Genome-Wide Introgression and Quantitative Trait Locus Mapping Reveals the Potential of Asian Cotton () in Improving Upland Cotton ().

(2=2=26, A), the putative progenitor of the A-subgenome of (2=4=52, AD), is a repository of genes of interesting that have been eliminated during evolution/domestication of . However, its valuable genes remain untapped so far due to species isolation. Here, using a synthetic amphiploid (AADDAA) previously reported, we developed a set of 289 chromosome segment introgression lines (ILs) in by expanding the backcrossing population and through precise marker-assisted selection (MAS) although complex chromosomal structural variations existed between parents which severely hindered introgression. Our results showed the total coverage length of introgressed segments was 1,116.29 Mb, representing 78.48% of the A-subgenome in the background, with an average segment-length of 8.69 Mb. A total of 81 co- quantitative trait loci (QTLs) for yield and fiber quality were identified by both the RSTEP-ADD-based QTL mapping and the genome-wide association study (GWAS) analysis, with 1.01-24.78% of the phenotypic variance explained. Most QTLs for boll traits showed negative additive effects, but still has the potential to improve boll-number traits in . Most QTLs for fiber quality showed negative additive effects, implying these QTLs were domesticated in compared with and, a small quantity of fiber quality QTLs showing positive additive effects, conversely; however, indicates that has the underlying genes of enhancing fiber quality of . This study provides new insights into the breeding genetic potential of , lays the foundation for further mining favorable genes of interest, and provides guidance for inter-ploidy gene transference from relatives into cultivated crops.