PDF(Pubmed)
Abstract：
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.
摘要：
世界各地土著保存的地方品种在表型和适应不同环境方面表现出较大的差异，这表明它们包含丰富的资源，可以作为水稻改良的基因库。尽管对栽培稻进行了广泛的研究，地方品种和现代栽培稻之间的变化和关系尚不清楚。在这项研究中,对总共20个品种进行了基因分型，其中包括10个来自全球不同国家的爪哇稻和10个来自中国的in稻，并产生了99.9GB的重测序原始数据。以粳稻品种Nipponbare的基因组序列为参考，以下单核苷酸多态性（SNP）的遗传特征范围为861,177至1,044,617，插入-缺失多态性（InDels）范围为164,018至211,135，结构变异（SV）范围为3,313至4,959。还确定了两个亚种之间的差异，即584,104个SNP，75,351InDels,104,606个SNP，和19,872种InDels，分别。此外，javanica特定SNP相关基因的基因本体论(GO)和KEGG揭示了它们参与DNA代谢过程,DNA复制,和DNA整合。通过Fst和扫描选择性分析鉴定序列变异和候选籽粒形状相关基因TGW2。TGW2的Hap4比其他的表现更好。本研究中说明的全基因组序列数据和遗传变异信息将作为分子育种的重要基因库，并有助于对javanicaOryza品种进行遗传分析。
