Ruperao Pradeep, Bajaj Prasad, Yadav Rashmi, Angamuthu Mahalingam, Subramani Rajkumar, Rai Vandana, Tiwari Kapil, Rathore Abhishek, Singh Kuldeep, Singh Gyanendra Pratap, Angadi Ulavappa B, Mayes Sean, Rangan Parimalan
Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, India.
Plant Genome. 2024 Jun;17(2):e20447. doi: 10.1002/tpg2.20447. Epub 2024 Apr 17.
Sesame (Sesamum indicum L.) is an ancient oilseed crop belonging to the family Pedaliaceae and a globally cultivated crop for its use as oil and food. In this study, 2496 sesame accessions, being conserved at the National Genebank of ICAR-National Bureau of Plant Genetic Resources (NBPGR), were genotyped using genomics-assisted double-digest restriction-associated DNA sequencing (ddRAD-seq) approach. A total of 64,910 filtered single-nucleotide polymorphisms (SNPs) were utilized to assess the genome-scale diversity. Applications of this genome-scale information (reduced representation using restriction enzymes) are demonstrated through the development of a molecular core collection (CC) representing maximal SNP diversity. This information is also applied in developing a mid-density panel (MDP) comprising 2515 hyper-variable SNPs, representing almost equally the genic and non-genic regions. The sesame CC comprising 384 accessions, a representative set of accessions with maximal diversity, was identified using multiple criteria such as k-mer (subsequence of length "k" in a sequence read) diversity, observed heterozygosity, CoreHunter3, GenoCore, and genetic differentiation. The coreset constituted around 15% of the total accessions studied, and this small subset had captured >60% SNP diversity of the entire population. In the coreset, the admixture analysis shows reduced genetic complexity, increased nucleotide diversity (π), and is geographically distributed without any repetitiveness in the CC germplasm. Within the CC, India-originated accessions exhibit higher diversity (as expected based on the center of diversity concept), than those accessions that were procured from various other countries. The identified CC set and the MDP will be a valuable resource for genomics-assisted accelerated sesame improvement program.
芝麻（Sesamum indicum L.）是一种古老的油料作物，属于胡麻科，是一种全球范围内种植的作物，用于生产油和食品。在本研究中，对保存在国际农业研究磋商组织-国家植物遗传资源局（NBPGR）国家基因库中的2496份芝麻种质进行了基因分型，采用了基因组辅助双酶切限制性内切酶相关DNA测序（ddRAD-seq）方法。共利用64910个经过筛选的单核苷酸多态性（SNP）来评估基因组规模的多样性。通过构建一个代表最大SNP多样性的分子核心种质库（CC），展示了这种基因组规模信息（使用限制性内切酶减少代表性）的应用。该信息还应用于开发一个包含2515个高变SNP的中密度芯片（MDP），这些SNP几乎平均代表基因区域和非基因区域。利用多种标准，如k-mer（序列读取中长度为“k”的子序列）多样性、观察到的杂合性、CoreHunter3、GenoCore和遗传分化，确定了由384份种质组成的芝麻CC，这是一组具有最大多样性的代表性种质。该核心种质库约占研究的总种质的15%，这个小的子集捕获了整个群体>60%的SNP多样性。在核心种质库中，混合分析显示遗传复杂性降低、核苷酸多样性（π）增加，并且在CC种质中按地理分布没有任何重复性。在CC内，原产于印度的种质表现出比从其他国家采购的种质更高的多样性（基于多样性中心概念预期）。所确定的CC集和MDP将成为基因组辅助加速芝麻改良计划的宝贵资源。
