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Gossypium arboreum  (2 n =2 x =26, A 2 ), the putative progenitor of the A t -subgenome of  Gossypium hirsutum  (2 n =4 x =52, AD), is a repository of genes of interesting that have been eliminated during evolution/domestication of  G. hirsutum . However, its valuable genes remain untapped so far due to species isolation. Here, using a synthetic amphiploid (AADDA 2 A 2 ) previously reported, we developed a set of 289  G. arboreum  chromosome segment introgression lines (ILs) in  G. hirsutum  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 t -subgenome in the  G. hirsutum  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  G. arboreum  still has the potential to improve boll-number traits in  G. hirsutum . Most QTLs for fiber quality showed negative additive effects, implying these QTLs were domesticated in  G. hirsutum  compared with  G. arboreum  and, a small quantity of fiber quality QTLs showing positive additive effects, conversely; however, indicates that  G. arboreum  has the underlying genes of enhancing fiber quality of  G. hirsutum . This study provides new insights into the breeding genetic potential of  G. arboreum , lays the foundation for further mining favorable genes of interest, and provides guidance for inter-ploidy gene transference from relatives into cultivated crops.

frontiers in plant science

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