Genome-Wide Quantification of Homeolog Expression Ratio in Synthetic Allotetraploid Arabidopsis kamchatica

Polyploidy plays an important role for evolutionary force in many eukaryotes including animals and plants. Allopolyploidization, or the whole genome duplication originated from two or more divergent genomes, is considered to contribute to flourish in broader and novel environmental niches. The acquisition of this environmental adaptation could be caused by an advantage of having duplicated gene pairs originated from the different species genomes (called homeolog). Until now, high sequence homologies between homeolog pairs have prevented genome-wide quantification of the homeolog expression levels. Here, we report a novel SNP-calling-free method to quantify the ratio of expression levels of homeolog pairs using RNA-seq, and the expression analysis of a synthetic allotetraploid Arabidopsis kamchatica derived from the diploid species A. halleri and A. lyrata. The comparison with an experimental SNP ratio analysis using PyroMark showed that the high accuracy of our method. By using our method, we analyzed the change of the homeolog expression ratio before and after cold stress treatment because the latitudinal distribution of A.lyrata is higher than A.halleri. As a result, the ratios of homeologs before and after the treatment were highly correlated (r=0.870), suggesting that the gene expression pattern in polyploids is less stochastic than previously estimated with other species. Moreover, our new statistical test incorporating overdispersion showed that homeologs whose ratio of homeolog was significantly changed were 1.11% of 20,369 expressed homeologs, many of which were related to stress responses. These homeologs may contribute to the environmental adaptation.