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Fiber quality improvement is a driving force for further cotton domestication and breeding. Here, QTLs for fiber quality were mapped in 115 introgression lines (ILs) first developed from two intraspecific populations of cultivated and feral cotton landraces. A total of 60 QTLs were found, which explained 2.03–16.85% of the phenotypic variance found in fiber quality traits. A total of 36 markers were associated with five fiber traits, 33 of which were found to be associated with QTLs in multiple environments. In addition, nine pairs of common QTLs were identified; namely, one pair of QTLs for fiber elongation, three pairs for fiber length, three pairs for fiber strength and two pairs for micronaire (qMICs). All common QTLs had additive effects in the same direction in both IL populations. We also found five QTL clusters, allowing cotton breeders to focus their efforts on regions of QTLs with the highest percentages of phenotypic variance. Our results also reveal footprints of domestication; for example, fourteen QTLs with positive effects were found to have remained in modern cultivars during domestication, and two negative qMICs that had never been reported before were found, suggesting that the qMICs regions may be eliminated during artificial selection.

Overuse of a small number of Upland cotton cultivars has narrowed cotton's genetic base, leading to major difficulties in developing cotton cultivars with diverse genetic backgrounds that are able to adapt to adverse conditions. To effectively broaden the genetic base, chromosome introgression lines (ILs) were developed, where TM‐1, the genetic standard of Upland cotton, was used as the common recipient and its two feral landraces, TX‐256 and TX‐1046, were used as the donors. A total of 115 ILs, with an average segment length of 11.15 cM, were first developed via intraspecific hybridization by marker‐assisted selection (MAS) in BC3F2 generations, spanning 3887.75 cM of the cotton genome. Association analysis showed that 63 markers were found to be associated with boll weight (BW), lint percentage (LP) and seed index. The percent of phenotypic variance explained by 148 QTLs detected was 4.12% on average. Eleven and five new QTLs for BW and LP (one stable QTL identified for LP in all environments) were detected, respectively, which can be used for efficiently pyramiding favourable alleles into one cultivar by MAS.

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