Data from: High-throughput genotyping for species identification and diversity assessment in germplasm collections

Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species and country of origin often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming species and genome composition of samples in germplasm collections, as well as providing valuable data about diversity and relationships between accessions. We genotyped 188 Brassicaceae accessions sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP array. Of these, 77 were provided on the basis of suspected misclassification and another 111 were sourced independently from the germplasm collection. Presence of the A and C genomes combined with hierarchical clustering and principle components analysis clearly separated B. rapa, B. oleracea, B. napus, B. carinata and B. juncea lines into distinct species groups. Several lines were further validated using chromosome counts. Overall, 18% of lines (32/180) were misclassified on the basis of species: 30% of the lines suspected to be misclassified (23/76), and 9% of the lines independently selected (9/105). Surprisingly, several lines were also found to be the product of interspecific hybridisation events. The SNP (Single Nucleotide Polymorphism) array proved effective at confirming species, and provided useful information related to genetic diversity. As similar genomic resources become available for different crop genera, high-throughput molecular genotyping will offer an efficient and cost-effective method to screen germplasm collections worldwide, facilitating more effective use of these valuable resources by breeders and researchers.