Genetic dissection of plant architecture, development, and seed morphology in exotic × elite Upland cotton...

Cotton (Gossypium hirsutum L.) breeding has primarily emphasized fiber yield and quality, yet plant architectural, developmental, and seed morphological traits also play key roles in productivity and management. Here, we dissect the genetic basis of four such traits: plant height (HT), number of nodes with one branch (N1B), days to flowering (DTF), and average surface area per seed (ASAS) using exotic × elite Upland cotton populations. Both population-specific and joint analyses of the populations identified 17 QTLs collectively, with ASAS having the largest number of detected QTLs. The exotic line T326 showed the highest potential for the improvement of ASAS. While HT, N1B, and DTF displayed limited genetic variance in these populations, gene ontology enrichment highlighted the CCR4-NOT complex as a potential shared regulatory hub connecting ASAS and DTF. In addition, ASAS showed a highly significant positive correlation and overlapping QTL regions with fiber strength and upper half mean length described in a companion paper, suggesting the possibility of strong linkage or pleiotropic effects of these genomic regions, which could be beneficial commercially. Overall, the data suggested no prevalence of negative allelic trade-offs or linkage drag from these secondary traits for the improvement of fiber quality traits, underscoring the value of exotic germplasm for simultaneous enhancement of fiber quality and seed morphology in Upland cotton breeding.