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

Bai, Jianfang; Wang, Yukun; Wang, Peng; Yuan, Shu; Gao, Jiangang; Duan, Wenjing; Wang, Na; Zhang, Fengting; Zhang, Wenjie; Qin, Mengying; Zhao, Changping; Zhang, Liping

doi:10.1186/s12864-018-5116-9

Cited by 21 publications

(32 citation statements)

References 84 publications

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“…More importantly, gibberelliin (GA), auxin (IAA), and methyl jasmonate (MeJA) responsive elements exist with TATA-boxes, TGA-elements, and CGTCA/TGACG-motifs, respectively, in the 2000 bp upstream region of NcEXPA8 ORF (Supplementary S3). However, only under GA 3 treatment did the expression level of NcEXPA8 show continuous upregulation over time, while under IAA/MeJA treatment its expression level fluctuated and was even downregulated at certain treatment time points (Figure 4), which was similar to the primary results reported in other gene expression studies under hormone treatments, showing downregualtion even though genes contained corresponding hormone-responsive elements [40]. As an important growth regulator, GA induces cell and stem growth through expansin-mediated loosening of the cell wall by increased expression and activity of expansins [41,42].…”

Section: Discussionsupporting

confidence: 87%

Internal Reference Gene Selection under Different Hormone Stresses in Multipurpose Timber Yielding Tree Neolamarckia cadamba

Deng

et al. 2020

Forests

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Neolamarckia cadamba, a member of the Rubiaceae family, is widely distributed throughout South Asia and South China. In order to acquire reliable and repeatable results, the use of a suitable internal reference gene to normalize the RT-qPCR data is essential. In this study, we reported the validation of housekeeping genes to identify the most suitable internal reference gene(s) for normalization of qPCR data obtained among different tissues (bud, leaf, cambium region) under different hormone stresses. Here, ΔCt, geNorm, NormFinder, and BestKeeper analyses were carried out to analyze the normalization of qPCR data of twenty-one reference gene families (ACT, CAC, CYP, EF1α, eIF, FPS1, FBK, GAPDH, RAN, PEPKR1, PP2A, RPL, RPS, RuBP, SAMDC, TEF, Tub-α, Tub-β, UBCE, UBQ, UPL) including 43 genes. The results showed that FPS1, RPL, and FBK were the most stable reference genes across all of the tested samples. In addition, the expression of NcEXPA8, one gene of interest that plays an important role in regulating cell wall extension, under different phytohormone stresses was used to further confirm the validated reference genes. Taken together, our results provide guidelines for reference gene selection under different phytohormone stresses and a foundation for more accurate and widespread use of RT-qPCR in N. cadamba.

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Section: Discussionsupporting

confidence: 87%

Internal Reference Gene Selection under Different Hormone Stresses in Multipurpose Timber Yielding Tree Neolamarckia cadamba

Deng

et al. 2020

Forests

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“…Apparently, jasmonate pathway-related genes are represented by large gene families in hexaploid wheat. According to WheatExp, a homologue-specific database of gene expression profiles [67], there are 12 expressed allene oxide synthase genes; based on the available published data, there are 18 COI genes [68] and 14 JASMONATE-ZIM DOMAIN transcription repressor genes in the wheat genome [69]. Further expression profiling study of the generated transgenic lines may shed light onto the jasmonate-dependent regulation of homolog gene expression in wheat.…”

Section: Discussionmentioning

confidence: 99%

Overexpression of Arabidopsis OPR3 in Hexaploid Wheat (Triticum aestivum L.) Alters Plant Development and Freezing Tolerance

Pigolev

Miroshnichenko

Pushin

et al. 2018

IJMS

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Jasmonates are plant hormones that are involved in the regulation of different aspects of plant life, wherein their functions and molecular mechanisms of action in wheat are still poorly studied. With the aim of gaining more insights into the role of jasmonic acid (JA) in wheat growth, development, and responses to environmental stresses, we have generated transgenic bread wheat plants overexpressing Arabidopsis 12-OXOPHYTODIENOATE REDUCTASE 3 (AtOPR3), one of the key genes of the JA biosynthesis pathway. Analysis of transgenic plants showed that AtOPR3 overexpression affects wheat development, including germination, growth, flowering time, senescence, and alters tolerance to environmental stresses. Transgenic wheat plants with high AtOPR3 expression levels have increased basal levels of JA, and up-regulated expression of ALLENE OXIDE SYNTHASE, a jasmonate biosynthesis pathway gene that is known to be regulated by a positive feedback loop that maintains and boosts JA levels. Transgenic wheat plants with high AtOPR3 expression levels are characterized by delayed germination, slower growth, late flowering and senescence, and improved tolerance to short-term freezing. The work demonstrates that genetic modification of the jasmonate pathway is a suitable tool for the modulation of developmental traits and stress responses in wheat.

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“…The Jasmonic acid (JA) signaling pathway is complicated and is involved in several regulatory processes, such as plant growth and development, fertility regulation, and plant immunity [1, 2]. In Arabidopsis , components of JA signaling pathway include F-box protein CORONATINE INSENSITIVE1 (COI1), Jasmonate-ZIM (JAZ) domain repressor, and the bHLH transcription factor MYC2, which can regulate the expression patterns of JA-response genes [3].…”

Section: Introductionmentioning

confidence: 99%

Genomic identification and characterization of MYC family genes in wheat (Triticum aestivum L.)

et al. 2019

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BackgroundMYC transcriptional factors are members of the bHLH (basic helix-loop-helix) superfamily, and play important roles in plant growth and development. Recent studies have revealed that some MYCs are involved in the crosstalk between Jasmonic acid regulatory pathway and light signaling in Arabidopsis, but such kinds of studies are rare in wheat, especially in photo-thermo-sensitive genic male sterile (PTGMS) wheat line.Results27 non-redundant MYC gene copies, which belonged to 11 TaMYC genes, were identified in the whole genome of wheat (Chinese Spring). These gene copies were distributed on 13 different chromosomes, respectively. Based on the results of phylogenetic analysis, 27 TaMYC gene copies were clustered into group I, group III, and group IV. The identified TaMYC genes copies contained different numbers of light, stress, and hormone-responsive regulatory elements in their 1500 base pair promoter regions. Besides, we found that TaMYC3 was expressed highly in stem, TaMYC5 and TaMYC9 were expressed specially in glume, and the rest of TaMYC genes were expressed in all tissues (root, stem, leaf, pistil, stamen, and glume) of the PTGMS line BS366. Moreover, we found that TaMYC3, TaMYC7, TaMYC9, and TaMYC10 were highly sensitive to methyl jasmonate (MeJA), and other TaMYC genes responded at different levels. Furthermore, we confirmed the expression profiles of TaMYC family members under different light quality and plant hormone stimuli, and abiotic stresses. Finally, we predicted the wheat microRNAs that could interact with TaMYC family members, and built up a network to show their integrative relationships.ConclusionsThis study analyzed the size and composition of the MYC gene family in wheat, and investigated stress-responsive and light quality induced expression profiles of each TaMYC gene in the PTGMS wheat line BS366. In conclusion, we obtained lots of important information of TaMYC family, and the results of this study was supposed to contribute novel insights and gene and microRNA resources for wheat breeding, especially for the improvement of PTGMS wheat lines.

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

Cited by 21 publications

References 84 publications

Internal Reference Gene Selection under Different Hormone Stresses in Multipurpose Timber Yielding Tree Neolamarckia cadamba

Internal Reference Gene Selection under Different Hormone Stresses in Multipurpose Timber Yielding Tree Neolamarckia cadamba

Overexpression of Arabidopsis OPR3 in Hexaploid Wheat (Triticum aestivum L.) Alters Plant Development and Freezing Tolerance

Genomic identification and characterization of MYC family genes in wheat (Triticum aestivum L.)

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