Phenotypic variation analysis and QTL mapping for cotton ( Gossypium hirsutum L.) fiber quality grown in different cotton-producing regions

Fiber quality, as an important target trait in cotton breeding programs, is easily affected by the environment, and thus results in great complexity in breeding selection. In this study, we compared phenotypic variation in main fiber quality parameters (including fiber length, fiber strength and fiber micronaire) and dissected the molecular genetic basis using a recombinant inbred line population containing 282 individual lines grown at three locations in two major cotton-producing regions; i.e., the Yellow River Valley and the Yangtze River Valley in China, over two cotton planting seasons. We found that fibers produced from the Yangtze River Valley location appeared shorter, stronger and thicker relative to that from the Yellow River Valley location. A total of 27 Quantitative Trait Loci (QTL) were identified for the main fiber quality parameters. Six QTLs were detected in more than five datasets, which explained 5.09–23.17 % of the phenotypic variance. One QTL ( qFL16.1 ) was detected at the Yellow River Valley location over two planting seasons while three QTLs ( qFL19.1, qFS03.1 and qFM19.1 ) were detected at the Yangtze River Valley location over the 2 years of planting seasons. Nine QTLs with significant additive × environment interactions (QEI) were also identified, and eight of these QTLs were detected at the Yangtze River Valley location. Moreover, four of twenty-three QTLs for boll weight and lint percentage were identified in more than five environments. These results may be beneficial for marker-assisted cotton breeding across different cotton-producing areas.