Identification Of Favourable SNP Allele And Haplotype Structure Analysis For Fiber Quality And Lint Percentage Traits By GWAS In Cotton

Cotton is one of the most important economic crops in the world.Its fiber can provide raw materials for the textile industry and can be used as fiber energy for industrial development.Studying the fiber development mechanism is an important part of cotton fiber improvement.In this study,278cotton accessions were collected to form the natural population,and SNP markers were developed using SLAF-seq method,and GWAS analysis and whole-genome LD blocks and haplotype structure analyses were performed based on SNPs markers and linkage disequilibrium relationship between two adjacent SNPs.Meanwhile,combining with bioinformatics and qRT-PCR experiments,we performed genome-wide identification and analysis of the evolution and expression patterns of the cellulose synthase gene superfamily in Gossypium species.These researches above may provide new insight into improving cotton fiber breeding work and studying fiber development molecule mechanism.By using SLAF-seq technology,3,464,561 SNPs were developed from 278 cotton materials and a total of 54,541 SNP markers were obtained with minInt of 0.85 and MAF of 0.05.Consequently,we performed population structure,PCA and phylogenetic tree analysis,which showed that the population can be divided into three sub-population including 31,235 and 12 lines in Q1,Q2 and Q3,respectively.Based on the pulation structure Q matrix and phenotypic values,a total of 670,678,1393 and 476significant(p<9.46e-8)SNPs loci were associated to the traits of fiber strength(FS),fiber length(FL),fiber micronaire(FM)and lint percentage(LP)by using GWAS analysis.The LD relationships between the two adjacent SNPs markers were calculated using Haploview 4.2 program and the conserved LD blocks and haplotypes were presented.A total of 15,14,25 and 31 blocks were identified to be associated with fiber traits of FS,FL,FM and LP,respectively.Further analysis of the three haplotypes within Block4 revealed that Hap1 is associated with LP trait and Hap3 is associated with traits of FS and FL.These excellent loci related to the target traits are helpful for candidate genes identification in our next research,and the results of blocks and haplotypes are feasible and would provide a further insights into genome organization and molecular breeding work.Among the candidate genes sourced from GWAS,there are two genes(Gh_A08G0421 and Gh_A05G3965)that are overexpressed in the 28 DPA stage of fiber development.The cellulose synthase gene superfamily,which includes the cellulose synthase(Ces)and cellulose synthase-like(Csl)families,is involved in the synthesis of cellulose and hemicellulose.This superfamily is critical for cotton fiber development in Gossypium species.Applying a series of bioinformatic methods,we identified 228 Ces/Csl genes from four Gossypium species(G.hirsutum,G.barbadense,G.arboreum,and G.raimondii).These genes were then grouped into 11 subfamilies based on phylogenetic relationships.A subsequent analysis of gene evolution revealed sites in CSLG and CSLJ genes that were under long-term positive selection pressure,with a posterior probability greater than 0.95.Moreover,the d_N:d_S value for the CSLJ clade was 1.305,suggesting this subfamily was under positive selection pressure.Our data indicated that the d_N:d_S value ranged from 0.0084 to 0.9693 among the homologous Ces/Csl genes,implying they were under purifying selection pressure.Our transcriptome and qRT-PCR analyses revealed that CesA genes were more highly expressed in tetraploids than in diploids.However,the Csl expression levels exhibited the opposite trend.Furthermore,changes to promoter sequences may have influenced the expression of homologous Ces/Csl genes.Our findings may provide novel insights into the evolutionary relationships and expression patterns of the Ces/Csl genes in Gossypium species.