Exploration Of Favorable Alleles Of Main Breeding Target Traits In Upland Cotton Based On Association Analysis

The Upland cotton is one of the most important economic crops in China,and the breeding of admirable varieties is a prerequisite for the production of cotton.It is very important to cotton breeding for xinjiang and the whole country that association analysis and exploration of elite alleles of breeding objective traits in upland cotton accessions of xinjiang excellent ecological environment.In this study,a diversity panel consisting of 403 upland cotton accessions was grown,and the 16 phenotypic traits were measured in different environments,including four main agronomic traits(plant height,the first fruit branch node,height of first fruit branch node,and fruit branch number)and six yield and its components traits(seed-cotton yield,lint percentage,boll weight,bolls per plant,lint index,and seed index)and fiber quality traits(fiber length,fiber strength,fiber micronaire,fiber uniformity and fiber elongation)and verticillium wilt resistance.Genotyping was performed with genome-wide Simple Sequence Repeats(SSR),and the genetic diversity,population structure,linkage disequilibrium(LD)of the 403 upland cotton accessions were analyzed,and were performed in association mapping of the 16 phenotypic traits,the favorable QTL alleles and typical accessions were mined.the results was follow:(1)403 upland cotton accessions were rich in phenotypic variation,the mean coefficients of variance ranged from 1.51% to 36.85%,the maximum was the verticillium wilt resistance and the minimum was the fiber uniformity;the broad heritability ranged from 46.23% to 91.99%,the maximum was the lint percentage and the minimum was the fruit branch number;The correlation analysis showed that there was a complex correlation between traits.(2)394 alleles were detected in 403 materials using 201 SSR markers,the number of allelic variation detected by different SSR markers varied from 1 to 4,with an average of 1.96,the average genetic diversity index was 0.556(ranging from 0.142 to 0.699),polymorphism information content(PIC)value was 0.483,ranging from 0.132 to 0.677.(3)The conclusions are the similar by using three kinds of analysis method(Population structure analysis based on STRUCTURE software,cluster analysis based on Nie's genetic distanceand PCAanalysis),this population should be classified into 2 subpopulations.Furthermore,the following association analysis is performed by using the Q matrix corresponding to K=2.The analysis of Linkage disequilibrium(LD)analysis were showed that whether the collinear marker loci or the non-collinear marker loci,there were different levels of linkage disequilibrium,at the P< 0.05 level,18.94% of the marker loci showed significant LD.(4)Based on the results of the genotype data,the phenotypic traits data of the BLUP results in six environments and phenotypic mean values of different environments,a mixed linear model(Q+K)in association mapping was performed to identify the associated SSR loci in upland cotton accessions,219 polymorphic loci were detected to be significant associations according to the BLUP and in at least two of the six environments,among which main agronomic traits,yield traits and fiber quality were 77,93 and 51,respectively.Using the identification of resistance to verticillium wilt in three environments,13 marker loci could be detected in more than two environments.Pleiotropism analysis of significant loci showed that 52 loci were associated with two or more traits at the same time.In comparison with previous studies,26 loci were found to be consistent with previous reports including 4 main agronomic traits,9 yield traits,12 fiber quality and 1 verticillium wilt resistance.the rest were newly discovered marker loci.These markers could provide marker source for molecular marker-assisted selection breeding in cotton.(5)73 elite alleles and 98 typical accessions that contained the favorable allele loci related to main breeding target traits were identified based on phenotypic effects and breeding practice,further study found that 24 materials had excellent elite alleles with multiple traits at the same time.The favorable QTL alleles and typical accessions for breeding target traits identified in this study will lay a good foundation for the selection of the best parents in hybrid breeding,the molecular marker assisted selection of hybrid progeny and the application of genome selection breeding.