GWAS combined with linkage analysis reveals major QTLs and candidate genes of salt tolerance in Japonica rice seedlings

文献类型： 外文期刊

第一作者： Xu, Shanbin

作者： Xu, Shanbin;Zheng, Jie;Du, Haoqiang;Li, Chong;Duan, Yuxuan;Cai, Yanan;Wang, Jingguo;Liu, Hualong;Yang, Luomiao;Xin, Wei;Jia, Yan;Zou, Detang;Zheng, Hongliang;Du, Xiaodong

作者机构：

关键词： Japonica rice seedling; salt tolerance; QTL; candidate gene; GWAS; linkage analysis

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：4.8； 五年影响因子：5.7 ）

ISSN： 1664-462X

年卷期： 2024 年 15 卷

页码：

收录情况： SCI

摘要： Background Soil salinization is one of the significant factors limiting high crop yields and expansion of arable land, seriously affecting global agricultural production. Rice is an essential food crop throughout the world, and its seedlings are particularly susceptible to salt stress, which can directly affect the growth and development of rice and its final yield. We used the natural population as the material for genome-wide association study (GWAS) and the recombinant inbred line (RIL) population from CD (salt sensitive)/WD20342 (salt tolerant) hybridization as the material for linkage analysis.Results The degree of salt tolerance was evaluated by using the relative root length (RRL), relative root number (RRN), relative root fresh weight (RRFW), and relative root dry weight (RRDW) as indicators. Fifteen and six major quantitative trait loci (QTLs) were identified by GWAS and linkage analysis, respectively. Meanwhile, the GWAS identified the lead SNP (Chr2_22340368), which was located within qRRL2 and qRRDW2 identified by linkage analysis. GWAS, combined with linkage analysis, selected a 196-kb overlapping region on chromosome 2, including 22 candidate genes. LOC_Os02g36880 was discovered as the candidate gene involved in salt tolerance by haplotype analysis, qRT-PCR, and sequence analysis. The score of salinity toxicity (SST) and seedling survival rate (SSR) were determined for CRISPR/Cas9 mutants (CR-1 and CR-15) and wild-type (ZH11), respectively.Conclusion The phenotypic validation indicated that LOC_Os02g36880 negatively regulated the salt tolerance at the seedling stage. This study provides resources for breeding Japonica rice to improve its response to salt stress.

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