Genome-Wide Identification and Expression Analysis of the HD-Zip Gene Family in Wheat (Triticum aestivum L.)

Abstract

The homeodomain-leucine zipper (HD-Zip) gene family, as plant-specific transcription factors, plays an important role in plant development and growth as well as in the response to diverse stresses. Although HD-Zip genes have been extensively studied in many plants, they had not yet been studied in wheat, especially those involved in response to abiotic stresses. In this study, 46 wheat HD-Zip genes were identified using a genome-wide search method. Phylogenetic analysis classified these genes into four groups, numbered 4, 5, 17 and 20 respectively. In total, only three genes with A, B and D homoeologous copies were identified. Furthermore, the gene interaction networks found that the TaHDZ genes played a critical role in the regulatory pathway of organ development and osmotic stress. Finally, the expression profiles of the wheat HD-Zips in different tissues and under various abiotic stresses were investigated using the available RNA sequencing (RNA-Seq) data and then validated by quantitative real-time polymerase chain reaction (qRT-PCR) to obtain the tissue-specific and stress-responsive candidates. This study systematically identifies the HD-Zip gene family in wheat at the genome-wide level, providing important candidates for further functional analysis and contributing to the better understanding of the molecular basis of development and stress tolerance in wheat.

Keywords: HD-Zip; abiotic stress; expression profiles; gene family; wheat.

Figure 1

Chromosomal localization and gene duplication identified in wheat. Seven chromosomes of wheat A, B and D sub-genomes are displayed in different colors. Duplicated gene pairs are exhibited in linked lines with the corresponding color.

Figure 2

Phylogenetic analysis of HD-Zip proteins among wheat (46), Arabidopsis (48) and rice (39).

Figure 3

The distribution of HD-Zip transcription factors from wheat, maize, Arabidopsis, rice and soybean.

Figure 4

The co-expression network of TaHDZ genes in wheat according to the orthologues in Arabidopsis.

Figure 5

(a) Phylogenetic relationships; (b) Expression patterns; (c) Conserved motifs compositions of the 46 HD-Zip genes in wheat. (a) The phylogenetic tree was constructed based on the full-length protein sequences using MEGA6.0 (http://web.megasoftware.net/); (b) Hierarchical clustering of the relative expression level of TaHDZ genes. RNA-Seq data of five tissues and four stresses in Chinese spring was used to analysis expression pattern. The heat map was drawn in Log₁₀-transformed expression values. Red or green colors represent decreased or increased expression level in each sample, respectively; (c) Multiple EM for motif elicitation (MEME) program [54] was used to predict conserved motifs. Each motif is represented by a different colored box.

Figure 6

The expression profiles of 28 TaHDZ genes that may be involved in the response to salt or drought stress in different wheat varieties using quantitative real-time polymerase chain reaction (qRT-PCR) analysis. For salt stress, two-week-old seedlings of variety Dekang No. 685 (DK) and Chinese Spring (CS) were treated with 200 mM sodium chloride (NaCl) for 24 h. Hanxuan No. 10 (HX) and CS were treated with 19.2% polyethylene glycol (PEG) for 24 h to represent the drought treatment. The control was an untreated seedling. Three biological replicates for each sample were performed and bars represented the standard deviations of the mean. Asterisks on top of the bars indicating statistically significant differences between the stress and counterpart controls (** p< 0.01, Student’s t-test). Gene expression profiles were evaluated using the 2^−∆∆C method.