As one of the major outputs of next‐generation sequencing (NGS), a large number of genome‐wide single‐nucleotide polymorphisms (SNPs) have been developed in pigeonpea [Cajanus cajan (L.) Huth.]. However, SNPs require a genotyping platform or assay to be used in different evolutionary studies or in crop improvement programs. Therefore, we developed an Axiom Cajanus SNP array with 56K SNPs uniformly distributed across the genome and assessed its utility in a genetic diversity study. From the whole‐genome resequencing (WGRS) data on 104 pigeonpea lines, ∼2 million sequence variations (SNPs and insertion–deletions [InDels]) were identified, from which a subset of 56,512 unique and informative sequence variations were selected to develop the array. The Axiom Cajanus SNP array developed was used for genotyping 103 pigeonpea lines encompassing 63 cultivars released between 1960 and 2014 and 40 breeding, germplasm, and founder lines. Genotyping data thus generated on 103 pigeonpea lines provided 51,201 polymorphic SNPs and InDels. Genetic diversity analysis provided in‐depth insights into the genetic architecture and trends in temporal diversity in pigeonpea cultivars. Therefore, the continuous use of the high‐density Axiom Cajanus SNP array developed will accelerate high‐resolution trait mapping, marker‐assisted breeding, and genomic selection efforts in pigeonpea.

中文翻译：

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具有56K SNP的高密度公理Cajanus SNP阵列的开发和应用，以了解已发布品种和创始人基因型的基因组架构。

作为下一代测序（NGS）的主要输出之一，木豆[ Cajanus cajan （L.）Huth。]已开发出许多全基因组范围的单核苷酸多态性（SNP）。但是，单核苷酸多态性需要基因分型平台或测定法，以用于不同的进化研究或作物改良计划中。因此，我们开发了一个在整个基因组中均匀分布的56K SNP的Axiom Cajanus SNP阵列，并评估了其在遗传多样性研究中的效用。从104个木豆系的全基因组重测序（WGRS）数据中，鉴定出约200万个序列变异（SNP和插入缺失[InDels]），从中选择了56,512个独特且信息丰富的序列变异的子集来开发阵列。公理卡雅努斯所开发的SNP阵列用于对103个木豆系进行基因分型，其中包括1960年至2014年发布的63个品种，以及40个育种，种质和创始人系。这样在103个木豆品系上生成的基因分型数据提供了51,201个多态性SNP和InDels。遗传多样性分析提供了对木豆品种遗传结构和时间多样性趋势的深入了解。因此，继续使用开发的高密度Axiom Cajanus SNP阵列将加快木豆的高分辨率性状作图，标记辅助育种和基因组选择工作。