Species misclassification (misidentification) and handling errors have been frequently reported in various plant species conserved at diverse gene banks, which could restrict use of germplasm for correct purpose. The objectives of the present study were to (i) determine the extent of genotyping error (reproducibility) on DArTseq-based single-nucleotide polymorphisms (SNPs); (ii) determine the proportion of misclassified accessions across 3134 samples representing three African rice species complex (Oryza glaberrima, O. barthii, and O. longistaminata) and an Asian rice (O. sativa), which are conserved at the AfricaRice gene bank; and (iii) develop species- and sub-species (ecotype)-specific diagnostic SNP markers for rapid and low-cost quality control (QC) analysis. Genotyping error estimated from 15 accessions, each replicated from 2 to 16 times, varied from 0.2 to 3.1%, with an overall average of 0.8%. Using a total of 3134 accessions genotyped with 31,739 SNPs, the proportion of misclassified samples was 3.1% (97 of the 3134 accessions). Excluding the 97 misclassified accessions, we identified a total of 332 diagnostic SNPs that clearly discriminated the three indigenous African species complex from Asian rice (156 SNPs), O. longistaminata accessions from both O. barthii and O. glaberrima (131 SNPs), and O. sativa spp. indica from O. sativa spp. japonica (45 SNPs). Using chromosomal position, minor allele frequency, and polymorphic information content as selection criteria, we recommended a subset of 24 to 36 of the 332 diagnostic SNPs for routine QC genotyping, which would be highly useful in determining the genetic identity of each species and correct human errors during routine gene bank operations.

中文翻译：

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开发用于4种水稻（Oryza L.）物种质量控制基因分型的物种诊断性SNP标记。

在不同基因库保存的各种植物物种中，经常出现物种分类错误（错误识别）和处理错误的报道，这可能会限制种质用于正确的目的。本研究的目的是（i）确定基于DArTseq的单核苷酸多态性（SNP）的基因分型错误（可重复性）的程度；（ii）确定3134个样品中错误分类的种质的比例，这些样品代表了非洲大米基因库中保存的三种非洲稻种复合体（Oryza glaberrima，O。barthii和O. longistaminata）和亚洲稻（O. sativa）；（iii）开发特定于物种和亚物种（生态型）的诊断SNP标记，以进行快速和低成本的质量控制（QC）分析。根据15个种质估计出的基因分型误差，每个复制品重复2到16次，从0.2％到3.1％不等，总体平均水平为0.8％。使用总共31134个SNP基因分型的3134个种质，错误分类的样本比例为3.1％（3134个种质中的97个）。除97个错误分类的登录外，我们共鉴定了332个诊断性SNP，它们清楚地区分了亚洲稻米中的三种非洲本土物种（156个SNP），长稻O. barthii和glaberrima的O. longistaminata登录（131个SNP），以及O. sativa spp。来自O. sativa spp。粳稻（45个SNP）。使用染色体位置，次要等位基因频率和多态信息含量作为选择标准，我们建议将332个诊断SNP中的24至36个子集用于常规QC基因分型，