Genome-wide integrative dissection of genetic basis of fiber color and whiteness regulation in upland cotton (Gossypium hirsutum)

Naturally colored cotton has gained renewed interest due to increasing environmental concerns over synthetic dyes. The genetic regulatory characteristics of fiber color are discovered by two perspectives in this study. Genome-wide association studies (GWAS) identified two major loci D11: 24.3–24.7 Mb and A07: 20.4–22.3 Mb controlling fiber color variation. Integrative QTL mapping and transcriptome profiling revealed three candidate genes Gh_D11G208100 , Gh_D11G207100 , and Gh_D11G207600 with distinct expression profiles in fiber whiteness on D11. In contrast, the A07 locus harbors key transcription regulators TT2 , C1 , and bHLH82 which are implicated in flavonoid-mediated brown pigmentation along with differentially expressed genes, Gh_A07G015400 , Gh_A07G019500 , and Gh_A07G019400 , further supporting their potential role in regulating fiber pigmentation. Segregation analysis of fiber color across three different F 2 populations revealed three gene models. The W1_W2 _loci were proposed to determine fiber whiteness located on D11 chromosome, while the fiber color gene locus Lb _ determined by genetic analysis is related to the key locus for transcription regulators TT2 on the A07 chromosome . The interaction of these three genes controls fiber color. Inheritance patterns were consistent pigment loss and a graded dilution model for pigmented phenotypes, with stable extreme classes white and near white, whereas intermediate pigmentation classes shifted between populations. We also identified overlapping QTLs of fiber quality and color attributes, indicating strongly linked genetic mechanisms. This integrated analysis supports a model of coordinated regulation, where transcriptional control from A07 influences pigment biosynthesis, while D11 modulates fiber surface or secondary metabolism to fine tune color intensity and whiteness.