Genome-wide Association Study And Candidate Genes Cloning Of Salt Tolerance Traits In Rice Fields

More than one-third of the world’s humans mainly use rice as one of the main foods,and the demand for rice is very large.However,due to unfavorable environmental factors,the yield of rice crops,especially drought and saline-alkali stress,is greatly restricted,which has a significant impact on crop yield.Rice prefers neutral or weakly acidic soils,which are very sensitive to salt damage,especially in rice reproductive growth period.Salt stress will directly affect the decline of rice biomass.However,the area of global saline-alkali land is still expanding.According to non-conservative estimates,more than one-fifth of the world’s saline-alkali fields have greatly reduced arable land,which has created a huge obstacle to increasing rice production.Therefore,it is important to mine the salt tolerance gene of rice and study the salt tolerance mechanism of rice for the genetic breeding of salt tolerance traits in rice.At present,methods for mining salt-tolerant genes include gene chip,GWAS,QTL mapping,etc.Among them,GWAS is one of the commonly used methods for mining genes in recent years,using high-throughput typing technology to analyze tens of thousands of Single nucleotide polymorphisms(SNPs)that correlate SNP molecular data with phenotypic traits to mine candidate genes.In this paper,we will use the genome-wide association analysis(GWAS)method to plant 268 rice landraces in normal and saline-alkali fields(salt alkalinity 3%-5%)for two years,and the phenotype of maturity,ie in normal fields.And the pH(plant height),PL(ear length),ENP(effective tiller),and YPR(single yield)of each variety in the saline-alkali field,calculate the ratio,and associate the salt-tolerant traits of Daejeon with the genome-wide association of 2,535,266 SNP markers.A total of 8 association sites related to salt tolerance traits were identified,at least one of which was associated with the associated site.In order to further predict the candidate genes in the loci obtained from the association analysis,we performed LD(linkage disequilibrium)analysis on the well-correlated loci associated with the correlation,and the related SNPs were annotated,and the genes in the LD interval we obtained were obtained.In contrast to the SNP annotation,the SNPs with 3’UTR,5’UTR and non-synonymous mutations were found in the related loci.Based on gene function annotation and further haplotype analysis,6 reported salt-tolerant genes and 3 were discovered.A new salt-tolerant-related locus,three candidate genes in chr1,was initially validated by a near-isogenic line(containing a chr1 32.26 Mb fragment in ASO/IR24 NIL),and the 105 family was significantly better than the background parent.In the background parent,the significant increase in salt tolerance also preliminarily proved that the salt-containing gene was indeed contained in this fragment,and SAP3 detected that 5 SNPs had missense_variant,and the gene was divided into three haplotypes.The SAP protein family has the characteristics of A20/AN1 zinc finger domain.SAP proteins with A20/AN1 zinc finger structure are ubiquitous in eukaryotes and have been studied in animals,but their functions in plants are not very clear.The other is the MATE protein,which was not involved in salt tolerance in previous studies,but its expression level was significantly induced under salt stress.In Chr.9,a base-ascorbate transporter was obtained,which undergoes a 4 base variation in the 3’UTR,and contains 10 transmembrane domains by transmembrane domain analysis and is regulated in different haplotypes.Different induction conditions have been reported in previous studies on the importance of ascorbic acid for salt tolerance,and the main research results are concentrated in mammals.There are few studies on NAT proteins in plants.Corn(lep1),Arabidopsis AtNAT1,AtNAT12 are transported.Astragalus and uric acid,apple MdNAT1,MdNAT1 have been reported to be involved in salt tolerance and drought,but the specific mechanism has not been studied.The role of ascorbate transporter in rice in salt tolerance,whether it is functional against salt tolerance,needs further verification.In Chr.10,all the genes in LD were screened by linkage disequilibrium analysis of related sites to obtain SNPs in 3’UTR,5’UTR and non-synonymous mutations,and a comment was obtained based on gene annotation and quantitative results.As a gene for pectin methylesterase inhibitor,the expression level of this gene was detected in different varieties after salt treatment.Pectin methylesterases(PME)are the first key enzymes that catalyze the pectin,an important component of plant cell walls.Its catalytic action can make pectin produce different structures and functions in plant physiological processes.And the stress response in stress is of great significance.PME belongs to a protein encoded by a multi-gene family,and there are many subtypes.The structural changes between different subtypes may be related to its cellular localization and function.Pectin methylesterase inhibitors(PMEIs)can inhibit the deesterification of pectin methylesterase and regulate the activity of PME.Whether the gene encoding the pectin methyl esterase inhibitor is involved in salt tolerance requires further validation.