An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

Junji Su,Juanjuan Liu,Ai Zhang,Caixiang Wang,Qi Ma,Xiongfeng Ma,Chunhui Shi,Xianliang Zhang,Delong Yang

doi:10.1186/s12870-020-02613-y

Abstract

BackgroundCotton (Gossypium spp.) fiber yield is one of the key target traits, and improved fiber yield has always been thought of as an important objective in the breeding programs and production. Although some studies had been reported for the understanding of genetic bases for cotton yield-related traits, the detected quantitative trait loci (QTL) for the traits is still very limited. To uncover the whole-genome QTL controlling three yield-related traits in upland cotton (Gossypium hirsutum L.), phenotypic traits were investigated under four planting environments and 9244 single-nucleotide polymorphism linkage disequilibrium block (SNPLDB) markers were developed in an association panel consisting of 315 accessions.ResultsA total of 53, 70 and 68 significant SNPLDB loci associated with boll number (BN), boll weight (BW) and lint percentage (LP), were respectively detected through a restricted two-stage multi-locus multi-allele genome-wide association study (RTM-GWAS) procedure in multiple environments. The haplotype/allele effects of the significant SNPLDB loci were estimated and the QTL-allele matrices were organized for offering the abbreviated genetic composition of the population. Among the significant SNPLDB loci, six of them were simultaneously identified in two or more single planting environments and were thought of as the stable SNPLDB loci. Additionally, a total of 115 genes were annotated in the nearby regions of the six stable SNPLDB loci, and 16 common potential candidate genes controlling target traits of them were predicted by two RNA-seq data. One of 16 genes (GH_D06G2161) was mainly expressed in the early ovule-development stages, and the stable SNPLDB locus (LDB_19_62926589) was mapped in its promoter region.ConclusionThis study identified the QTL alleles and candidate genes that could provide important insights into the genetic basis of yield-related traits in upland cotton and might facilitate breeding cotton varieties with high yield.

Highlights

Cotton (Gossypium spp.) fiber yield is one of the key target traits, and improved fiber yield has always been thought of as an important objective in the breeding programs and production
Phenotypic variations of three yield-related traits among accessions Three yield-related traits (BN, boll weight (BW) and lint percentage (LP)) of the natural population were evaluated in four planting environments (E1–4) during 2014 and 2015
By utilizing the RTM-genome-wide association studies (GWAS) procedure of the multiple environments, we identified respectively 53, 70 and 68 significant single-nucleotide polymorphism linkage disequilibrium block (SNPLDB) loci associated with boll number (BN), BW and LP (P < 0.05; Fig. 2; Table S4)

Summary

Introduction

Cotton (Gossypium spp.) fiber yield is one of the key target traits, and improved fiber yield has always been thought of as an important objective in the breeding programs and production. Over the past 5 years, a lot of significant single-nucleotide polymorphisms (SNPs) associated with fiber yield component traits have been identified by using genome-wide association studies (GWAS) methods in upland cotton [1, 4, 6,7,8,9]. These GWAS findings laid a good foundation for deciphering the genetic basis underlying cotton yieldrelated traits. The detected QTL for the target traits still remained limited, because only a handful of major QTL were identified through the conventional GWAS procedures

Methods

Results

Discussion

Conclusion