Genome-wide Association Study Of Salt Stress Tolerance At Seedling Stage In Rice

Salt stress is one of the most damaging abiotic factors that hindered the growth and production of crops.Because of global warming and climatic change,every year a considerable amount of cultivable land are swamped with salinity and creating shortage of world food production.Rice plants are sensitive to salinity and the extent of vulnerability of salinity is observed at seedling stage.So,improving salt tolerance is an important target in rice breeding.Salinity tolerance is a complex trait,and many physiological processes as well as environmental factors are related with salinity and governed by many QTLs/genes.Thus,the exploitation of genetic difference of available germplasm using molecular tools(gene/QTL mapping,GWAS)is necessary for adaptive breeding.The objective was set up to find out better salt tolerant genotypes and genes based on their physiological performance as well as genetic dissection at seedling stage of rice plant.We used 426 rice germplasms from 3K Rice Genome Project developed by the China National Crop Gene Bank and International Rice Gene Bank Collection;belongs to indica(62%),Japonica(28%),Aus(1%),Aromatic(1%)and Admixture(8%)from different countries though the germplasms were evaluated for morpho-physiological traits.11 morpho-physiological traits i.e.seedling survival index(SSI),shoot length(SL),RL(RL),shoot dry weight(SDW),root dry weight(RDW),Na~+conc.of shoot(SNC)as well as root(RNC),K~+conc.of shoot(SKC)as well as root(RKC),Na~+/K~+of shoot(SNK)as well as root(RNK)were measured under control(no salt)and salt stress,salinity response index(SRI)was also calculated.We performed a genome-wide association study(GWAS)to detect the trait-SNP association for all measured traits.A total of 28,20594 SNPs including 20,94607 SNPs for indica and 14,49167 SNPs for japonica sub-group were used in the GWAS considering<20%missing rate and MAF>0.05.The phenotypic variations of the germplasms were significant for all the studied traits under both control and salt stress conditions.Under salt stress,Na~+and Na~+/K~+ratio in shoot showed the negative significant correlation with K~+concentration of shoot and the plant growth parameters i.e.SL,RL,SDW and RDW,illustrated the detrimental effect of high Na~+accumulation in plant tissue.We have selected 10 most tolerant germplasms out of 426 germplasms considering the response of SNC,SKC and SNK as well as SSI>0.50.The salinity response of Na~+and Na~+/K~+in shoot was positive over the control condition.In total,82 QTLs were identified under control,salt stress and SRI including the QTLs of four(04)for SSI,six(06)for SL,five(05)for RL,two(02)for SDW,thirteen(13)for RDW,nine(09)for SNC,eighteen(18)for RNC,seventeen(17)for RKC,and eight(08)for SNK.Among these QTLs,26 QTLs were previously reported and 56 QTLs were newly identified in our experiment.We have identified ten(10)QTL clusters controlled different traits on chromosome 1,2,4,5,8,9 and 10 of which 4.186-4.397Mb,12.43-12.52Mb,23.10-23.30Mb&28.52-28.54Mb regions belongs to chromosome 1,23.89-24.74 Mb regions belongs to chromosome 2,29.07-29.13Mb region belongs to chromosome 4,1.745-2.180Mb belongs to chromosome 5,19.43-20.03Mb region belongs to chromosome 8,12.56-13.11 Mb region belongs to chromosome 9 and 3.97-4.59Mb belongs to chromosome 10.These QTL regions are very important for salt tolerant study.Based on gene based association analysis,we have identified seventeen(17)candidate genes of different traits from the region harboring strong linkage disequilibrium(r~2>0.8)SNP.These genes played significant roles on plant growth and development process.Out of 17 candidate genes,LOC_Os07g18560,LOC_Os07g18600 and LOC_Os07g22720 for SSI,LOC_Os09g17850 for SLR,LOC_Os09g21660,LOC_Os09g21700,LOC_Os11g20190 and LOC_Os11g20260 for RNCR,LOC_Os03g51060,LOC_Os10g07480 and LOC_Os10g07520 for RKCR,LOC_Os10g22039 for SNKR,functional markers also detected for those candidate genes.Moreover,LOC_Os09g21660 and LOC_Os09g21700 on chromosome 9,LOC_Os10g07480 and LOC_Os10g07520 on chromosome 10located on the QTL clusters.These functional SNPs allelic variants of these candidate genes can be used to hasten marker assisted selection(MAS)which contribute to design climate-resilient salt tolerant rice varieties.