Abstract Recently, Li and his team hosted a project on roles of inversion in upland cotton population differentiation. Strikingly, genomic comparison identified, and subsequent RIL population and germplasm panel haplotype analyses confirmed, that large-scale inversions on chromosome A t 08 are widely distributed and have over time mediated the reduction of meiotic recombination that has ultimately driven genetically isolated haplotypes of G. hirsutum . This work is likely to become the new benchmark for cotton functional genomics research, and the scientific insights from the comparative analyses contributed substantially to our basic understanding of how genomic inversions influence meiotic recombination and thus lower genetic diversity in plant populations.