Phenotype Identification And Genome-wide Association Study Of Salt Tolerance-related Traits Of Rice

Soil salinization is becoming more and more serious,and it is one of the common abiotic stresses that affect crop growth and yield.Rice is an important crop with moderate sensitivity to salt stress.Studying the molecular mechanism of rice salt tolerance and cultivating salttolerant varieties can improve salt tolerance while maintaining high and stable yield,which has important theoretical significance and practical application value.Genome-wide Association Study(GWAS)can simultaneously identify the loci of the complex traits of germplasm resources.In this study,a rice population containing 159 varieties were investigated for salt tolerance-related traits for three years and GWAS analysis was performed to identify the loci related to rice salt tolerance.The candidate genes were predicted and analyzed.The main contents are as follows:1.Investigation and analysis of field salt-tolerant phenotypes of rice population.The salt-tolerance related traits of rice population were investigated and the plant height(PH),tiller number(TN),effective panicle number(EPN),panicle length(PL)under normalsoil field and saline-soil field were counted.The ratios of saline-soil-field values to normalsoil-field values were used as the salt tolerance identification index.The results showed that both the PH,TN,EPN,PL of rice decreased under saline-soil-field conditions.The four statistical traits in the population all showed a continuous normal distribution,indicating that the rice salt tolerance traits were controlled by multiple QTLs.2.Genome-wide association analysis and analysis of candidate genes.The rice population contained 3 types: indica,japonica and Aus.Through SNP Calling,the whole-genome SNPs of 159 varieties were separated from Rice 3k population and quality control was performed,and a total of 3,013,743 SNPs were obtained.The population was divided into 5 subgroups through population structure analysis.Based on the population structure,phenotypic data and SNP data,genome-wide association analysis were performed and a total of 7 repetitive QTLs were identified,which located on Chromosome 1,2,3,4,5and 11.After analyzing these QTLs,2 candidate genes were obtained which were Os CHX13 and Os ERF138.The Os CHX13 CDS region could be divided into 5 haplotypes,Hap B was an superior haplotype,and Hap E was an inferior haplotype.The promoter region of Os CHX13 could be divided into 5 haplotypes,Hap A was an inferior haplotype,and Hap B was a superior haplotype.The expression of Os CHX13 had a significant response to salt stress.The Os ERF138 CDS region could be divided into 4 haplotypes,there was no difference between Hap A to Hap C,and Hap D was an inferior haplotype.The promoter region of Os ERF138 could be divided into 6 haplotypes,there was no difference between Hap A to Hap E,and Hap F was an inferior haplotype.Under salt stress,Os ERF138 was expressed in both shoot tissues and root tissues,and the expression level of shoot tissues was significantly higher than that in root tissues.