Resequencing of 1,143 indica rice accessions reveals important genetic variations and different heterosis patterns

Qiming Lv, Weiguo Li, Zhizhong Sun, Ning Ouyang, Xin Jing, Qiang He, Jun Wu, Jiakui Zheng, Jiatuan Zheng, Shaoqing Tang, Renshan Zhu, Yan Tian, Meijuan Duan, Yanning Tan, Dong Yu, Xiabing Sheng, Xuewu Sun, Gaofeng Jia, Hongzhen Gao, Qin Zeng, Yufei Li, Li Tang, Qiusheng Xu, Bingran Zhao, Zhiyuan Huang, Hongfeng Lu, Na Li, Jian Zhao, Lihuang Zhu (), Dong Li (), Longping Yuan () and Dingyang Yuan ()
Additional contact information
Qiming Lv: Hunan Academy of Agricultural Sciences
Weiguo Li: Huazhi Biotech Co. Ltd
Zhizhong Sun: Hunan Academy of Agricultural Sciences
Ning Ouyang: Hunan Academy of Agricultural Sciences
Xin Jing: Novogene Bioinformatics Institute
Qiang He: Hunan Academy of Agricultural Sciences
Jun Wu: Hunan Academy of Agricultural Sciences
Jiakui Zheng: Sichuan Academy of Agricultural Sciences
Jiatuan Zheng: Fujian Academy of Agricultural Sciences
Shaoqing Tang: China National Rice Research Institute
Renshan Zhu: Wuhan University
Yan Tian: Hunan Academy of Agricultural Sciences
Meijuan Duan: Hunan Academy of Agricultural Sciences
Yanning Tan: Hunan Academy of Agricultural Sciences
Dong Yu: Hunan Academy of Agricultural Sciences
Xiabing Sheng: Hunan Academy of Agricultural Sciences
Xuewu Sun: Hunan Academy of Agricultural Sciences
Gaofeng Jia: Huazhi Biotech Co. Ltd
Hongzhen Gao: Huazhi Biotech Co. Ltd
Qin Zeng: Huazhi Biotech Co. Ltd
Yufei Li: Huazhi Biotech Co. Ltd
Li Tang: Hunan Academy of Agricultural Sciences
Qiusheng Xu: Hunan Academy of Agricultural Sciences
Bingran Zhao: Hunan Academy of Agricultural Sciences
Zhiyuan Huang: Hunan Academy of Agricultural Sciences
Hongfeng Lu: Novogene Bioinformatics Institute
Na Li: Novogene Bioinformatics Institute
Jian Zhao: Novogene Bioinformatics Institute
Lihuang Zhu: Hunan Academy of Agricultural Sciences
Dong Li: Huazhi Biotech Co. Ltd
Longping Yuan: Hunan Academy of Agricultural Sciences
Dingyang Yuan: Hunan Academy of Agricultural Sciences

Nature Communications, 2020, vol. 11, issue 1, 1-10

Abstract: Abstract Obtaining genetic variation information from indica rice hybrid parents and identification of loci associated with heterosis are important for hybrid rice breeding. Here, we resequence 1,143 indica accessions mostly selected from the parents of superior hybrid rice cultivars of China, identify genetic variations, and perform kinship analysis. We find different hybrid rice crossing patterns between 3- and 2-line superior hybrid lines. By calculating frequencies of parental variation differences (FPVDs), a more direct approach for studying rice heterosis, we identify loci that are linked to heterosis, which include 98 in superior 3-line hybrids and 36 in superior 2-line hybrids. As a proof of concept, we find two accessions harboring a deletion in OsNramp5, a previously reported gene functioning in cadmium absorption, which can be used to mitigate rice grain cadmium levels through hybrid breeding. Resource of indica rice genetic variation reported in this study will be valuable to geneticists and breeders.

Date: 2020
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DOI: 10.1038/s41467-020-18608-0

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