Identifying QTL for fiber quality traits with three upland cotton (Gossypium hirsutum L.) populations

Cotton fiber quality was quantitative trait, controlled by multiple genes. Identification of stable quantitative trait loci (QTL) effectively contributing to favorable fiber quality traits would provide the key basis for marker-assisted selection used in molecular breeding projects. Three upland cotton F2 populations were established with a common parent Chinese cultivar Yumian 1 and three American commercial cultivars/lines (Acala Maxxa, CA3084 and TAM94L-25), each of which had unique fiber quality characteristic that was favorable economically. Three whole genome genetic maps were constructed with 323, 302 and 262 SSR loci for population (Yumian 1 × Acala Maxxa), (Yumian 1 × CA3084), and (Yumian 1 × TAM 94L-25) respectively, spanning 1,617.2, 1,639.9 and 1,441.4 cM. Based on these genetic maps and three generation phenotypic data of fiber quality traits (F2, F2:3 and F2:4), 77 QTL were detected, including 19 for fiber length, 14 for fiber uniformity, 17 for micronaire, 10 for fiber elongation, and 17 for fiber strength. Among these QTL, 46 QTL were significant QTL and 31 were putative QTL, including that one QTL (qFL05.1) and four QTL (qFL23.1, qFM06.1, qFM06.2 and qFE25.1) were detected across three and two populations respectively; two QTL qFL10.1 (Yumian 1 × TAM 94L-25) and qFL15.1 (Yumian 1 × Acala Maxxa) were detected in three generations; qFM23.1, qFE18.1 and qFS21.2 detected in population (Yumian 1 × CA3084), qFE10.1, and qFS10.2 detected in population (Yumian 1 × TAM 94L-25), and qFS15.1 detected in population (Yumian 1 × Acala Maxxa), were all detected in two generations. Alleles underlying these stable QTL were valuable candidate gene for fine mapping, cloning, and favorable gene pyramiding projects. Our study also verified that QTL mapping of fiber quality traits using multiple populations with a common parent had higher efficiency compared to single population crossed with two parents and favorable alleles contributed to QTL effect could be conferred by parents with inferior fiber quality traits.