Abstract
Background Cotton is the most important natural fiber-producing crop globally. High yield, super quality fiber, and early maturity are equally important breeding goals in the cotton industry. However, it remains challenging to synchronously improve these traits through conventional breeding techniques.Methods To identify additional genetic information relating to yield, fiber quality, and early maturity, a high-density genetic map was constructed using Jifeng 1271 and Jifeng 173 cultivars as parents. Sixteen phenotypic traits were tested and quantitative trait locus (QTL) mapping was performed. Candidate genes were analyzed using published RNA-seq data and qRT-PCR assays.Results All 16 tested traits showed bi-directional transgressive segregation and most traits followed an approximately normal distribution. Overall, 33 and 12 trait pairs showed significant positive and significant negative correlations, respectively. A total of 317 QTL and 39 chromosomal regions containing overlapping QTL were mapped based on the generated high-density genetic map, including 18 stable and 18 major QTL. Three outstanding QTL—qLP-A13-3, qSI-A2-1, and qFL-D13-1—that could be repeatedly mapped and had a major additive effect on phenotypic variation were screened out. Thirteen trait pairs exhibiting significant positive correlations contained overlapping QTL, and overlapping QTL within the same region exhibited the same additive-effect directions. Ten trait pairs showing significant negative correlations also had overlapping QTL; for 8 of these pairs, the QTL within a region had opposite additive-effect directions. Four genes locating in the mapped QTL regions were screened out due to their high expression levels in the evaluated RNA-seq datasets and their annotated functions. Ghir_A04G014830.1, covered by qBW-A4-1, qSI-A401, qHNFFB-A4-1, and qFU-A4-1, encoded ACLA-1. Ghir_D07G023700.1, covered by qFT-D7-1, qNFFB-D7-1, qHNFFB-D7-1, qFU-D7-1, qFE-D7-1, and qFE-D7-2, encoded ALDH2B4. Ghir_D13G015010.1, encoding VTC2, and Ghir_D13G016670.1, encoding GA2OX1, were in the stable QTL qFL-D13-1 region. The qRT-PCR results relating to the expression patterns of these four genes in ovules and fibers suggested that these four genes may be involved in promoting seed development, fiber initiation, and fiber elongation.Conclusions Overall, these findings contribute additional information for the breeding of high-yield, super fiber quality, and early-maturity varieties as well as research on related molecular mechanisms.