Genome-Wide Identification and Characterization of the OPR Gene Family in Wheat (Triticum aestivum L.)

Abstract

The 12-oxo-phytodienoic acid reductases (OPRs), which belong to the old yellow enzyme (OYE) family, are flavin mononucleotide (FMN)-dependent oxidoreductases with critical functions in plants. Despite the clear characteristics of growth and development, as well as the defense responses in Arabidopsis, tomato, rice, and maize, the potential roles of OPRs in wheat are not fully understood. Here, forty-eight putative OPR genes were found and classified into five subfamilies, with 6 in sub. I, 4 in sub. II, 33 in sub. III, 3 in sub. IV, and 2 in sub. V. Similar gene structures and conserved protein motifs of TaOPRs in wheat were identified in the same subfamilies. An analysis of cis-acting elements in promoters revealed that the functions of OPRs in wheat were mostly related to growth, development, hormones, biotic, and abiotic stresses. A total of 14 wheat OPR genes were identified as tandem duplicated genes, while 37 OPR genes were segmentally duplicated genes. The expression patterns of TaOPRs were tissue- and stress-specific, and the expression of TaOPRs could be regulated or induced by phytohormones and various stresses. Therefore, there were multiple wheat OPR genes, classified into five subfamilies, with functional diversification and specific expression patterns, and to our knowledge, this was the first study to systematically investigate the wheat OPR gene family. The findings not only provide a scientific foundation for the comprehensive understanding of the wheat OPR gene family, but could also be helpful for screening more candidate genes and breeding new varieties of wheat, with a high yield and stress resistance.

Keywords: OPR; expression pattern; gene family; stress response; wheat.

Figure 1

Phylogenetic tree of the wheat OPR family. The maximum-likelihood (ML) phylogenetic tree was constructed based on the amino acid sequence alignments of wheat (48), Arabidopsis (3), Oryza sativa (13), and Zea mays (8), using the MEGA7.0 software, with 1000 replicates. OPR genes in wheat are classified into five subfamilies, and the names of each subfamily are shown in different colors outside of the circle.

Figure 2

Phylogenetic relationship, gene structure, and conserved motif analysis of TaOPR genes. (a) Phylogenetic tree of 48 wheat OPR proteins. The maximum-likelihood phylogenetic tree was constructed using MEGA7.0, with 1000 replicates. (b) Exon-intron structures of TaOPR genes. Orange boxes represent exons, black lines represent introns, and the upstream/downstream regions of TaOPR genes are represented by blue boxes. (c) Conserved motifs of TaOPR proteins. Ten conserved motifs are shown in different colored boxes, and the details of the motifs are provided in Table S3.

Figure 3

Number of various cis-acting regulatory elements of TaOPR genes. The cis-acting regulatory elements were identified from PlantCARE online by an analysis at 1.5 kb upstream of the transcription start site of TaOPR genes. The graph was generated using cis-acting element names and functions of TaOPR genes, and the number of elements in five different subfamilies are shown in different colors.

Figure 4

Genomic distribution of TaOPR genes and gene homology analysis in wheat. Gray lines are all synteny blocks in the wheat genome, and the different color lines indicate duplicated OPR gene pairs on different chromosome. 1A, 1B, 1D indicate chromosome 1A, chromosome 1B and chromosome 1D, respectively.

Figure 5

(a) Expression profiles of TaOPRs in five different tissues and organs (leaf, root, spike, stem, and grain). The heatmap was constructed using the Heml software, and the FPKM (fragments per kilobase of transcript per million fragments) values of TaOPR genes were transformed by log2. The red and blue colors represent the higher and lower relative abundance of the transcript, respectively. (b) Analysis of expression profiles of five TaOPR genes in leaf and root by qRT-PCR. Data were presented as mean ± SD (n = 3), and the values differed significantly when p < 0.05. Varied letters within a figure meant a significant difference.

Figure 6

The expression profiles of 46 TaOPR genes under drought and heat stress treatments. FPKM (fragments per kilobase of transcript per million fragments)values of TaOPR genes were transformed by log2 to create the heat map using the Heml software. The red and blue colors represent the higher and lower relative abundance of each OPR gene, respectively.

Figure 7

Analysis of the relative expression level of TaOPRs by qRT-PCR. Expression profiles of five TaOPR genes, TaOPRI-B2, TaOPRII-B1, TaOPRIII-B7, TaOPRIV-A1, and TaOPRV-B1, under drought, heat, salt, wound, MeJA, ABA, SA, and aphid stresses. Data were presented as mean ± SD (n = 3), and the values differed significantly when p < 0.05. Varied letters within a figure meant a significant difference.