Introducing the inherent genetic diversity of wild species into cultivars has become one of the hot topics in crop genetic breeding and genetic resource research. Fiber- and seed-related traits, which are critical to the global economy and people's livelihoods, are the principal focus of cotton breeding. Here, the wild cotton species Gossypium tomentosum was used to broaden the genetic basis of G. hirsutum and identify QTLs for fiber- and seed-related traits. A population of 559 chromosome segment substitution lines (CSSLs) was established with various chromosome segments from G. tomentosum in a G. hirsutum cultivar background. Totals of 72, 89, and 76 QTLs were identified for three yield traits, five fiber quality traits, and six cottonseed nutrient quality traits, respectively. Favorable alleles of 104 QTLs were contributed by G. tomentosum. Sixty-four QTLs were identified in two or more environments, and candidate genes for three of them were further identified. The results of this study contribute to further studies on the genetic basis of the morphogenesis of these economic traits, and indicate the great breeding potential of G. tomentosum for improving the fiber- and seed-related traits in G. hirsutum.

Naturally colored cotton fiber is environment-friendly but has monotonous color and poor fiber quality. Identification of green fiber or fuzz genes would aid in investigating the biosynthesis of green pigments in cotton fibers. In this study, we established a mapping population and found that the trait (white lint and green fuzz) from Gossypium hirsutum race latifolium is controlled by an incompletely dominant gene. The locus was mapped to a 71-kb interval on chromosome 21 containing seven genes, including a transcription factor with similarity to Arabidopsis MYB9. Harboring 13 SNPs and a 4-bp insertion/deletion in its promoter, GhMYB9 was highly up-regulated in the critical period for green pigment development in fuzz. Virus-induced gene silencing of GhMYB9 in a green-fuzz accession of G. hirsutum race latifolium TX-41 conferred white or light green fuzz. These results suggest that GhMYB9 is an important contributor to green pigments in cotton fiber and shed light on the regulatory mechanism controlling green pigmentation.