Comprehensive Evaluation of Salt Tolerance and Genome-Wide Association Study of Japonica Rice Germplasms at Seedling Stage
To investigate the distribution characteristics of Na+and K+in japonica rice germplasms at seedling stage under salt stress,identify elite salt-tolerant germplasms and detect ion homeostasis-related loci,181 japonica rice germplasms were used to determine the salt tolerance score(STS),shoot Na+content(SNC),root Na+content(RNC),shoot K+content(SKC),root K+content(RKC),calculate shoot Na+/K+(SNK),root Na+/K+(RNK)and comprehensive evaluation value(D),and conduct genome-wide association study(GWAS).The results showed that seven indexes STS,SNC,RNC,SKC,RKC,SNK and RNK showed abundant variation,and the variation coefficient ranged from 23.7%to 70.5%.The correlation analysis result showed that,SNC was extremly significantly positively correlated with RNC,SNK and RNK;RNC was extremly significantly positively correlated with SNK and RNK;SKC was significantly positively correlated with RKC and extremly significantly negatively correlated with SNK.Principal component analysis(PCA)results showed that four major components were extracted,with a cumulative contribution rate of 89.545%.Subsequently,five salt-tolerant germplasms,including Bertone,Cigalon,Banat2951,Zaonuodao and Shennong 2,were selected by D value,and Jiahe 1,Yueguang,Xingshi,Shanfuliya and Qianchonglang were salt-sensitive germplasms.The GWAS analysis revealed a total of 16 salt tolerance related InDel loci and 32 allelic variants,with contribution rate of 10.82%—20.57%.Among them,nine InDel loci were significantly associated with RNC,which were located on chromosomes 1,4,6,8,9 and 11;seven InDel loci were significantly associated with RNK,which were located on chromosomes 4,5,6,7,9 and 10,with contribution rate of 11.04%—18.79%.The allele 6IM20.68Mb-2 was detected in RNC and RNK,respectively.The InDel locus 9IM20.21Mb,which was significantly associated with RNK,showed three haplotypes.The RNK of Hap1 was significantly lower than that of Hap2 and Hap3,so it was a typical salt-tolerant haplotype.
Japonica riceSalt toleranceComprehensive evaluationGenome-wide association study(GWAS)
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