Genome-wide quantitative trait loci reveal the genetic basis of cotton fibre quality and yield-related traits in a Gossypium hirsutum recombinant inbred line population

Abstract

Cotton is widely cultivated globally because it provides natural fibre for the textile industry and human use. To identify quantitative trait loci (QTLs)/genes associated with fibre quality and yield, a recombinant inbred line (RIL) population was developed in upland cotton. A consensus map covering the whole genome was constructed with three types of markers (8295 markers, 5197.17 centimorgans (cM)). Six fibre yield and quality traits were evaluated in 17 environments, and 983 QTLs were identified, 198 of which were stable and mainly distributed on chromosomes 4, 6, 7, 13, 21 and 25. Thirty-seven QTL clusters were identified, in which 92.8% of paired traits with significant medium or high positive correlations had the same QTL additive effect directions, and all of the paired traits with significant medium or high negative correlations had opposite additive effect directions. In total, 1297 genes were discovered in the QTL clusters, 414 of which were expressed in two RNA-Seq data sets. Many genes were discovered, 23 of which were promising candidates. Six important QTL clusters that included both fibre quality and yield traits were identified with opposite additive effect directions, and those on chromosome 13 (qClu-chr13-2) could increase fibre quality but reduce yield; this result was validated in a natural population using three markers. These data could provide information about the genetic basis of cotton fibre quality and yield and help cotton breeders to improve fibre quality and yield simultaneously.

Keywords: QTL clusters; consensus genetic map; fibre quality; fibre yield; gene expression level; genetic correlation; upland cotton.

Figure 1

The phenotype of the parents and a transgressive segregation line in 22 environments and the correlation analysis. (a) The phenotype of the parents and transgressive segregation line in 22 environments. (b) The correlation analysis between the different traits in the same environments.

Figure 2

Detailed information about the consensus genetic map. (a) The density of markers in the genetic map in a 5 cM window. (b) The density of markers in the physical map in a 500 kb window. (c) The distribution of the SSR markers, SLAF‐SNP, markers and chip makers in the consensus genetic map. (d) Collinearity analysis of markers between the physical map and genetic map in the A subgenome. (e) Collinearity analysis of markers between the physical map and genetic map in D subgenome.

Figure 3

Detailed information about the QTLs and QTL clusters. (a) The position of the QTLs on the consensus genetic map. (b) The distribution of the stable QTLs for the six traits on the 26 chromosomes. (c) The position of QTL clusters on the consensus genetic map of A_t. (d) The position of QTL clusters on the consensus genetic map of D_t. (e) The number of two‐pair‐trait QTL clusters with the same and different direction for additive effect.

Figure 4

Heatmap of the expression level of candidate genes in six QTL clusters during cotton fibre development. (a–f) Heatmap of the expression level of candidate genes in qClu‐chr7‐2, qClu‐chr11‐1, qClu‐chr6‐2, qClu‐chr13‐2, qClu‐chr5‐1 and qClu‐chr25‐4 during cotton fibre development. (g–i) The qRT‐PCR result of the genes Gh_A13G0393, Gh_A13G0394 and Gh_A13G0395.

Figure 5

The detail information of the QTL cluster qClu‐chr13‐2. (a) The QTLs located in the QTL cluster qClu‐chr13‐2. (b) The genotype of the three markers in the QTL cluster qClu‐chr13‐2 based on the RIL population. (c) The genotype of the three markers in the QTL cluster qClu‐chr13‐2 based on the breeding parents. (d) The t‐test of the three markers in the QTL cluster qClu‐chr13‐2 based on the breeding parents in 2017. (e) The t‐test of the three markers in the QTL cluster qClu‐chr13‐2 based on the breeding parents in 2016.