Genome-wide identification and analysis of the COI gene family in wheat (Triticum aestivum L.)

Abstract

Background: COI (CORONATINE INSENSITIVE), an F-box component of the Skp1-Cullin-F-box protein (SCF^COI1) ubiquitin E3 ligase, plays important roles in the regulation of plant growth and development. Recent studies have shown that COIs are involved in pollen fertility. In this study, we identified and characterized COI genes in the wheat genome and analyzed expression patterns under abiotic stress.

Results: A total of 18 COI candidate sequences for 8 members of COI gene family were isolated in wheat (Triticum aestivum L.). Phylogenetic and structural analyses showed that these COI genes could be divided into seven distinct subfamilies. The COI genes showed high expression in stamens and glumes. The qRT-PCR results revealed that wheat COIs were involved in several abiotic stress responses and anther/glume dehiscence in the photoperiod-temperature sensitive genic male sterile (PTGMS) wheat line BS366.

Conclusions: The structural characteristics and expression patterns of the COI gene family in wheat as well as the stress-responsive and differential tissue-specific expression profiles of each TaCOI gene were examined in PTGMS wheat line BS366. In addition, we examined SA- and MeJA-induced gene expression in the wheat anther and glume to investigate the role of COI in the JA signaling pathway, involved in the regulation of abnormal anther dehiscence in the PTGMS wheat line. The results of this study contribute novel and detailed information about the TaCOI gene family in wheat and could be used as a benchmark for future studies of the molecular mechanisms of PTGMS in other crops.

Keywords: COI; Gene family; JA signaling; Male sterile; Quantitative real-time PCR; Triticum aestivum L..

Fig. 1

Bio Neighbor-Joining (BioNJ) phylogenetic tree (1000 bootstrap replicates), based on a protein alignment of COIs from T. aestivum (Ta), P. patens (Pp), P. trichocarpa (Pt), A. thaliana (At), S. bicolor (Sb), Z. mays (Zm), O. sativa (Os), B. distachyon (Bd), S. moellendorffii (Sm), Ae. tauschii (Aet), T. urartu (Tu), and H. vulgare (Hv). Each TaCOI protein is indicated by a red dot

Fig. 2

Analysis of specific cis-elements in promoters. The 2 k-bp promoter sequences of corresponding COI genes were used to analyze five specific hormone-related cis-elements, including ABRE, TGA-element, TATC-box, CGTCA/TGACG-motif, TCA-element which respond to ABA, auxin (IAA), gibberellin (GA), methyl jasmonate (MeJA), salicylic acid (SA) and two stress-responsive regulatory elements, TC-rich repeats and LTR which respond to stress/defence and low temperature, which are color-coded

Fig. 3

Exon-intron structures (a) of the COI genes in T. aestivum (Ta), O. sativa (Os), B. distachyon (Bd), T. urartu (Tu), and H. vulgare (Hv) and a motif distribution analysis (b). Exons are shown as yellow boxes, introns are shown as thin lines, and UTRs are shown as blue lines. The sizes of exons and introns can be estimated using the scale below. Ten motif types are shown as colored boxes

Fig. 4

Chromosomal localizations and syntenic relationships among TaCOI genes in wheat. The positions of TaCOI genes are marked directly on chromosomes. “+” and “-” in front of gene names mean sense and anti-sense strand of genome

Fig. 5

Real-time PCR analysis of TaCOI genes in six wheat tissues (root, stem, leaf, pistil, stamen, and glume) in the heading stage. Actin was used as a reference control gene. The 2^-∆∆Ct method was used to calculate the relative expression levels of the target genes. The error bars indicate the standard deviation obtained from three replicates

Fig. 6

Expression profiling of TaCOI genes at three anther development stages in fertile (20 °C with 12-h day/12-h night for daily mean temperature during pollen development stages) and sterile conditions (10 °C with 12-h day/12-h night for daily mean temperature during pollen development stages). I, II and III are mean stage 1: secondary sporogenous cells had formed, stage 2: all cell layers were present and mitosis had ceased and stage 3: meiotic division stage, respectively. The error bars indicate the standard deviation of three replicates

Fig. 7

Expression profiling of TaCOI genes under five phytohormone (MeJA, ABA, GA, IAA, and SA), drought (PEG 6000), salt (NaCl), and cold (10 °C) treatments in BS366. Actin was used as a reference control gene. ABA (100 mM), Cold (10 °C), GA (100 mM), IAA (50 mM), MeJA (100 mM), NaCl (200 mM), PEG 6000 (− 0.5 MPa) and SA (2 mM), were preformed in this study. The 2^-∆∆Ct method was used to calculate the relative expression levels of the target genes. There are three replicates

Fig. 8

The dehiscence of glumes (a–h) and anthers (i–p) treated with MeJA and SA. a–d and I–L represent the glumes and anthers treated with MeJA (0 mM, 0.5 mM, 2 mM, and 4 mM from left to right), respectively. e–h and m–p represent the glumes and anthers treated with MeJA (0 mM, 0.5 mM, 2 mM, and 4 mM from left to right) and SA (10 mM). MeJA: spikelets were treated with MeJA (0 mM, 0.5 mM, 2 mM, and 4 mM from left to right). MeJA+SA: SA (10 mM) and MeJA interaction treatment

Fig. 9

Expression profiling of TaCOI genes in glumes (a) and anthers (b) treated with MeJA (0 mM 0.5 mM, 2 mM, and 4 mM) and SA (10 mM). Values on the x-axis indicate the MeJA concentration. MeJA: spikelets were treated with MeJA (0 mM, 0.5 mM, 2 mM, and 4 mM). MeJA + SA: SA (10 mM) and MeJA interaction treatment. The error bars indicate the standard deviation of three replicates