Table_5_Whole Genome Resequencing of 20 Accessions of Rice Landraces Reveals Javanica Genomic Structure Variation and Allelic Genotypes of a Grain Weight Gene TGW2.XLSX

The landraces preserved by indigenous worldwide exhibited larger variation in the phenotypes and adaption to different environments, which suggests that they comprise rich resources and can be served as a gene pool for rice improvement. Despite extensive studies on cultivated rice, the variations and relationships between landraces and modern cultivated rice remain unclear. In this study, a total of 20 varieties that include 10 Oryza javanica collected from different countries worldwide and 10 Oryza indica from China were genotyped and yielded a sum of 99.9-Gb resequencing raw data. With the genomic sequence of the japonica cultivar Nipponbare as a reference, the following genetic features of single-nucleotide polymorphism (SNP) ranged from 861,177 to 1,044,617, insertion–deletion polymorphisms (InDels) ranged from 164,018 to 211,135, and structural variation (SV) ranged from 3,313 to 4,959 were identified in Oryza javanica. Variation between the two subspecies was also determined that 584,104 SNPs, 75,351 InDels, 104,606 SNPs, and 19,872 InDels specific to Oryza indica and Oryza javanica, respectively. Furthermore, Gene Ontology (GO) and KEGG of Oryza javanica-specific SNP-related genes revealed that they participated in DNA metabolic process, DNA replication, and DNA integration. The sequence variation and candidate grain shape-related gene TGW2 were identified through Fst and sweep selective analysis. Hap4 of TGW2 is performed better than others. The whole genome sequence data and genetic variation information illustrated in this study will serve as an important gene pool for molecular breeding and facilitate genetic analysis of Oryza javanica varieties.

全球各地本土社群保存的水稻地方品种（landrace）展现出更为丰富的表型变异与环境适应性，这表明其蕴含极为丰富的遗传资源，可作为水稻遗传改良的核心基因库。尽管学界对栽培水稻已开展大量研究，但地方品种与现代栽培稻之间的遗传变异及演化关系仍未明确。本研究共选取20份水稻材料，其中包括从全球多国采集的10份爪哇稻（Oryza javanica）以及10份来自中国的籼稻（Oryza indica），对其进行基因分型后共获得99.9 Gb的重测序原始数据。本研究以粳稻品种日本晴（Nipponbare）的基因组序列作为参考基因组，在爪哇稻中鉴定得到如下遗传变异：单核苷酸多态性（single-nucleotide polymorphism, SNP）数量介于861,177至1,044,617之间，插入缺失多态性（insertion–deletion polymorphisms, InDels）数量介于164,018至211,135之间，结构变异（structural variation, SV）数量介于3,313至4,959之间。本研究同时明确了两个亚种间的遗传变异特征：籼稻特异性拥有584,104个单核苷酸多态性与75,351个插入缺失多态性，爪哇稻则特异性存在104,606个单核苷酸多态性与19,872个插入缺失多态性。此外，对爪哇稻特异性单核苷酸多态性相关基因开展基因本体（Gene Ontology, GO）与京都基因与基因组百科全书（KEGG）富集分析，结果显示这些基因参与了DNA代谢过程、DNA复制及DNA整合等生物学过程。本研究通过Fst与选择性清除分析，鉴定到了与谷粒形状相关的候选基因TGW2及其序列变异，其中TGW2的单倍型Hap4表现优于其余单倍型。本研究产出的全基因组测序数据与遗传变异信息，将作为分子育种的重要遗传资源库，同时可为爪哇稻品种的遗传解析提供关键支撑。