGS) technology to genebanks holds the promise of increasing knowledge about germplasm collections, without needing to phenotype every accession. Genotyping and extensive phenotyping of a subset of accessions may allow the discovery of genotype-phenotype associations, through which predictions can be made as to the phenotype of other accessions based on genotypic data alone.

In this presentation I will present some ideas as to how genebanks may be sequenced using current technologies, mentioning specific projects where different approaches are already in use (e.g. whole genome resequencing, genotyping-by-sequencing and Restriction site Associated DNA (RAD) sequencing). I will also outline some thoughts on best practices for data standards and practical approaches for analysing and sharing NGS data for genebanks. These recommendations have been further described in a technical report submitted to the Global Crop Diversity Trust entitled 'Strategic approaches to large-scale germplasm evaluation' which is available at http://goo.gl/faMav.