Data_Sheet_1_Genome-Wide DArTSeq Genotyping and Phenotypic Based Assessment of Within and Among Accessions Diversity and Effective Sample Size in the Diverse Sorghum, Pearl Millet, and Pigeonpea Landraces.zip

Germplasm should be conserved in such a way that the genetic integrity of a given accession is maintained. In most genebanks, landraces constitute a major portion of collections, wherein the extent of genetic diversity within and among landraces of crops vary depending on the extent of outcrossing and selection intensity infused by farmers. In this study, we assessed the level of diversity within and among 108 diverse landraces and wild accessions using both phenotypic and genotypic characterization. This included 36 accessions in each of sorghum, pearl millet, and pigeonpea, conserved at ICRISAT genebank. We genotyped about 15 to 25 individuals within each accession, totaling 1,980 individuals using the DArTSeq approach. This resulted in 45,249, 19,052, and 8,211 high-quality single nucleotide polymorphisms (SNPs) in pearl millet, sorghum, and pigeonpea, respectively. Sorghum had the lowest average phenotypic (0.090) and genotypic (0.135) within accession distances, while pearl millet had the highest average phenotypic (0.227) and genotypic (0.245) distances. Pigeonpea had an average of 0.203 phenotypic and 0.168 genotypic within accession distances. Analysis of molecular variance also confirms the lowest variability within accessions of sorghum (26.3%) and the highest of 80.2% in pearl millet, while an intermediate in pigeonpea (57.0%). The effective sample size required to capture maximum variability and to retain rare alleles while regeneration ranged from 47 to 101 for sorghum, 155 to 203 for pearl millet, and 77 to 89 for pigeonpea accessions. This study will support genebank curators, in understanding the dynamics of population within and among accessions, in devising appropriate germplasm conservation strategies, and aid in their utilization for crop improvement.

种质资源保育需以维持特定入库种质份样的遗传完整性为前提。在多数基因库中，地方品种构成了收集保存材料的主体，作物地方品种内部及品种间的遗传多样性程度，取决于农民所施加的异交水平与选择强度。本研究通过表型与基因型鉴定手段，对108份多样化地方品种及野生种质份样的内部及群体间多样性水平进行了评估，供试材料包括保存于国际半干旱热带作物研究所（ICRISAT）基因库的高粱、珍珠粟以及木豆各36份种质份样。本研究采用DArTseq技术，对每份种质份样内的15~25个个体进行基因型鉴定，总计完成1980个个体的分型，最终分别在珍珠粟、高粱、木豆中获得45249、19052以及8211个高质量单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点。高粱的份样内平均表型距离（0.090）与基因型距离（0.135）均为最低，而珍珠粟的份样内平均表型距离（0.227）与基因型距离（0.245）则为最高；木豆的份样内平均表型距离为0.203，基因型距离为0.168。分子方差分析结果同样证实，高粱种质份样内的变异占比最低（26.3%），珍珠粟则最高（80.2%），木豆的变异占比处于中间水平（57.0%）。在种质更新过程中，为捕获最大遗传变异并保留稀有等位基因所需的有效样本量，高粱种质份样为47~101，珍珠粟为155~203，木豆为77~89。本研究可为基因库管理员理解种质份样内及群体间的种群动态、制定合理的种质资源保育策略提供支撑，并有助于推动其在作物遗传改良中的应用。