Genome-Wide Identification of the AGC Protein Kinase Gene Family Related to Photosynthesis in Rice (Oryza sativa)

Abstract

The cAMP-dependent protein kinase A, cGMP-dependent protein kinase G and phospholipid-dependent protein kinase C (AGC) perform various functions in plants, involving growth, immunity, apoptosis and stress response. AGC gene family is well described in Arabidopsis, however, limited information is provided about AGC genes in rice, an important cereal crop. This research studied the AGC gene family in the AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza nivara, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, Oryza glumaepatula and Oryza longistaminata were searched and classified into six subfamilies, and it was found that these species have similar numbers of members. The analysis of gene duplication and selection pressure indicated that the AGC gene family expanded mainly by segmental or whole genome duplication (WGD), with purifying selection during the long evolutionary period. RNA-seq analysis revealed that OsAGCs of subfamily V were specifically highly expressed in leaves, and the expression patterns of these genes were compared with that of photosynthesis-related genes using qRT-PCR, discovered that OsAGC9, OsAGC20, and OsAGC22 might participate in photosynthesis. These results provide an informative perspective for exploring the evolutionary of AGC gene family and its practical application in rice.

Keywords: AGC protein kinase; Oryza genus; gene family; photosynthesis; rice.

Figure 1

Phylogenetic relationship of AGC proteins identified in Oryza species and Arabidopsis.

Figure 2

Phylogenetic relationship, gene structure and conserved motifs of AGC family members. (a) Phylogenetic relationship of AGCs in rice and Arabidopsis. (b) Structure of exons and introns of AGCs, exons and introns were represented using rectangles and bars, respectively. (c) Distributions of conserved motifs.

Figure 3

Collinearity analysis of AGCs in Oryza species.

Figure 4

Haplotype analysis of the AGC gene family in 3010 rice genomes (3KRG). (a) Distribution of gene–CDS–haplotype number (gcHapN) in different populations. (b) Distribution of equitability values (E_H) in different populations. Bas, Basmati; Adm, Admixtures; XI, Xian/Indica; GJ, Geng/Japonica; Different colors represent different populations; * Difference is significant at p < 0.05 level among different populations; ** Difference is significant at p < 0.01 level among different populations; *** Difference is significant at p < 0.001 level among different populations.

Figure 5

Predicted cis-elements of the OsAGC gene family.

Figure 6

Expression patterns analysis of OsAGCs in O. sativa, japonica.

Figure 7

The expression profiles of four OsAGCs and three photosynthesis-related genes were evaluated by qRT–PCR in leaf-level at 47, 50, 53, and 56 days after sowing (DAS).