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

- Genome-wide identification and analysis of the COI gene family in wheat ( Triticum.
- 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.
- In this study, we identified and characterized COI genes in the wheat genome and analyzed expression patterns under abiotic stress..
- 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..
- 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.
- Jasmonates (JAs), including jasmonic acid (JA), methyl jasmonate (MeJA), and its derivatives, play important roles in the regulation of biotic and abiotic stresses as well as plant growth, development, and defense [1–4]..
- JA is also involved in the regulation of floral organ development, such as pollen maturation, anther dehis- cence, and male fertility [5–8].
- OsCOI1b is involved in leaf senescence [35].
- Recently, it has been reported that male sterility of the female parent can be attributed to lack of anther development or dehis- cence in the two line hybrid wheat system [43].
- However, there are few studies of COI in the wheat jasmonic acid regulatory path- way.
- In this study, we first systematically identified and characterized the COI genes of wheat (TaCOI), and ana- lyzed its architectural features, evolutionary history, and expression patterns in anther tissues in the PTGMS wheat line.
- In addition, the expression profiles of TaCOI genes in different tissues as well in response to several stresses were analyzed.
- The anther and glume dehiscence and the expression of TaCOI genes after.
- For the SA and MeJA interaction treatment, 0.5 mM, 2 mM, and 4 mM MeJA were applied every day for 5 days when spikelets were treated with 10 mM SA (20 °C, 12-h day/12-h night) in the artificial climate incubator.
- The hidden Markov model (HMM) profiles were constructed using the hmmbuild procedure (HMMER3.0) (http://hmmer.org/) for comparisons of the COI con- served protein structure domain in the wheat protein database (E-value ≤1.0E-10).
- The sequences of the COI promoters are listed in Additional file 2: Table S3..
- To determine the roles of COIs in the JA signaling path- way, a multiple sequence alignment of the amino acid sequences of COI in selected plant genomes was gener- ated using DNAMAN (ver.
- In addition, These COI genes were distinguished by their positions in the wheat sub-genome (A, B, and D).
- It was showed that these TaCOI genes exhibited cytoplasmic, nuclear, and.
- TaCOI4-A and TaCOI4-B were located in the cytoplasm and nuclei.
- The remaining genes were located in the cytoplasm and chloroplasts.
- Table 1 Characteristics of TaCOI gene family members from wheat.
- Analysis of stress response-related cis -regulatory elements in the promoter regions of TaCOI genes.
- To analyze how the ex- pression levels of TaCOI genes responded to stress stimuli, 2.0-kb upstream promoter regions of TaCOI genes were scanned for stress-related cis-regulatory elements using the Plant CARE online service (http://bioinformatics.psb.u- gent.be/webtools/plantcare/html/) [18].
- 2 and Table 3, five hormone-responsive regulatory elements, ABRE, TGA-element, TATC-box, CGTCA/TGACG-motif, and TCA-element, associated with ABA, auxin (IAA), gib- berellin (GA), methyl jasmonate (MeJA), and salicylic acid (SA) responses, were identified in the promotor region of TaCOIs.
- Additionally, two stress-responsive regulatory elements, TC-rich repeats and LTR, associated with defense/stress and low-temperature responses, respectively, were identified in the TaCOI promoter regions.
- Different types and numbers of regulatory elements were present in the distinct TaCOI promoters (Table 2), indicating that TaCOI genes might be involved in the response to various stress and hormone treatments via participating different.
- The CGTCA/TGACG-motif, which was associated with a methyl jasmonate (MeJA) responsive element, was enriched in the promoters of TaCOI genes (Fig.
- It was also found that ABRE-motif was also enriched in the promoters of most of all TaCOI genes (Fig.
- The numbers and types of stress-related cis-elements in the 2.0-kb up- stream regions of TaCOI family genes are listed in Table 2 and Table 3..
- The majority of TaCOI genes contained two or three copies, and the number of exons ranged from one to four (Fig.
- Furthermore, most COIs in the same sub- group shared the same structures.
- The distribution of TaCOI family members in the wheat genome is depicted in Fig.
- Each of the remaining chromosomes included a single TaCOI gene.
- The TaCOI genes showed a scattered chromosomal distribution.
- Table 3 Functions of cis- acting regulatory elements in promoter regions of TaCOI genes.
- TC-rich repeats Nicotiana tabacum GTTTTCTTAC cis-acting element involved in defense and stress responsiveness TCA-element Nicotiana tabacum CCATCTTTTT cis-acting element involved in salicylic acid responsiveness CGTCA-motif Hordeum vulgare CGTCA cis-acting regulatory element involved in the MeJA-responsiveness TGACG-motif Hordeum vulgare TGACG cis-acting regulatory element involved in the MeJA-responsiveness.
- TATC-box Oryza sativa TATCCCA cis-acting element involved in gibberellin-responsiveness ABRE Arabidopsis thaliana TACGTG cis-acting element involved in the abscisic acid responsiveness.
- The COI gene family is primarily involved in plant growth [60], development [21, 35], and stress re- sponses [61].
- To study the biological functions of these genes in wheat, the expression profiles of the eight TaCOI genes were analyzed in six tissue types (i.e., root, stem, leaf, petal, pistil, stamen, and glume tissues) of PTGMS line BS366 at the heading stage by qRT-PCR.
- 5, eight TaCOI genes were expressed in different tissues, suggesting that the TaCOI genes were constitutively expressed in BS366.
- TaCOI1, TaCOI2, and TaCOI4 expression levels in the stamen were rela- tively highly than those in other tissues.
- To further investigate the role of TaCOI genes in pollen fertility, the TaCOI expression profiles at three stages of stamen development in different fertility envi- ronments (fertile conditions and sterile condition) were analyzed.
- 6, TaCOI1, TaCOI3, TaCOI5, and TaCOI7 exhibited higher expression levels in all three stamen developmental stages in sterile condition than that in fertile condition, while the expression levels of TaCOI6 and TaCOI8 in the three stamen develop- mental stages were lower in sterile condition.
- These results suggested that these TaCOI genes may be in- volved in stamen development and participate in fertile transformation via some unknown pathway..
- To determine the mechanisms involved in.
- 3 Exon-intron structures (a) of the COI genes in T.
- The results showed that all TaCOI genes responded to plant hormones and stress (Fig.
- Under ABA treatment, the transcript profiles of TaCOI genes showed the up- regulation of TaCOI and the down-regulation of TaCOI2, 6, 8 at early treatment time points (0-4 h post-treatment).
- 4 Chromosomal localizations and syntenic relationships among TaCOI genes in wheat.
- The positions of TaCOI genes are marked directly on chromosomes.
- Interestingly, all TaCOI genes were inhib- ited to different degrees under SA treatment.
- These results revealed that these TaCOI genes responded to various plant hormones and were involved in complex regu- latory networks in the PTGMS wheat line BS366..
- The regulation of COIs in wheat anther/glume dehiscence To investigated the regulation of COIs in the JA signal- ing pathway during anther dehiscence, wheat spikelets.
- The expression levels of TaCOI3, 4, 5, and 6 were up-regulated with increasing MeJA concentrations in the glume (Fig.
- After treatment of MeJA-treated plants with SA (10 mM), the expression of all TaCOI genes was repressed in glumes (Fig.
- In the anther, the expression levels of TaCOI5 and 6 were up-regulated as the MeJA concentration increased, and the levels of the remaining TaCOIs peaked after treat- ment with 2 mM MeJA and subsequently decreased (Fig.
- 5 Real-time PCR analysis of TaCOI genes in six wheat tissues (root, stem, leaf, pistil, stamen, and glume) in the heading stage.
- The 2 - ΔΔ Ct method was used to calculate the relative expression levels of the target genes.
- JAs are oxylipin signaling molecules involved in the control of various aspects of plant developmental processes, such as plant fertility anthocyanin accumulation [64], fruit ripening [65], root growth [66], and leaf senescence [24, 25].
- In the present study, 18 candidate COI.
- The analyses of TaCOI genes provided insight into the important roles underlying the roles of MeJA in pollen fertility in wheat.
- 2, five hormone-responsive (ABA, IAA, GA, MeJA, and SA) and two stress-responsive (high salinity, drought, and cold) regulatory elements were found in the TaCOI promoter.
- 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).
- regions, suggesting that TaCOI genes have different regula- tory mechanisms in response to various stress and hor- mone treatments.
- However, there were some differences between TaCOI genes with respect to the number and type of cis-acting regulatory elements.
- Therefore, we investigated the expression profiles of TaCOI genes in wheat seedlings under different stress con- ditions were evaluated.
- In Arabidopsis, COI1 functions in the JA signaling pathway.
- These TaCOI genes were also induced by some abiotic stresses (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.
- The 2 -ΔΔCt method was used to calculate the relative expression levels of the target genes.
- FLOR1 is a flower-specific LRR protein involved in the development of floral organs in A..
- For example, TaCOI6 and TaCOI2 shared similar structures and con- tained the same ten motifs, and 9 out of 10 motifs were LRR domains or leucine-rich sequences, which was con- sistent with the conclusion obtained by the previous scholar [76, 77], suggesting that these TaCOI genes may play a role in plant defense.via these enriched domains..
- The tissue expression profiles of TaCOI genes were also investigated to further examine TaCOI gene functions.
- In this study, the expression levels of TaCOI2, TaCOI6, and TaCOI7 in the glume and TaCOI1 and TaCOI4 in the stamen were higher than those in other tissues (Fig.
- Additionally, all TaCOI genes showed lower expression levels in root tissues than in other tissues (Fig.
- These results suggested that TaCOI genes are involved in stamen and glume development.
- It has been reported that JAs are involved in the regulation of anther dehiscence, filament elongation, and pollen fertility in plants [48, 83.
- MeJA and SA may have antagonistic effect on expressions TaCOI genes in PTGMS wheat line (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)..
- The expression of TaCOI genes in the glume and anther under various concentrations of MeJA and SA were also investigated (Fig.
- In the present study, some TaCOI genes were inhibited by SA and induced by MeJA (Fig.
- For example, the expression levels of TaCOI 3, 4, 5, and 6 were up-regulated with increasing concentrations of MeJA in the glume and the expression levels of TaCOI 5 and 6 were up-regulated with increasing concentrations of MeJA in the anther (Fig.
- In addition, all TaCOI genes were inhibited by SA in the glume and anther (Fig.
- In addition, the expression re- sults for TaCOI genes during anther development in different fertility environments showed that TaCOI1, TaCOI3, TaCOI5, and TaCOI7 exhibit higher expression, while the expression levels of TaCOI6 and TaCOI8 were lower at all three anther development stages in the sterile environment (Fig.
- 6), suggesting that TaCOI genes have dif- ferent roles in fertility..
- Structural analyses and the expression patterns of the TaCOI genes would provide a more comprehensive understanding of gene functions.
- The roles of TaCOI gene expression differences in anther development and in the responses to vari- ous abiotic stresses provide insight into the roles of MeJA signaling in the anther and glume dehiscence of wheat..
- Specific primers for TaCOI genes for qRT-PCR..
- Promoter sequences of TaCOI genes.
- TaOPR2 encodes a 12-oxo-phytodienoic acid reductase involved in the biosynthesis of jasmonic acid in wheat (Triticum aestivum L.
- The arabidopsis DELAYED DEHISCENCE1 gene encodes an enzyme in the jasmonic acid synthesis pathway.
- COI1, a jasmonate receptor, is involved in ethylene- induced inhibition of Arabidopsis root growth in the light.
- A critical role of two positively charged amino acids in the Jas motif of Arabidopsis JAZ proteins in mediating coronatine- and jasmonoyl isoleucine-dependent interactions with the COI1 F-box protein..
- Fertility alteration in the photo- thermo-sensitive male sterile line BS20 of wheat ( Triticum aestivum L.)..
- Genome interplay in the grain transcriptome of hexaploid bread wheat.
- The RNA polymerase II core promoter: a key component in the regulation of gene expression.
- Pieterse CM, Van Loon LC: NPR1: the spider in the web of induced resistance signaling pathways.
- After-ripening alters the gene expression pattern of oxidases involved in the ethylene and gibberellin pathways during early imbibition of Sisymbrium officinale L.
- Structural and functional diversity in the leucine-rich repeat family of proteins

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