Genome Wide Association Analysis Of Salt Tolerance And Alkali Tolerance In Japonica Rice Seedlings

Salinie-alkali stress is a common abiotic stress that affects grain yield.As one of the most important food crops in the world,rice planting area and yield affect the national food security.However,due to the deterioration of rice growing environment and the decrease of cultivated area year by year,it is difficult to guarantee the planting area and yield of rice.The results show that rice planting in saline alkali soil can not only improve the utilization rate of saline alkali soil,but also improve the situation of saline alkali soil.Therefore,it is of great significance to study the genetic mechanism of salt tolerance and alkali tolerance of rice and to cultivate salt tolerant rice varieties by molecular means.In this study,295 japonica rice varieties were used as experimental materials.Under salt stress and alkali stress,seven salt and alkali tolerance correlations,including salt(alkali)damage level,Na~+concentration in the shoot,K~+concentration in the shoot,Na~+/K~+concentration in the shoot,Na~+concentration in the root,K~+concentration in the root and Na~+/K~+concentration in the root,were investigated.788396 high-quality SNPs were obtained by resequencing The whole genome association analysis was carried out,and the candi date genes of important QTLs were further screened,in order to analyze the genetic mechanism of salt tolerance and alkali tolerance of Japonica rice,and lay the foundation for mining and using salt tolerance genes.The main results of this study are as follows:1.Statistical analysis of the phenotypes of 7 salt tolerance and 7 alkali tolerance related traits showed that there were abundant phenotypic variations in each trait in this study,the variation coefficient of salt tolerance was between 20.13%-41.31%,and the variation coefficient of alkali tolerance was between 25.00%-52.99%.According to the level of salt and alkali damage,40 salt resistant(salt damage level?3)materials and 57 alkali resistant(alkali damage level?3)materials were selected.2.The correlation analysis showed that the correlation coefficients between most salt tolerant and alkali tolerant traits were significant or extremely significant.Among the salt tolerance characters,the salt damage level was positively correlated with the Na~+concentration in the upper part,negatively correlated with the Na~+/K~+concentration in the upper part,negatively correlated with the Na~+concentration in the upper part,positively correlated with the K~+concentration in the root and positively correlated with the Na~+concentration in the root.Among the alkali tolerance characters,the alkali damage level had a significant negative correlation with the K~+concentration above ground and root,and a significant positive correlation with the Na~+concentration at root;the Na~+concentration above ground had a significant negative correlation with the K~+concentration above ground;the Na~+concentration at the K~+concentration above ground and the K~+concentration at root had a significant negative correlation;the Na~+/K~+above ground had a significant positive correlation with the Na~+/K~+at root There was a significant negative correlation between Na~+concentration and K~+concentration in roots.3.Using the mixed linear model(MLM)of tassle5.0 software,19 salt tolerance SNPs with a total of 15 QTLs and 76 alkali tolerance SNPs with a total of 34 QTLs were detected at the P<5.46×10-6 level.q SNCS4,q SNKS12 and q RNKS11 contributed more than 10 salt tolerance QTLs.The highest contribution rate of QTL to alkali resistance was q SNKA9-2,with a contribution rate of 18.13.In addition to the overlapping of q SNKS12 of chromosome 12 affecting Na~+/K~+and q RNKA12-2 of Na~+/K~+above ground under salt stress and alkali stress,the rest QTLs were located in different chromosomes or different regions,indicating that the genetic overlap of salt stress and alkali stress at seedling stage was very small,and the inhe ritance of salt tolerance and alkali tolerance might be independent of each other.4.A total of 52 candidate genes were screened for QTLs that simultaneously affected the salt tolerance and alkali tolerance of Japonica rice seedlings,including 4 hypothet ical proteins,10retrotransposon proteins,7 transposon proteins,13 expression proteins with unknown functions,and 18 function annotation genes.q SNKA9-2,which had the highest contribution rate to alkali tolerance of japonica rice seedlings,was selected as candidate gene Because of the screening,a total of 18 candidate genes were found,including 1 hypothetical protein,2 retrotransposon proteins,1 transposon protein,4 expression proteins with unknown functions,and 10 functional annotation genes.