Rathinasabapathi Pasupathi, Purushothaman Natarajan, Parani Madasamy
Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu-603 203, India.
Genome. 2016 May;59(5):363-6. doi: 10.1139/gen-2016-0025. Epub 2016 Mar 24.
Although rice genome was sequenced in the year 2002, efforts in resequencing the large number of available accessions, landraces, traditional cultivars, and improved varieties of this important food crop are limited. We have initiated resequencing of the traditional cultivars from India. Kavuni is an important traditional rice cultivar from South India that attracts premium price for its nutritional and therapeutic properties. Whole-genome sequencing of Kavuni using Illumina platform and SNPs analysis using Nipponbare reference genome identified 1 150 711 SNPs of which 377 381 SNPs were located in the genic regions. Non-synonymous SNPs (62 708) were distributed in 19 251 genes, and their number varied between 1 and 115 per gene. Large-effect DNA polymorphisms (7769) were present in 3475 genes. Pathway mapping of these polymorphisms revealed the involvement of genes related to carbohydrate metabolism, translation, protein-folding, and cell death. Analysis of the starch biosynthesis related genes revealed that the granule-bound starch synthase I gene had T/G SNPs at the first intron/exon junction and a two-nucleotide combination, which were reported to favour high amylose content and low glycemic index. The present study provided a valuable genomics resource to study the rice varieties with nutritional and medicinal properties.
尽管水稻基因组已于2002年完成测序，但对这种重要粮食作物的大量现有种质、地方品种、传统品种和改良品种进行重测序的工作仍很有限。我们已启动对印度传统品种的重测序工作。卡武尼是印度南部一种重要的传统水稻品种，因其营养和治疗特性而售价高昂。使用Illumina平台对卡武尼进行全基因组测序，并使用日本晴参考基因组进行单核苷酸多态性（SNP）分析，共鉴定出1150711个SNP，其中377381个SNP位于基因区域。非同义SNP（62708个）分布在19251个基因中，每个基因中的数量在1到115个之间。3475个基因中存在7769个具有较大效应的DNA多态性。这些多态性的通路映射显示，与碳水化合物代谢、翻译、蛋白质折叠和细胞死亡相关的基因参与其中。对淀粉生物合成相关基因的分析表明，颗粒结合淀粉合酶I基因在第一个内含子/外显子连接处有T/G SNP和一个双核苷酸组合，据报道这有利于高直链淀粉含量和低血糖指数。本研究为研究具有营养和药用特性的水稻品种提供了宝贵的基因组资源。
