Evolution of Homeologous Gene Expression in Polyploid Wheat

Abstract

Polyploidization has played a prominent role in the evolutionary history of plants. Two recent and sequential allopolyploidization events have resulted in the formation of wheat species with different ploidies, and which provide a model to study the effects of polyploidization on the evolution of gene expression. In this study, we identified differentially expressed genes (DEGs) between four BBAA tetraploid wheats of three different ploidy backgrounds. DEGs were found to be unevenly distributed among functional categories and duplication modes. We observed more DEGs in the extracted tetraploid wheat (ETW) than in natural tetraploid wheats (TD and TTR13) as compared to a synthetic tetraploid (AT2). Furthermore, DEGs showed higher Ka/Ks ratios than those that did not show expression changes (non-DEGs) between genotypes, indicating DEGs and non-DEGs experienced different selection pressures. For A-B homeolog pairs with DEGs, most of them had only one differentially expressed copy, however, when both copies of a homeolog pair were DEGs, the A and B copies were more likely to be regulated to the same direction. Our results suggest that both cis- and inter-subgenome trans-regulatory changes are important drivers in the evolution of homeologous gene expression in polyploid wheat, with ploidy playing a significant role in the process.

Keywords: differentially expressed gene; polyploidy; transcriptome; wheat; whole genome duplication.

Figure 1

Diagram of wheat ploidy history and targeted genotypes. (a) Timeline of the two allopolyploidization events in wheat evolutionary history that resulted in three different ploidy levels, diploid, tetraploid, and hexaploidy (Marcussen et al., 2014) [18]. (b) The four tetraploid wheats (red color) used in this study and their relationships in different ploidy backgrounds. In synthetic tetraploid wheat (AT2, S^lS^lAA), both AA and BB (S^l~B) evolved in the diploid background; in wild tetraploid wheat (TD, BBAA) and domesticated tetraploid wheat (TTR13, BBAA), both AA and BB evolved in tetraploid background after the whole genome duplication 0.36–0.5 Mya; In the extracted tetraploid wheat (ETW, BBAA), both AA and BB evolved in a hexaploid background before being extracted.

Figure 2

Analysis of differentially expressed genes (DEGs). Number and direction of change of DEGs identified in comparisons between different wheat genotypes in leaves (upper panel) and young inflorescences (lower panel). The total number of upregulated and downregulated genes are shown at top and bottom of x-axis for each comparison. The proportions of AA and BB upregulated DEGs are shown in red and beige, respectively; The proportions of AA and BB downregulated DEGs were shown in dark blue and light blue, respectively.

Figure 3

Functional enrichment of DEGs. GO (gene ontology) (lower) or Pfam (upper) terms that were significantly (q-value < 0.05) over-represented in DEGs of three or more comparisons are shown. The dot sizes correspond to proportions of DEGs and colors correspond to the q-values.

Figure 4

Proportion of DEGs in five duplication modes in different comparisons. The percentages of DEGs in AA and BB genome are shown on the up and down sides of x-axis. Different duplicate modes are shown in different colors in leaves (upper panel) and young inflorescences (lower panel) for each comparison.

Figure 5

Distribution Ka/Ks ratios for genes in DEG category (red) and non-DEG category (blue). Any gene differentially expressed between genotypes in either tissue was grouped into DEG category, while, others were grouped into non-DEG category. The significance of Mann–Whitney–Wilcoxon test between DEG category and non-DEG category are shown as ** p-value < 0.01.