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 B. 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 Genebank were misclassified. Surprisingly, several individuals 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 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）为育种者与科研人员提供了极具价值的研究资源。然而，种质材料的物种误鉴定问题时常阻碍这些资源的高效利用。本研究提出，采用高通量基因分型工具，可为种质资源库的物种身份确认提供快速、高效且经济的解决方案，同时还能获取宝贵的遗传多样性数据。我们使用新近发布的Illumina Infinium Brassica 60K单核苷酸多态性（Single Nucleotide Polymorphism, SNP）芯片，对来自澳大利亚谷物种质库（Australian Grains Genebank）的180份十字花科（Brassicaceae）样本开展基因分型实验。其中76份为预先疑似存在物种误鉴定的样本，剩余104份则从种质库中随机抽取获取。结合A、C基因组的检出结果与主成分分析（principle components analysis），可将芸薹属（Brassica）的B. rapa、B. oleracea、B. napus、B. carinata及B. juncea样本清晰区分为不同的物种类群。另有部分株系通过染色体计数实验得到了进一步验证。整体来看，18%的样本（32/180）存在物种误鉴定情况。在上述180份样本中，76份疑似误鉴定样本里有23份（占比30%）确为误鉴定；而从种质库随机抽取的105份样本中，则有9份（占比9%）存在物种误鉴定问题。令人意外的是，本研究还发现数个个体为种间杂交事件的产物。该SNP芯片被证实可有效用于物种身份确认，同时能够提供与遗传多样性相关的有效信息。随着针对不同作物的同类基因组学资源逐步普及，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高效且经济的技术方案，助力育种者与科研人员更高效地利用这些宝贵的种质资源。