Homoeologous Imbalance of Gene Expression in Polyploid Wheat

Advances in next-generation sequencing technologies and new genomic resources available for wheat provide new opportunities for the analysis of gene expression in polyploid genomes. In a set of 43,832 genes we have identified mutations differentiating duplicated genes in the wheat A, B and D genomes. RNA-seq data generated for hexaploid (genome formula is AABBDD) and tetraploid (genome formula is AABB) wheat and their diploid ancestors was used to investigate the evolution of gene expression in wheat. About 37% of genes demonstrated the evidence of homoeologous imbalance in expression. From 3% to 9% of genes were silenced in one of the three wheat genomes with the higher proportion of silenced genes in the A and B genomes than in the D genome. Positive correlation was found between the rate of gene silencing and ploidy level. Consistent with “gene balance” hypothesis, gene silencing in one of the genomes was compensated by the increase of gene expression in other genomes. The analysis of gene expression in a set of seven wheat accessions showed that the majority of silenced genes were not shared among accessions. Gene silencing established in tetraploid wheat showed tendency to be inherited by hexaploid wheat. Our data showed substantial level of expression divergence between duplicated genes suggesting that genetic redundancy have had significant impact on the evolution of gene expression in polyploid wheat. This study provides first insights into the homoeolog-specific patterns of gene expression in wheat laying foundation for detailed analysis of expression regulation in this polyploid genome.