MIKC-type MADS-box transcription factor gene family in peanut: Genome-wide characterization and expression analysis under abiotic stress

Abstract

Peanut (Arachis hypogaea) is one of the most important economic crops around the world, especially since it provides vegetable oil and high-quality protein for humans. Proteins encoded by MADS-box transcription factors are widely involved in regulating plant growth and development as well as responses to abiotic stresses. However, the MIKC-type MADS-box TFs in peanut remains currently unclear. Hence, in this study, 166 MIKC-type MADS-box genes were identified in both cultivated and wild-type peanut genomes, which were divided into 12 subfamilies. We found a variety of development-, hormone-, and stress-related cis-acting elements in the promoter region of peanut MIKC-type MADS-box genes. The chromosomal distribution of peanut MADS-box genes was not random, and gene duplication contributed to the expansion of the MADS-box gene family. The interaction network of the peanut AhMADS proteins was established. Expression pattern analysis showed that AhMADS genes were specifically expressed in tissues and under abiotic stresses. It was further confirmed via the qRT-PCR technique that five selected AhMADS genes could be induced by abiotic and hormone treatments and presented different expressive profiles under various stresses. Taken together, these findings provide valuable information for the exploration of candidate genes in molecular breeding and further study of AhMADS gene functions.

Keywords: MADS-box transcription factor; abiotic stress; expression patterns; peanut; phylogenetic analysis.

Figure 1

Phylogenetic tree of the peanut MIKC-type MADS-box gene family. Phylogenetic tree of 116 MADS-box proteins from peanut (93) and Arabidopsis (23). Twelve subfamilies are highlighted with specific colors.

Figure 2

Phylogenetic relationship, conserved motifs, and exon−intron structure analysis of the MADS-box genes in peanut. (A) The maximum-likelihood phylogenetic tree was constructed using MEGA X with 1000 replicates. (B) Conserved motifs of MADS-box proteins. Ten conserved motifs are shown in different-colored boxes. (C) Exon−intron structures of MADS-box genes. The yellow boxes represent exons, and the black lines represent introns.

Figure 3

Interaction networks of AhMADS in peanut based on Arabidopsis data.

Figure 4

Chromosomal location of MIKC-type MADS-box proteins. In total, 93 AhMADS genes were located on 18 chromosomes. Genes from different subfamilies are shown in different colors.

Figure 5

Chromosomal distributions and synteny relationships of MADS-box genes in peanut. Red lines indicate the duplicated AhMADS gene pairs in peanut.

Figure 6

Cis-acting regulatory elements in the peanut MADS-box gene promoters. (A) The distribution of cis-acting elements in the promoter of each peanut MADS-box. (B) Various functional cis-acting elements are shown with different colors in the pie charts.

Figure 7

Expression profiles of MIKC-type MADS-box genes in 22 different peanut tissues. The heatmap was generated by Heml software, and the fragments per kilobase of transcript per million fragments (FPKM) values of peanut MADS-box genes were log2-transformed. The red and blue colors represent the maximum and minimum values, respectively.

Figure 8

Expression levels of MADS-box genes under salt and drought stress treatments in peanut. The FPKM values of the peanut MADS-box genes were log2-transformed to create the heatmap using Heml software. The blue and red colors represent the expression levels of AhMADS genes from low to high.

Figure 9

Analysis of the relative expression levels of peanut AhMADS genes by qRT-PCR. The expression profiles of five peanut AhMADS genes (AhMADS9, AhMADS21, AhMADS34, AhMADS50, and AhMADS64) under four stresses (cold, hot, drought, and salt) were validated. The data are presented as the mean ± SD (n = 3), and the values differed significantly at p < 0.05. Different letters indicate significant differences.

Figure 10

Analysis of the relative expression levels of peanut AhMADS genes by qRT-PCR. The expression profiles of five peanut AhMADS genes (AhMADS9, AhMADS21, AhMADS34, AhMADS50, and AhMADS64) under two hormone treatments (MeJA and ABA) were validated. The data are presented as the mean ± SD (n = 3), and the values differed significantly at p < 0.05. Different letters indicate significant differences.