Large-scaled genomic variation investigations for germplasm are critical for understanding the formation and evolution of favorable traits in crops. This study demonstrated that two extensive chromosomal inversions derived from landraces were the essential causes for subpopulation divergence in the Upland cotton (cultivars) population via analyzing approximately 3,000 Gossypium hirsutum accessions.  Moreover, genomic analyses also confirmed that the introgressed genomic fragments from diploid cotton were the key factor in improving fiber quality. This study provides insight into adaptation evolution and the theoretical basis for cotton fiber improvement.

Extensive inversions of two chromosomes caused population divergence

The major loci for fiber quality of Upland cotton

The fiber quality improvement effect for introgressed fragments derived from diploid cotton