Identification of candidate genes for salinity tolerance in Japonica rice at the seedling stage based on genome-wide association study and linkage mapping

Frontiers in Plant Science

Plant Science

Jingnan Cui¹  Tianze Ma¹  Hu Cao¹  Shaoming Liang¹  Hongliang Zheng¹  Shanbin Xu¹  Jingguo Wang¹  Wei Xin¹  Hualong Liu¹  Luomiao Yang¹  Yan Jia¹  Detang Zou¹ 

[1] Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China;

关键词: Japonica;    GWAS;    linkage mapping;    salinity tolerance;    seedling stage;   

DOI  :  10.3389/fpls.2023.1184416

 received in 2023-03-11, accepted in 2023-04-11,  发布年份 2023

来源: Frontiers

【 摘 要 】

BackgroundSalinity tolerance plays a vital role in rice cultivation because the strength of salinity tolerance at the seedling stage directly affects seedling survival and final crop yield in saline soils. Here, we combined a genome-wide association study (GWAS) and linkage mapping to analyze the candidate intervals for salinity tolerance in Japonica rice at the seedling stage.ResultsWe used the Na+ concentration in shoots (SNC), K+ concentration in shoots (SKC), Na+/K+ ratio in shoots (SNK), and seedling survival rate (SSR) as indices to assess the salinity tolerance at the seedling stage in rice. The GWAS identified the lead SNP (Chr12_20864157), associated with an SNK, which the linkage mapping detected as being in qSK12. A 195-kb region on chromosome 12 was selected based on the overlapping regions in the GWAS and the linkage mapping. Based on haplotype analysis, qRT-PCR, and sequence analysis, we obtained LOC_Os12g34450 as a candidate gene.ConclusionBased on these results, LOC_Os12g34450 was identified as a candidate gene contributing to salinity tolerance in Japonica rice. This study provides valuable guidance for plant breeders to improve the response of Japonica rice to salt stress.

【 授权许可】

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Copyright © 2023 Xu, Cui, Cao, Liang, Ma, Liu, Wang, Yang, Xin, Jia, Zou and Zheng