Decryption of favourable haplotypes and potential candidate genes for five fibre quality properties using a relatively novel genome-wide association study procedure in upland cotton

Abstract

To understand the genetic basis of crop economic characteristics, identifying whole-genome quantitative trait loci (QTLs) in breeding resources via genome-wide association studies (GWASs) is important, but conventional GWAS procedures have mainly concentrated on identifying regions of major QTLs. In this study, to reveal whole-genome QTLs controlling cotton fibre quality traits, a total of 1,236,418 single-nucleotide polymorphism (SNP) markers were explored in a natural population of 315 upland cotton accessions using the specific-locus amplified fragment sequencing (SLAF-seq) method, and 13,391 high-quality SNPs were organized into 9244 SNP linkage disequilibrium blocks (SNPLDBs) to develop molecular markers with multiple haplotypes/alleles. A relatively novel procedure for restricted two-stage multi-locus multi-allele GWAS (RTM-GWAS) involving two methods was applied, including multiple environments and four single environments. In total, 75, 77, 66, 66, and 60 significant SNPLDBs associated with the upper half mean length (UHML), fibre strength (FS), fibre micronaire (FM), fibre uniformity index (FUI), and fibre elongation (FE), respectively, were identified via the multiple-environment RTM-GWAS method. Based on these results, the haplotype/allele effects of the significant SNPLDB loci were estimated, and QTL-allele matrices were established to provide the abbreviated genetic composition of the population. Most importantly, nine stable SNPLDB loci were simultaneously detected in multiple environments and two or more single test environments with large –lg(P) values and percentages of explained phenotypic variation. Furthermore, favourable haplotypes/alleles of the nine stable SNPLDB loci were identified, and 79 potential candidate genes related to UHML and FS traits were predicted from RNA-seq data. Favourable haplotypes/alleles, potential candidate genes and QTL-allele matrices can offer important insights into the genetic basis of fibre quality traits in upland cotton and may facilitate the breeding of cotton varieties with excellent fibre quality properties.