Loci Related To Defoliant Sensitivity Of Upland Cotton Were Located Based On Association Analysis

Genome-wide Association Analysis was used to detect SNP sites significantly related to defoliator sensitivity in upland cotton,and candidate genes related to defoliator sensitivity were screened out,providing theoretical basis for machine-picked molecular assisted breeding.In this study,a natural population composed of 334 upland cotton(GOssypium hirsutae l.)germplasm resources was used as research materials.SNP sites were developed by high-throughput whole genome resequencing technology,and the population structure and genetic relationship of the natural population were analyzed;Atthe same time,phenotypic identification of defoldable agent sensitivity,yield and fiber quality related traits was carried out at 2 points in 2 years(2018 and 2019,Shihezi city and Wujiaqu City,Xinjiang Province).Stability and variation trend of 19 phenotypic traits in 4 environments were analyzed using R3.6.1 software.EMMAX software was used to conduct genome-wide association analysis of defoliant sensitivity based on MLM(P+K)model,combined with gene functional annotation and SNP haplotype analysis,and then screened out candidate genes related to defoliant sensitivity.The main research results are as follows:1.Compared with the reference genome,2366003 SNPS and 137361 In Del were detected,with an average of 1.06 SNPS per 1 KB and 0.07 In Del per 1 KB.Chromosome A08 had the largest number of SNPS(256991).The lowest number of SNPS was 32,644 on Chromosome D04.A total of 37108 SNPs and822 In Del were located in the gene coding region,including 17,560 SNPs causing non-synonymous mutations,one In Del 816 causing frameshift mutations,and 542 mutations causing significant effects such as coding loss or coding termination.About 82 percent of the mutations occurred in the intergene region,and only 14 percent occurred upstream or downstream.2.Population structure and genetic relationship analysis were carried out based on 2366003 SNPS,and 334 upland cotton varieties(lines)were divided into 2 subgroups.3.Based on the comprehensive analysis of phenotypic data of 19 phenotypic traits under 4environments,the variation coefficient of BLUP ranged from 0.02% to 1.88%;heritability varies from 0.00 to 0.89.The variation coefficient of 7 phenotypic traits related to defoliant sensitivity ranged from 0.14% to1.88%,and the heritability ranged from 0.00 to 0.69.4.Under the threshold p=3.99×10-6,three genes related to defolient sensitivity were identified from chromosome A08,A09 and D11 by GWAS analysis,namely Ghi＿A08G14871,Ghi＿A09G11721 and Ghi＿D11G05221.Haplotype analysis was performed on the three genes related to defoliating agent sensitivity,and the results showed that there were extremely significant differences in the sensitivity of the three genes to different haplotypes of defoliating agent.Ghi＿A08G14871 contained non-synonymous mutation 8＿125084770＿SNV(T/A),and materials carrying AA(mutant)genotype.The opened boll percentage was significantly higher than that of TT genotypes.Ghi＿A09G11721 contained the non-synonymous mutation 9＿79668969＿SNV(TA/T),and the opened boll percentage of the material carrying the TT(mutant)genotype was significantly higher than that of the material carrying the TATA(reference)genotype.Ghi＿D11G05221 contained non-synonymous mutation 24＿9433534＿SNV(T/C),and the defoliated percentage of materials carrying CA(mutant)genotype was significantly higher than that of materials carrying TC(reference)genotype.Combined with gene functional annotation,the arabidopsis homolog of Ghi＿A08G14871 was AtGC1,which was related to golgi formation.The arabidopsis homolog of Ghi＿A09G11721 is AtASPG1.In Arabidopsis,AtASPG1 is involved in abscisic acid(ABA)mediated stress response,and ASPG1 expression is induced by ABA in Arabidopsis.The Ghi＿D11G05221Arabidopsis homology is AtCYSC1,which not only encodes the-cyanoalanine synthase,but also is part of the cyanide detoxification pathway,which is a byproduct of ethylene synthesis pathway.In Arabidopsis,AtCYSC1 regulates its expression in response to biological stress,and mutations in this gene result in a root-hairless phenotype.