| Cotton(Gossypium spp.)is the most important natural textile fiber source worldwide.Upland cotton(Gossypium hirsutum L.)is the most widely cultivated tetraploid cotton species and accounts for 95% of annual worldwide cotton production.The Verticillum wilt resistance is the most important breeding target traits in cotton.Over the last two decades,many quantitative trait loci(QTLs)related to the above-mentioned target traits have been identified using QTL-mapping methods and association mapping based on simple sequence repeat(SSR)markers.However,few QTL for the most important breeding target traits have been identified genome-wide association studies based on single nucleotide polymorphism(SNP)loci in upland cotton.To better understand the genetic architecture of the most important breeding target traits in upland cotton,a population consisting of 355 upland cotton germplasm accessions was phenotypically characterized for Verticillum wilt resistance traits in six environments and was genotyped using the specific-locus amplified fragment sequencing(SLAF-seq)approach,A total of 93,250 SNPs covered all 26 chromosomes in 355 upland cotton accessions were discovered using SLAF-seq.1.There were extensive variations of phenotype resistance to Verticillum wilt in 355 upland cotton germplasm materials.The mean value of the disease of Verticillum wilt was in17.5-37.6 range,among which the lowest was 17.5 in the sick bed(2015)and the largest was37.6 in the greenhouse(2017).The resistance to Verticillum wilt of the natural population in many years was the trend of the near normal distribution.2.There was a significant difference in resistance to disease among different years.The disease resistance was the best in 2015,second in 2016,and the weakest in 2017.There were significant differences between different sites on the disease resistance,among which the disease resistance in greenhouse was weaker than that in the sick bed.The influence of the interaction between the year and the site on the disease resistance was significant,and the disease resistance from high to low was in the sick bed(2015),in the greenhouse(2015),in the greenhouse(2016),in the sick bed(2017),in the sick bed(2016),in the greenhouse(2017),orderly.On the whole,the disease resistance in the disease nursery was stronger than that in the greenhouse.It may be related to the climate and environmental impact.3.A total of 140 SSR markers distributing on the 26 cotton chromosomes were employed to detect the genetic diversity and the genetic structure of 186 upland cotton cultivars.A total of 355 alleles were obtained from 140 polymorphic SSR markers in the 186 materials,with an average of 2.54 alleles per SSR primer,and polymorphism information content of primers ranged from 0.50 to 0.99,with an average of 0.76;a total of 22 SSR loci were associated with Verticillum wilt resistance both in the GLM and the MLM models,and two loci,NAU998 and CGR5258,could be detected in more than two environments,explaining 5.53% and 12.07% of the observed phenotypic variances,respectively.4.According to the correlation analysis of the resistance to Verticillum wilt,these SNP markers covered all 26 chromosomes of upland cotton,of which the maximum of SNP markerswas 7,560 on the A06 chromosome,however,the lowest was 1,476 on D04 chromosome.Three significant associations with resistance to Verticillum wilt were obtained.In order to study the phenotypic effects of the significant association of SNP alleles,we selected three significant associated SNP loci.We selected three SNP loci for a significant association between Verticillum wilt,and 74 candidate genes were found near the site of rs A10:4209077;43 candidate genes were found near the site of rs A11:25550007;100 candidate genes were found near the site of rs D04:48805600.The molecular markers and candidate genes associated with Verticillum wilt were identified in this study,it can lay a theoretical foundation for molecular assisted breeding of Verticillum wilt resistance in cotton,and application to cotton disease resistance breeding. |
