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 (AD 1 ) and G. barbadense (AD 2 ) to evaluate the effects of immediate changes in ploidy. We compared the transcriptomes of diploid cotton species G. arboreum (A 2 ), G. raimondii (D 5 ), their F 1 hybrid (A 2 × D 5 ), natural allotetraploids (AD 1 and AD 2 ), and their derived haploids (hAD 1 via the GhDMP knockout system and hAD 2 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 AD 1 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 F 1 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.