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

Shanbin Xu; Jingnan Cui; Hu Cao; Shaoming Liang; Tianze Ma; Hualong Liu; Jingguo Wang; Luomiao Yang; Wei Xin; Yan Jia; Detang Zou; Hongliang Zheng

doi:10.3389/fpls.2023.1184416

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

Front Plant Sci. 2023 May 10:14:1184416. doi: 10.3389/fpls.2023.1184416. eCollection 2023.

Authors

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

Affiliation

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

Abstract

Background: Salinity 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.

Results: We 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.

Conclusion: Based 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.

Keywords: GWAS; Japonica rice; linkage mapping; salinity tolerance; seedling stage.

Grants and funding

This research was funded by the National Natural Science Foundation of China (grant No. U20A2025, 31872884), and the “Academic Backbone” Project of Northeast Agricultural University (grant No. 20XG24).