A Genome-Wide Analysis of the Jasmonic Acid Biosynthesis Gene Families in Peanut Reveals Their Crucial Roles in Growth and Abiotic Stresses

Abstract

Abiotic stress is a limiting factor in peanut production. Peanut is an important oil crop and cash crop in China. Peanut yield is vulnerable to abiotic stress due to its seeds grown underground. Jasmonic acid (JA) is essential for plant growth and defense against adversity stresses. However, the regulation and mechanism of the jasmonic acid biosynthesis pathway on peanut defense against abiotic stresses are still limitedly understood. In this study, a total of 64 genes encoding key enzymes of JA biosynthesis were identified and classified into lipoxygenases (AhLOXs), alleno oxide synthases (AhAOSs), allene oxide cyclases (AhAOCs), and 12-oxo-phytodienoic acid reductases (AhOPRs) according to gene structure, conserved motif, and phylogenetic feature. A cis-regulatory element analysis indicated that some of the genes contained stress responsive and hormone responsive elements. In addition to proteins involved in JA biosynthesis and signaling, they also interacted with proteins involved in lipid biosynthesis and stress response. Sixteen putative Ah-miRNAs were identified from four families targeting 35 key genes of JA biosynthesis. A tissue expression pattern analysis revealed that AhLOX2 was the highest expressed in leaf tissues, and AhLOX32 was the highest expressed in shoot, root, and nodule tissues. AhLOX16, AhOPR1, and AhOPR3 were up-regulated under drought stress. AhLOX16, AhAOS3, AhOPR1, and AhAOC4 had elevated transcript levels in response to cold stress. AhLOX5, AhLOX16, AhAOC3, AhOPR1, and AhOPR3 were up-regulated for expression under salt stress. Our study could provide a reference for the study of the abiotic stress resistance mechanism in peanut.

Keywords: abiotic stress; genome-wide; jasmonic acid biosynthesis; peanut.

Figure 1

The distribution of the LOX, AOS, AOC, and OPR genes in A. duranensis, A. ipaensis (A), and A. hypogaea (B).

Figure 2

The phylogenetic analysis of proteins implicated in JA biosynthesis-related enzymes in Arabidopsis thaliana, Oryza sativa, Zea mays, Glycine max, Phaseolus vulgaris, Cicer arietinum, A. duranensis, A. ipaensis, and A. hypogaea. A phylogenetic tree was created using the maximum-likelihood (ML) method with 1000 replications by MEGA11 software (version v11.0.13). (A) AhLOXs; (B) AhAOSs; (C) AhAOCs; (D) AhOPRs.

Figure 3

Distribution of conserved domains of JA biosynthesis-related enzyme genes in A. hypogaea. (A) AhLOXs; (B) AhAOSs; (C) AhAOCs; (D) AhOPRs.

Figure 4

Distribution and composition of exons–introns of JA biosynthesis-related enzyme genes in A. hypogaea. (A) AhLOXs; (B) AhAOSs; (C) AhAOCs; (D) AhOPRs.

Figure 5

Distribution of conserved motifs of JA biosynthesis-related enzyme genes in A. hypogaea. (A) AhLOXs; (B) AhAOSs; (C) AhAOCs; (D) AhOPRs. Various conservative motifs are represented by different colors.

Figure 6

Protein structure and 3D analysis of JA biosynthesis genes in peanut. (A) AhLOXs; (B) AhAOSs; (C) AhAOCs; (D) AhOPRs. Three-dimensional structure predictions of 64 proteins; domains are represented by different colors, with PLAT_LH2 in green, lipoxygenase in red, CYP74 in blue, p450 in yellow, Allene_ox_cyc in purple, Oxidored_FMN in light blue, and uncharacterized regions are shown in gray.

Figure 7

Cis-regulatory elements in the promoters of peanut JA biosynthesis-related enzyme genes. (A) Distribution of various cis-regulatory elements in AhLOX, AhAOS, AhAOC, and AhOPR promoter regions. (B) Number of elements in different families is counted. (C) Classification and percentage of different cis-regulatory elements.

Figure 8

Interactions and regulation networks of genes involved in JA biosynthesis of peanut. (A) Predicted protein–protein interaction network of AhLOXs, AhAOSs, AhAOCs, and AhOPRs. (B) Regulatory network of putative miRNAs and their targeted candidate genes. Yellow, green, blue, and orange circles represent target genes. The pink circles represent miRNAs. The putative regulatory relationships between miRNAs and their targeted JA biosynthesis-related enzyme genes are shown as gray lines.

Figure 9

Heatmap of JA biosynthesis-related enzyme genes in 22 peanut tissues by RNA-seq. (A) AhLOXs; (B) AhAOSs; (C) AhAOCs; (D) AhOPRs. Leaf 1: Lateral stem leaf; leaf 2: Mainstem leaf; leaf 3: Seedling leaf; veg shoot: Vegetative shoot tip; repr shoot: Reproductive shoot tip; root: Root; nodule: Module; perianth: Perianth; stamen: Stamen; pistil: Pistils; peg tip 1: Peg tip aerial; peg tip 2: Peg tip below soil; peg tip Pat. 1: Peg tip to fruit Pattee 1; fruit Pat. 1: Fruit Pattee 1; fruit Pat. 3: Fruit Pattee 3; pericarp Pat. 5: Pericarp Pattee 5; pericarp Pat. 6: Pericarp Pattee 6; seed Pat. 5: Seed Pattee 5; seed Pat. 6: Seed Pattee 6; seed Pat. 7: Seed Pattee 7; seed Pat. 8: Seed Pattee 8; seed Pat 10: Seed Pattee 10. The relative expression values are shown on left side of heatmap.

Figure 10

Heatmap of JA biosynthesis-related enzyme genes under drought stress by qRT-PCR. (A) AhLOXs; (B) AhAOSs; (C) AhAOCs; (D) AhOPRs. Relative expression values of green (low) to purple (high) are shown in right side of heatmap. Expression levels above 30 times were shown in red.

Figure 11

Key enzyme proteins of JA biosynthesis-mediated drought (A), cold (B), and salt stress (C) responses in peanut. Solid arrows represent direct promotion and solid horizontal bars represent suppression of expression. Gene expression range increasing from blue to red and placed on right side of figure. Solid arrows indicate promotion.