The Effect of Promoter Region Indels on Expression Bias in Polyploid Cotton Species

Many species of cotton (Gossypium hirsutum, G. barbadense, G. tomentosum, etc.) are allotetraploid (A_T and D_T genomes). RNAseq data identified 478 gene pairs with common homoeologous expression biases between G. hirsutum, G. tomentosum, and a diploid F₁-hybrid. Of that group, 19 gene pairs in the diploid F₁ (Dt > At) were biased in the opposite direction than the natural polyploids (G. Hirsutum and G. tomentosum, e.g. At > Dt). Possible influences on this biased expression are indels in the promoter regions of one of the two genomes, thus altering how expression regulators bind to the gene promoters. Perhaps, the biased expression of homoeologous genes is due to different promoter efficiencies between duplicated copies. While much has been said about subfunctionalization and genome fractionation, these two hypotheses have not been investigated. This project examines WGS data of the promoter regions of genes where the diploid F₁-hybrid exhibits biased expression opposite of the tetraploids, with confirmation by cloning and Sanger sequencing promoter regions of exemplary genes.