Homoeolog gene expression analysis reveals novel expression biases in upland hybrid cotton under intraspecific hybridization

Hybridization is useful to enhance the yield potential of agronomic crops in the world. Cotton has genome doubling due to the allotetraploid process and hybridization in coordination with duplicated genome can produce more yield and adaptability. Therefore, the expression of homoeologous gene pairs between hybrids and inbred parents is vital to characterize the genetic source of heterosis in cotton. Investigation results of homoeolog gene pairs between two contrasting hybrids and their respective inbred parents identified 36853 homoeolog genes in hybrids. It was observed both high and low hybrids had similar trends in homoeolog gene expression patterns in each tissue under study. An average of 96% of homoeolog genes had no biased expression and their expressions were derived from the equal contribution of both parents. Besides, very few homoeolog genes (an average of 1%) showed no biased or novel expression in both hybrids. The functional analysis described secondary metabolic pathways had a majority of novel biased homoeolog genes in hybrids. These results contribute preliminary knowledge about how hybridization affects expression patterns of homoeolog gene pairs in upland cotton hybrids. Our study also highlights the functional genomics of metabolic genes to explore the genetic mechanism of heterosis in cotton.