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Long W, Li Y, Yuan Z, Luo L, Luo L, Xu W, Cai Y, Xie H. Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing. PLoS One 2022; 17:e0274418. [PMID: 36215240 PMCID: PMC9550083 DOI: 10.1371/journal.pone.0274418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 08/30/2022] [Indexed: 11/07/2022] Open
Abstract
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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Affiliation(s)
- Weixiong Long
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Yonghui Li
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Zhengqing Yuan
- State key Laboratory of Hybrid Rice, Wuhan University, Wuhan, China
| | - Lihua Luo
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Laiyang Luo
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Weibiao Xu
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Yaohui Cai
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Hongwei Xie
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China,* E-mail:
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