Mining Of Major Loci Of Maize Salt Tolerance Genes And Development Of Linked Molecular Markers

Expanding the area of cultivated land to solve the shortage of land resources in China,is one of the most effective solutions to transforming the vast saline-alkali land into cultivated land reserve resources.However,the vast majority of crops as well as corn are not resistant to saline-alkali.Therefore,it is essential to dissect the genetic basis of salt-tolerance in maize and identify salt-tolerant genes,thus to provide the basis for cultivating new salt-tolerant varieties in theory.This study used 258 IBM（B73×Mo17）Syn10 double haploid（DH）lines to identify salt-tolerance related traits such as seedling length（SL）,mesocotyl length（ML）,and root length（RL）.QTL analysis was performed by combining with 6618 high-resolution genetic bin markers.Meanwhile,392 inbred lines with/without salt stress were utilized for GWAS analysis,with the average distribution of more than 1.68 million single nucleotide polymorphisms（SNP）markers across the whole genome.Our data indicated significant differences between 0 mmol/L NaCl treatment and salt tolerance treatment with 150 mmol/L NaCl.Four QTL,associated with RL,ML,and SL,were identified in the IBM Syn10 DH populations.The LOD scores range from 2.66-4.15,explaining4.7-7.2%of the observed phenotypic variations.A total of 2489 SNP sites(P<1×10^-5)associated with salt tolerance were detected across ten chromosomes in the GWAS panel.To further screen for genes that might be associated with salt tolerance,we defined the region containing three or more significant salt-tolerant SNP loci within the chromosomal 1Mb region as the salt-tolerant candidate region.Finally,a total of 579 genes were detected in the salt-tolerant candidate region.Besides,we selected a salt-tolerant line from the IBM Syn10 DH population.After being treated with 150 mmol/L NaCl for ten days,the RNA was extracted for transcriptomic sequencing.In total,3623 differentially expressed genes were identified,among which 1598 genes are up-regulated,and the other 2025 genes showed decreased expression in salt-tolerance treatment.Based on the genome-wide association analysis,we searched for significant SNPs associated with salt tolerance traits located within the QTL regions,and 139 SNPs were detected consistent with the QTL regions associated with salt-tolerance（q ML-1,q RL-1,q SL-1,q SL-2）.Finally,the genes identified by QTL and genome-wide association analysis were co-localized with the differentially expressed genes,and 266 and 59 genes were detected,respectively.We used the SMART website’s search function to annotate the protein sequence corresponding to the gene,analyzed its conserved domain,predicted the possible role of the coding protein,and finally screened out 12 candidate genes that may be related to the salt tolerance of maize.These 12 genes mainly encode transporters,protein kinases,and ion channel-related proteins,which may be involved in signal transduction and ion transport pathways in response to salt stress.Meanwhile,at 106Mb of chromosome 7,the candidate gene haplotypes were detected by linkage disequilibrium analysis of SNP loci significantly associated with phenotype.These results provided a basis for the study of maize salt tolerance-related functions and marker-assisted breeding.