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

Jie Yuan,Fusen Tang,Fengbin Wang,Zichao Li,Zhiqiang Zhao,Xueqiang Wang,Yanhong Zhang,Najeeb Ullah Khan,Xiaorong Wen,Yan Zhao

doi:10.1038/s41598-020-66604-7

Abstract

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.

Highlights

Soil salinity is a major factor affecting rice growth and productivity worldwide especially at seedling stage
Prior to genome-wide association study (GWAS) we performed a Principal component (PC) and kinship matrix analysis based on 3.5 million SNPs to characterize the population structure (Fig. 1)
For confirmation of the superior haplotype and functional site of OsSTL1 we investigated 446 wild rice (O. rufipogon) accessions using publicly available sequence data[23] to determine the origin of OsSTL1

Summary

Introduction

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. Thirty-three candidate genes in a protein interaction network were associated with salt tolerance in rice seedlings in a genome-wide association study (GWAS) using 295 accessions[13]. Because molecular marker-assisted selection (MAS) demands explicit genetic architecture of agronomic traits[19] identification of new QTLs/genes related to salt tolerance in rice and confirmation of elite alleles is necessary for their utilization in modern molecular breeding. Our results provide insight into the genetic architecture of salt tolerance and markers derived from the newly identified genes will be useful in improving salinity stress tolerance in rice seedlings

Methods

Results

Conclusion