Whole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in Rice

文献类型： 外文期刊

第一作者： Fan, Jiongjiong

作者： Fan, Jiongjiong;Hua, Hua;Luo, Zhaowei;Zhang, Qi;Chen, Mengjiao;Wei, Xin;Huang, Zonghua;Huang, Xuehui;Wang, Qin;Gong, Junyi

作者机构：

关键词： Rice; Chromosome segment substitution lines (CSSLs); QTL mapping; Heading date; RFT1

期刊名称：RICE （ 影响因子：5.638； 五年影响因子：6.097 ）

ISSN： 1939-8425

年卷期： 2022 年 15 卷 1 期

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收录情况： SCI

摘要： Rice is one of the most important food crops in Asia. Genetic analyses of complex traits and molecular breeding studies in rice greatly rely on the construction of various genetic populations. Chromosome segment substitution lines (CSSLs) serve as a powerful genetic population for quantitative trait locus (QTL) mapping in rice. Moreover, CSSLs containing target genomic regions can be used as improved varieties in rice breeding. In this study, we developed a set of CSSLs consisting of 117 lines derived from the recipient 'Huanghuazhan' (HHZ) and the donor 'Basmati Surkb 89-15' (BAS). The 117 lines were extensively genotyped by whole-genome resequencing, and a high-density genotype map was constructed for the CSSL population. The 117 CSSLs covered 99.78% of the BAS genome. Each line contained a single segment, and the average segment length was 6.02 Mb. Using the CSSL population, we investigated three agronomic traits in Shanghai and Hangzhou, China, and a total of 25 QTLs were detected in both environments. Among those QTLs, we found that RFT1 was the causal gene for heading date variance between HHZ and BAS. RFT1 from BAS was found to contain a loss-of-function allele based on yeast two-hybrid assay, and its causal variation was a P to S change in the 94th amino acid of the RFT1 protein. The combination of high-throughput genotyping and marker-assisted selection (MAS) is a highly efficient way to construct CSSLs in rice, and extensively genotyped CSSLs will be a powerful tool for the genetic mapping of agronomic traits and molecular breeding for target QTLs/genes.

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