Genome-wide selection and introgression of Chinese rice varieties during breeding

Jinyue Ge; Junrui Wang; Hongbo Pang; Fei Li; Danjing Lou; Weiya Fan; Ziran Liu; Jiaqi Li; Danting Li; Baoxuan Nong; Zongqiong Zhang; Yanyan Wang; Jingfen Huang; Meng Xing; Yamin Nie; Xiaorong Xiao; Fan Zhang; Wensheng Wang; Jianlong Xu; Sung Ryul Kim; Ajay Kohli; Guoyou Ye; Weihua Qiao; Qingwen Yang; Xiaoming Zheng

doi:10.1016/j.jgg.2022.02.025

Volume 49 Issue 5

May 2022

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Article Navigation > Journal of Genetics and Genomics > 2022 > 49(5): 492-501

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Genome-wide selection and introgression of Chinese rice varieties during breeding

doi: 10.1016/j.jgg.2022.02.025

a National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
b Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, Jiangsu 530006, China;
c College of Life Science, Shenyang Normal University, Shenyang, Jilin 110034, China;
d Liaoning Institute of Pomology, Yingkou, Liaoning 115009, China;
e Rice Research Institute, Guangxi Academy of Agricultural Science, Nanning, Guangxi 530007, China;
f National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572000, China;
g International Rice Research Institute, DAPO box 7777, Metro, Manila, Philippines;
h. Crop Biotech Institute & Department of Genetic Engineering, Kyung Hee University, Yongin 446-701, Republic of Korea

Funds:

This work was supported by the National Key Research and Development Program of China (2016YFD0100301 to Z.X.M.), the National Natural Science Foundation of China (31670211 and 31970237 to Z.X.M.), Sanya Yazhou Bay Science and Technology City (SKJC-2020-02-001 to Z.X.M.), the Central Public-interest Scientific Institution Basal Research Fund (S2021ZD01 to Z.X.M.), the Major Incubation Project of Shenyang Normal University (ZD20210 to P.H.B.), and the Hundred Talent Program of Shenyang Normal University (SSDBRJH2002012 to P.H.B.).

Received Date: 2021-10-31
Accepted Date: 2022-02-16
Rev Recd Date: 2022-02-11
Publish Date: 2022-03-12

Abstract

Abstract

China is the largest rice-producing country, but the genomic landscape of rice diversity has not yet been clarified. In this study, we re-sequence 1070 rice varieties collected from China (400) and other regions in Asia (670). Among the six major rice groups (aus, indica-I, indica-II, aromatic, temperate japonica, and tropical japonica), almost all Chinese varieties belong to the indica-II or temperate japonica group. Most Chinese indica varieties belong to indica-II, which consists of two subgroups developed during different phases of rice breeding. The genomic segments underlying the differences between these subgroups span 36.32 Mb. The Chinese japonica rice varieties fall into the temperate japonica group, consisting of two subgroups based on their geographical distribution. The genomic segments underlying the differences between these subgroups span 27.69 Mb. These differentiated segments in the Chinese indica varieties span 45 genes with nonsynonymous mutations that are closely related to variations in plant height and grain width. Fifty-four genes with nonsynonymous mutations are associated with the differences in heading date between the two Chinese japonica subgroups. These findings provide new insights into rice diversity in China that will facilitate the molecular breeding.
- Rice,
- Genome selection,
- Introgression,
- Agronomic traits,
- Breeding

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