Genetic dissection of cotton fiber quality and yield components using an interspecific introgression population

The 66 stable QTLs related to fiber quality and yield components were identified using Gh-Gb introgression population. A keratin-associated gene GbKAP from qFU-D04-1^b is verified to modulate cell elongation and seed yield. Chromosome segment substitution lines (CSSLs) are a powerful tool for genetic dissection of complex quantitative traits. Here, we re-sequenced 117 CSSLs introgressed from Gossypium barbadense acc. Hai7124 into G. hirsutum acc. TM-1. A total of substitution segment length of 4572 Mb, with a total genome coverage of 68.78%, were identified. Utilizing both regression stepwise-likelihood ratio test (RSTEP-LRT) and composite interval mapping (CIM) methods, 145 common QTLs (co-QTLs) were detected simultaneously across four environments/years, including 65 associated with fiber quality traits and 80 related to yield components. Among these, 66 co-QTLs were detected in two or more environments/years as stable QTLs. We further verified a stable fiber uniformity (FU)-related QTL qFU-D04-1^b using F₂ and F_2:3 secondary segregating populations derived from a cross between the elite introgression line CSSL25 and TM-1 and fine-mapped the QTL to the region of 762 kb on D04 chromosome. Within this interval, GB_D04G0512 named as GbKAP, encoding a keratin-associated protein, exhibited higher transcript level during fiber elongation stages in CSSL25 than in TM-1. There was a non-synonymous SNP in the coding region and three specific transcription factor binding sites in the promoter of GbKAP in CSSL25 compared to its homolog in TM-1. Heterologous expression of GbKAP in Arabidopsis resulted in increased root length, root cell length, hypocotyl length, rosette leaf growth, plant height, and seed size and weight, indicating GbKAP plays an important role in cell elongation and seed yield. This study provides valuable resources for the improvement of upland cotton fiber quality and yield traits.