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（germplasm collections）可为育种工作者与科研人员提供极具价值的研究资源。然而，因物种鉴定失误导致的种质入库材料分类错误，常阻碍此类资源库的高效利用。本研究提出，借助高通量基因分型工具（high-throughput genotyping tool），既可快速、高效且经济地完成种质资源库内材料的物种鉴定，亦可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 SNP芯片（Illumina Infinium Brassica 60K SNP array），对取自澳大利亚谷物种质基因库（Australian Grains Genebank）的180份十字花科（Brassicaceae）样本开展基因分型。其中76份为疑似分类错误的送检样本，剩余104份则从种质资源库中独立抽取获取。结合A基因组与C基因组的存在情况以及主成分分析（principal components analysis），可将芸薹（Brassica rapa）、甘蓝（B. oleracea）、甘蓝型油菜（B. napus）、埃塞俄比亚芥（B. carinata）以及芥菜型油菜（B. juncea）的样本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完成了进一步验证。整体而言，18%的样本（32/180）存在物种分类错误。在该180份样本中，76份疑似分类错误的样本里有23份（占比30%）存在分类错误，而从澳大利亚谷物种质基因库随机抽取的105份样本中，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（单核苷酸多态性，single nucleotide polymorphism）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为全球范围内的种质资源库筛查提供一种高效且经济的方法，助力育种工作者与科研人员更高效地利用这些珍贵资源。