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 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 in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP array. Of these, 76 were provided on the basis of suspected misclassification and another 104 were sourced independently from the germplasm collection. Presence of the A- and C-genomes combined with principle components analysis clearly separated Brassica rapa, B. oleracea, B. napus, B. carinata and B. juncea samples into distinct species groups. Several lines were further validated using chromosome counts. Overall, 18% of samples (32/180) were misclassified on the basis of species. Within these 180 samples, 23/76 (30%) supplied on the basis of suspected misclassification were misclassified, and 9/105 (9%) of the samples randomly sourced from the Australian Grains Genebank were misclassified. Surprisingly, several individuals were also found to be the product of interspecific hybridization 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 crops, 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.

种质资源库为育种工作者与科研人员提供了极具价值的研究资源。然而，种质份样的物种分类错误时常阻碍这些资源的高效利用。本研究提出，借助高通量基因分型技术，不仅可快速、高效且经济地完成种质资源库的物种鉴定，还能获取极具价值的遗传多样性数据。本研究利用最新发布的Illumina Infinium Brassica 60K单核苷酸多态性（single nucleotide polymorphism, SNP）芯片，对取自澳大利亚谷物种质库的180份十字花科种质样品进行了基因分型。其中76份为疑似存在分类错误的送检样品，剩余104份则直接从种质库中随机抽取。结合A、C基因组存在性分析与主成分分析（Principal Components Analysis），可将芸苔（Brassica rapa）、甘蓝（Brassica oleracea）、甘蓝型油菜（Brassica napus）、埃塞俄比亚芥（Brassica carinata）以及芥菜型油菜（Brassica juncea）的样品清晰划分为不同的物种类群。部分株系还通过染色体计数法进行了进一步验证。整体而言，18%的样品（32/180）存在物种分类错误。在这180份样品中，76份疑似分类错误的样品里有23份（占比30%）确实存在分类错误，而从澳大利亚谷物种质库随机抽取的105份样品中则有9份（占比9%）存在分类错误。令人意外的是，部分个体被证实为种间杂交的产物。该SNP芯片可有效完成物种鉴定，并能提供与遗传多样性相关的有效信息。随着不同作物的同类基因组学资源陆续问世，高通量分子基因分型技术将成为全球范围内种质资源库筛查的高效经济手段，助力育种工作者与科研人员更高效地利用这些珍贵资源。