Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing
文献类型： 外文期刊
作者： Long, Weixiong 1 ; Li, Yonghui 1 ; Yuan, Zhengqing 2 ; Luo, Lihua 1 ; Luo, Laiyang 1 ; Xu, Weibiao 1 ; Cai, Yaohui 1 ; Xie, Hongwei 1 ;
作者机构： 1.Jiangxi Acad Agr Sci, Jiangxi Super Rice Res & Dev Ctr, Natl Engn Lab Rice, Nanchang, Jiangxi, Peoples R China
2.Wuhan Univ, State Key Lab Hybrid Rice, Wuhan, Peoples R China
期刊名称：PLOS ONE （ 影响因子：3.7； 五年影响因子：3.8 ）
ISSN： 1932-6203
年卷期： 2022 年 17 卷 10 期
页码：
收录情况： SCI
摘要： Oryza sativa ssp. javanica rice varieties exhibit a wide variation in the phenotypes of several important agronomic traits, including grain quality, grain shape, plant architecture, disease resistance, and high adaption to an unfavorable environment, indicating a great potential for rice improvement. DNA molecular markers are basic and critical tools in genetic analysis and gene mining. However, only a few whole-genome variation analyses have been performed in Oryza sativa ssp. Javanica (tropical japonica rice), and this has hampered the utilization of such an important resource. In this study, the length of insertions/deletions variation greater larger than 10 bp from 10 Oryza sativa ssp. indica rice and 10 Oryza sativa ssp. tropical japonica rice were extracted by using the Nipponbare genome as a reference. A total of 118 primer pairs which were almost evenly distributed on each chromosome corresponding to the loci of InDels were designed by the Primer 5 program. We confirmed 85 InDel markers from 60 rice varieties, including indica and tropical japonica, by running polyacrylamide gels. The InDel markers function like SSRs in identifying hybrids, calculating genetic distance, constructing the genetic linkage map, and gene mining. The InDel markers developed in this study might help in genetic studies and to investigate the tropical japonica rice varieties.
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