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

Abstract

Hybridization is useful to enhance yield potential of agronomic crops in the world. Cotton has genome doubling due to alloteraploidy process and hybridization process in coordinate with duplicated genome can produce more yield and adaptability. Therefore, expression of homoeolog gene pairs between hybrids and inbred parents are vital to characterize genetic source of heterosis in cotton. Investigation results of homoeolog gene pairs between two contrasting hybrids and their respective inbred parents identi ed 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. BackgroundHybridization or polyploidy is a vital process, produces exceptional phenotypes through the interaction of two distinct genomes, and has a substantial in uence on the plant genome (1, 2). The novel phenotypes in plants can be consequent of many modi cations not only at genomic and epigenetic levels but also in gene expression patterns (3, 4). Several examples in cotton (5) Brassica napus (6), and Spartina (7) stated that hybridization (genome merger) modi ed more transcriptome than polyploidy. About 15% of owering plants are polyploidy (8) and divided into categories of autopolyploid and allopolyploid. Autopolyploid is evolved from a genome merger of the same or similar species but allopolyploids contain a genomic combination of two different species (3). Allopolyploids have enhanced growth and wider adaptations relative to autopolyploid. Many important crops are allopolyploids together with upland cotton (Gossypium hirsutum). In allopolyploids, hybridization or polyploidy is allied with various kinds of exchanges and interactions between homoeolog genes (duplicate genes) (9-11). Further modi cations are consisting of epigenetic (3, 12), gene activation (4, 13), and sequence removal (14,15). The result of different genomic interactions by hybridization or polyploidy produced several expression patterns of duplicate or genes with similar functions. For instance, these may be gene silencing, gene activation, novel expression, and altered parental contribution (2, 16). However, the direction and magnitude of duplicate gene expression are varied with crop, tissue, and organ (17)(18)(19)(20).Previous studies have identi ed four different expression forms of duplicated genes in plants e.g., one duplicate gene copy ...