Transgressive and subgenome expression level dominance and co-expression network analyses at the early fiber development in allopolyploid Gossypium

Polyploidization can lead to the emergence of new species. Allotetraploid cotton arose through hybridization and whole genome duplication of its diploid A and D genome progenitors. As a prominent global fiber crop, cotton serves as an excellent model organism for exploring plant evolutionary biology and fiber development, particularly in polyploidization. This study utilized transcriptomics to analyze expression difference between diploid and allotetraploid cotton, aiming to further the understanding of transcriptomic dynamics associated at different fiber developmental stages during polyploidization process. In this study, we identified additive and non-additive genes and clarified the contributions of non-additive genes during the tetraploid formation process. Furthermore, we constructed a gene co-expression network, providing new insights into the transcriptional regulation of polyploid cotton fiber development. Among non-additive genes, more A genome-biased expression level dominance (ELD-A) than D genome (ELD-D) occurred in the tetraploids. In Gossypium hirsutum, ELD-A genes played major roles during initial elongation, exerting greater dominance in fiber development. Transgressive genes impacted early fiber development in Gossypium barbadense. While the At subgenome profoundly influences tetraploid fiber development, Dt sub-genome activation, inheritance and sub/neo-functionalization promote superior high-yield traits. By constructing co-expression networks, we identified key fiber developmental candidate genes, providing valuable resources for functional research and breeding perspectives to develop superior cotton varieties. •Transcriptional expression patterns of diploid and allotetraploid cotton are different.•At the early stage of fiber development, ELD-A gene plays a major role in Gh, while transgressive genes in Gb.•Dt subgenome contributed to superior high-yield traits through activation, inheritance, and sub/neofunctionalization.•The candidate genes were identified providing important genetic resources for improving cotton fiber quality.