Genome-Wide Identification and Homoeologous Expression Analysis of Genes in Wheat ( L.)

Plant protein phosphatase 2Cs (PP2Cs) play crucial roles in phytohormone signaling, developmental processes, and both biotic and abiotic stress responses. However, little research has been conducted on the gene family in hexaploid wheat ( L.), which is an important cereal crop. In this study, a genome-wide investigation of gene family was performed. A total of 257 homoeologs of 95 genes were identified, of which 80% of genes had all the three homoeologs across A, B, and D subgenomes. Domain analysis indicated that all the homoeologs harbored the type 2C phosphatase domains. Based on the phylogenetic analysis, TaPP2Cs were divided into 13 groups (A-M) and 4 single branches, which corresponded to the results of gene structure and protein motif analyses. Results of chromosomal location and synteny relationship analysis of homoeologs revealed that known chromosome translocation events and pericentromeric inversions were responsible for the formation of gene family. Expression patterns of homoeologs in various tissues and under diverse stress conditions were analyzed using publicly available RNA-seq data. The results suggested that genes regulate wheat developmental processes and stress responses. Homoeologous expression patterns of triad homoeologs from A, B, and D subgenomes, revealed expression bias within triads under the normal condition, and variability in expression under different stress treatments. Quantitative real-time PCR (qRT-PCR) analysis of eight genes in group A revealed that they were all up-regulated after abscisic acid treatment. Some genes in group A also responded to other phytohormones such as methyl jasmonate and gibberellin. Yeast two-hybrid assays showed that group A TaPP2Cs also interacted with TaSnRK2.1 and TaSnRK2.2 from subclass II, besides with subclass III TaSnRK2s. in group A was transformed into and germination assay revealed that ectopic expression of in enhanced its tolerance to ABA. Overall, these results enhance our understanding of the function of TaPP2Cs in wheat, and provide novel insights into the roles of group A TaPP2Cs. This information will be useful for in-depth functional analysis of TaPP2Cs in future studies and for wheat breeding.