Genome-wide analysis of the MADS-box gene family in Brachypodium distachyon

Abstract

MADS-box genes are important transcription factors for plant development, especially floral organogenesis. Brachypodium distachyon is a model for biofuel plants and temperate grasses such as wheat and barley, but a comprehensive analysis of MADS-box family proteins in Brachypodium is still missing. We report here a genome-wide analysis of the MADS-box gene family in Brachypodium distachyon. We identified 57 MADS-box genes and classified them into 32 MIKC(c)-type, 7 MIKC*-type, 9 Mα, 7 Mβ and 2 Mγ MADS-box genes according to their phylogenetic relationships to the Arabidopsis and rice MADS-box genes. Detailed gene structure and motif distribution were then studied. Investigation of their chromosomal localizations revealed that Brachypodium MADS-box genes distributed evenly across five chromosomes. In addition, five pairs of type II MADS-box genes were found on synteny blocks derived from whole genome duplication blocks. We then performed a systematic expression analysis of Brachypodium MADS-box genes in various tissues, particular floral organs. Further detection under salt, drought, and low-temperature conditions showed that some MADS-box genes may also be involved in abiotic stress responses, including type I genes. Comparative studies of MADS-box genes among Brachypodium, rice and Arabidopsis showed that Brachypodium had fewer gene duplication events. Taken together, this work provides useful data for further functional studies of MADS-box genes in Brachypodium distachyon.

Figure 1. Phylogenetic analysis of MADS-box proteins in Brachypodium, rice and Arabidopsis.

A total of 57 MADS-box proteins in Brachypodium, 75 in rice and 98 in Arabidopsis were used to construct the NJ tree. The MADS-box proteins in Brachypodium were marked by solid triangles. Branches with less than 50% bootstrap support were collapsed.

Figure 2. Phylogenetic relationship and gene structure analysis of MADS-box genes in Brachypodium.

Un-rooted neighbor-joining tree was constructed from the alignment of full-length amino acid sequences using the MEGA5 package. Branches with less than 50% bootstrap values were collapsed. Lengths of exons and introns of each MADS-box gene were displayed proportionally. The green solid boxes represent exons; black lines represent introns.

Figure 3. Conserved motif analysis of Brachypodium MADS-box proteins according to the phylogenetic relationship.

Each motif is represented by a number in a colored box. Motif 1 is the MADS-box domain; 2 and 3 are two different components of the K domain; 4 and 20 are I domains; 6 is a 129 amino acid MADS-box domain; 8 is a structure; 5, 7 and 9–19 are unidentified regions. Box length corresponds to motif length. Specific lengths, locations and p-values of each motif can be found in Table S4 in File S1.

Figure 4. Genomic locations of MADS-box genes and duplicated gene pairs in the Brachypodium genome.

Gene pairs located in the segmental duplicated chromosome region are linked using red lines.

Figure 5. Expression patterns of Brachypodium MADS-box genes in vegetative and reproductive organs.

Sources of the samples are as follow: root (R), stem (S), leaf (L), lodicule (Lo), lemma (Le), palea (Pa), stamen (St), carpel (Ca) and young seed (YS).

Figure 6. Differential expressions of MADS-box genes in response to the salt, drought, and cold stress.

The Mα, Mβ and MIKC*-type genes were highlighted with green, blue and red background respectively.