A genome-wide analysis of the auxin/indole-3-acetic acid gene family in hexaploid bread wheat (Triticum aestivum L.)

Abstract

The Auxin/indole-3-acetic acid (Aux/IAA) gene family plays key roles in the primary auxin-response process and controls a number of important traits in plants. However, the characteristics of the Aux/IAA gene family in hexaploid bread wheat (Triticum aestivum L.) have long been unknown. In this study, a comprehensive identification of the Aux/IAA gene family was performed using the latest draft genome sequence of the bread wheat "Chinese Spring." Thirty-four Aux/IAA genes were identified, 30 of which have duplicated genes on the A, B or D sub-genome, with a total of 84 Aux/IAA sequences. These predicted Aux/IAA genes were non-randomly distributed in all the wheat chromosomes except for chromosome 2D. The information of wheat Aux/IAA proteins is also described. Based on an analysis of phylogeny, expression and adaptive evolution, we prove that the Aux/IAA family in wheat has been replicated twice in the two allopolyploidization events of bread wheat, when the tandem duplication also occurred. The duplicated genes have undergone an evolutionary process of purifying selection, resulting in the high conservation of copy genes among sub-genomes and functional redundancy among several members of the TaIAA family. However, functional divergence probably existed in most TaIAA members due to the diversity of the functional domain and expression pattern. Our research provides useful information for further research into the function of Aux/IAA genes in wheat.

Keywords: Aux/IAA family; bread wheat genome; chromosome location; expansion pattern; function prediction.

Figure 1

Phylogenetic relationship, motif and gene structure of wheat Aux/IAA genes. (A) The phylogenetic tree of TaIAAs constructed from a complete alignment of 84 wheat Aux/IAA genes using MEGA 6.0 by the neighbor-joining method with 1000 bootstrap replicates. Bootstrap scores are indicated on the nodes and the 34 members of TaIAA, most of which contain duplicated genes, are indicated by blue or pink block. (B) The conserved motifs of TaIAAs. Motifs were identified by MEME software using the deduced amino-acid sequences of the TaIAAs. The relative position of each identified motif in all TaIAA proteins is shown as 1, 2, 3, and 4, which represented the four conserved domains of IAA. (C) Exon/intron structures of TaIAA genes. Exons are represented by black boxes and introns by black lines. The sizes of exons and introns can be estimated using the scale below.

Figure 2

Chromosome distribution of TaIAA family in wheat. White ovals on the chromosomes (vertical bar) indicate the position of centromeres. The arrows next to gene names show the direction of transcription. The position of each gene can be estimated using the left scale. The chromosome numbers are indicated at the top of each bar.

Figure 3

Duplicated TaIAA genes of wheat homologous groups and the collinearity among TaIAAs, TuIAAs, and AetIAAs. Seven homologous groups of wheat chromosomes are displayed in different colors. Duplicated genes of each homo-group are linked using lines with corresponding color. The gray annulus on the periphery represents chromosomes of T. urartu and A. tauschii. The collinearity among TaIAAs, TuIAAs, and AetIAAs were signified by the lines between the orthologous gene-pairs.

Figure 4

Motifs of wheat Aux/IAA proteins. The sequence logos are based on multiple alignment analysis of 84 wheat Aux/IAA proteins performed with Clustal W. The bit score indicates the information content for each position in the sequence. Positions of conserved domains are boxed.

Figure 5

Phylogenetic relationship of Aux/IAA proteins among wheat and another species. The full-length amino-acid sequences of 85 wheat, 31 rice, 29 Arabidopsis, 7 tomato, 2 maize, 2 grape, 1 sorghum, and 1 pear genes were aligned by Clustal W and the phylogenetic tree was constructed using MEGA 6.0 by the neighbor-joining method with 1000 bootstrap replicates. Each TaIAA protein is indicated by a black dot. Two major groups, group A and B, are represented by the red and blue. The functions of some clades were annotated.

Figure 6

Heatmap of expression profiles for TaIAA genes across different organs of seedling and adult stages. The expression data were generated from GeneVestigator database and viewed in MeV software. The relative expression level of a particular gene in each row was normalized against the mean value by log₂ transformation. The color scale below represents expression values, green indicating low levels and red indicating high levels of transcript abundance.