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Genetic basis and identification of candidate genes for salt tolerance in rice by GWAS

Yuan JieInstitute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, ChinaXueqiang WangState Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, ChinaYan ZhaoState Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, ChinaNajeeb Ullah KhanState Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, ChinaZhiqiang ZhaoInstitute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, ChinaYanhong ZhangInstitute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, ChinaXiaorong WenRice Experiment Stations in WenSu, Xinjiang Academy of Agricultural Sciences, Aksu, 843000, ChinaFusen TangRice Experiment Stations in WenSu, Xinjiang Academy of Agricultural Sciences, Aksu, 843000, ChinaFengbin WangInstitute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China. [email protected]Zichao LiState Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China. [email protected]

2020en

ABI

Annotatsiya

Soil salinity is a major factor affecting rice growth and productivity worldwide especially at seedling stage. Many genes for salt tolerance have been identified and applied to rice breeding, but the actual mechanism of salt tolerance remains unclear. In this study, seedlings of 664 cultivated rice varieties from the 3000 Rice Genome Project (3K-RG) were cultivated by hydroponic culture with 0.9% salt solution for trait identification. A genome-wide association study (GWAS) of salt tolerance was performed using different models of analysis. Twenty-one QTLs were identified and two candidate genes named OsSTL1 (Oryza sativa salt tolerance level 1) and OsSTL2 (Oryza sativa salt tolerance level 2) were confirmed using sequence analysis. Haplotype and sequence analysis revealed that gene OsSTL1 was a homolog of salt tolerance gene SRP1 (Stress associated RNA-binding protein 1) in Arabidopsis. The hap1 of OsSTL1 was identified as the superior haplotype and a non-synonymous SNP was most likely to be the functional site. We also determined that the level of salt tolerance was improved by combining haplotypes of different genes. Our study provides a foundation for molecular breeding and functional analysis of salt tolerance in rice seedlings.

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DOI: 10.1038/s41598-020-66604-7

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