Fig. 5

Identification of the cotton fiber quality trait-associated candidate gene Gh_D09G2376 on Dt09. a Manhattan plots for FE, FS, FL and FU on Dt09. The dashed line indicates the significance threshold (P < 10^− 3). b Local Manhattan plot and LD heatmap of the genomic region 49.0–50.7 Mb on Dt09. The red dashed line indicates the candidate region. c Gene structure of Gh_D09G2376. Black rectangles and black lines represent exons and introns, respectively. d Box plots of FE, FS, FL and FU based on the SNP allele i52359Gb. The significance levels of the differences were assessed using two-tailed t-tests. e RT-qPCR of Gh_D09G2376. GhHis3 was used as a housekeeping gene. Error bars represent the standard deviations of three independent biological replicates