School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh 201314, India.
Genomics. 2021 May;113(3):1458-1468. doi: 10.1016/j.ygeno.2021.03.020. Epub 2021 Mar 17.
Crop productivity in legumes is determined by number and size/weight of seeds. To understand the genetic basis of seed size/weight in chickpea, we performed genome resequencing of 13 small- and 5 large-seeded genotypes using Illumina platform. Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) differentiating small- and large-seeded genotypes were identified. A total of 17,902 SNPs and 2594 InDels located in promoter and/or coding regions that may contribute to seed size/weight were detected. Of these, 266 SNPs showed significant association with seed size/weight trait. Twenty-three genes including those involved in cell growth/division, encoding transcription factors and located within QTLs associated with seed size/weight harbored SNPs within transcription factor binding motif(s) and/or coding region. The non-synonymous SNPs were found to affect the mutational sensitivity and stability of the encoded proteins. Overall, we provided a high-quality SNP map for large-scale genotyping applications and identified candidate genes that determine seed size/weight in chickpea.
豆类作物的生产力取决于种子的数量和大小/重量。为了了解鹰嘴豆种子大小/重量的遗传基础，我们使用 Illumina 平台对 13 个小粒和 5 个大粒基因型进行了基因组重测序。鉴定出区分小粒和大粒基因型的单核苷酸多态性 (SNP) 和插入/缺失 (InDel)。总共检测到 17902 个位于启动子和/或编码区的 SNP 和 2594 个 InDel，这些 SNP 和 InDel 可能有助于种子大小/重量。其中，266 个 SNP 与种子大小/重量性状显著相关。23 个基因包括参与细胞生长/分裂的基因、编码转录因子的基因，以及位于与种子大小/重量相关的 QTL 内的基因，这些基因在转录因子结合基序内或编码区内含有 SNP。非同义 SNP 被发现影响编码蛋白的突变敏感性和稳定性。总的来说，我们为大规模基因分型应用提供了高质量的 SNP 图谱，并鉴定出了决定鹰嘴豆种子大小/重量的候选基因。
