The evolution of gene expression in allopolyploid cotton relative to parental diploids and induced haploids

Allopolyploidization, a process involving interspecific hybridization and whole-genome duplication, has both immediate and long-term evolutionary effects on plants. However, the immediate impact of genome doubling in cotton (Gossypium spp.) remains understudied due to the lack of resynthesized allopolyploids. In this study, we used haploid lines from the allotetraploid species Gossypium hirsutum (AD₁) and G. barbadense (AD₂) to evaluate the effects of immediate changes in ploidy. We compared the transcriptomes of diploid cotton species G. arboreum (A₂), G. raimondii (D₅), their F₁ hybrid (A₂ × D₅), natural allotetraploids (AD₁ and AD₂), and their derived haploids (hAD₁ via the GhDMP knockout system and hAD₂ via semigamy). We determined that haploidization has a minor effect on changes in gene expression compared to hybridization and allopolyploidization, highlighting the large effect of species-specific long-term evolution. Specifically, ploidy changes in AD₁ were linked to chromosome separation and nucleosome dynamics. Moreover, haploidization appeared to obscure homologous expression divergence due to changes in the trans environment, leading to a decreased amount of homoeolog expression bias (HEB). While significant associations were detected between nonadditive patterns of total homoeolog expression, HEB, and cis-trans regulatory categories, no apparent differences in these association patterns were observed among the F₁ hybrid, tetraploids, and haploids. These findings provide a more detailed view of the transcriptomic consequences of allopolyploidization in cotton, offering insight into the temporal dynamics of gene expression evolution and the underlying regulatory mechanisms.