Genome-wide analysis of JMJ-C histone demethylase family involved in salt-tolerance in Gossypium hirsutum L.

Sun, Zhimao; Wang, Xiaoyan; Qiao, Kaikai; Fan, Shiliang; Ma, Qin

doi:10.1016/j.plaphy.2020.11.029

Cited by 22 publications

(19 citation statements)

References 44 publications

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“…To examine the evolutionary relationships of JmjC genes in cotton, O. sativa and A. thaliana , we constructed a phylogenetic tree of JmjC based on 145 full-length JmjC protein sequences, including 51, 25, 28, 20, and 21 sequences from G. hirsutum , G. raimondii , G. arboreum, O. sativa , and A. thaliana , respectively. It appears that JmjC could be categorized into six distinct groups rather than the five groups reported in recent studies ( Zhang et al, 2020 ; Sun et al, 2021 ), which are denoted group I to group VI ( Figure 1 ). Group VI, relative to other five groups, contains more genes from each of the five species.…”

Section: Resultsmentioning

confidence: 80%

“…Previous studies in rice and maize revealed that hypomethylation events were observed more frequently than hypermethylation in the process of tissue culture and somatic embryogenesis ( Stroud et al, 2013 ; Stelpflug et al, 2014 ). A number of G. hirsutum JmjC genes have been found to respond to cold, salt, and osmotic stress to some extent ( Zhang et al, 2020 ; Sun et al, 2021 ), the question of whether JmjC plays a role in cotton tissue culture and somatic embryogenesis remains unanswered until this study.…”

Section: Discussionmentioning

confidence: 97%

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Genome-wide Characterization of the JmjC Domain-Containing Histone Demethylase Gene Family Reveals GhJMJ24 and GhJMJ49 Involving in Somatic Embryogenesis Process in Cotton

Zhu

Yao

et al. 2022

Front. Mol. Biosci.

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The Jumonji C (JmjC) domain-containing protein family, an important family of histone demethylase in plants, can directly reverse histone methylation and play important roles in various growth and development processes. In the present study, 51 JmjC genes (GhJMJs) were identified by genome-wide analysis in upland cotton (Gossypium hirsutum), which can be categorized into six distinct groups by phylogenetic analysis. Extensive syntenic relationship events were found between G. hirsutum and Theobroma cacao. We have further explored the putative molecular regulatory mechanisms of the JmjC gene family in cotton. GhJMJ24 and GhJMJ49 were both preferentially expressed in embryogenic callus compared to nonembryogenic callus in cotton tissue culture, which might be regulated by transcription factors and microRNAs to some extent. Further experiments indicated that GhJMJ24 and GhJMJ49 might interact with SUVH4, SUVH6, DDM1, CMT3, and CMT1 in the nucleus, potentially in association with demethylation of H3K9me2. Taken together, our results provide a foundation for future research on the biological functions of GhJMJ genes in cotton, especially in somatic embryogenesis in cotton tissue culture, which is crucial for the regeneration of transgenic plants.

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Section: Resultsmentioning

confidence: 80%

Section: Discussionmentioning

confidence: 97%

Genome-wide Characterization of the JmjC Domain-Containing Histone Demethylase Gene Family Reveals GhJMJ24 and GhJMJ49 Involving in Somatic Embryogenesis Process in Cotton

Zhu

Yao

et al. 2022

Front. Mol. Biosci.

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“…The GWAS undertaken on the shoot biomass identified one significant QTL of interest at 5HL. Within the region at 5HL there are a number of genes encoding for proteins of interest such as a) Lysine-specific demethylase REF6—selected as it has a histone demethylase domain and over expression of a histone demethylase gene in Arabidopsis has been shown to improve salinity tolerance ( Shen et al, 2014 ) as well as associations of a histone demethylase family with salinity tolerance in cotton ( Sun et al, 2021 ); b) Actin 7—selected as salinity stress has been shown to affect actin filament assembly and has shown to be necessary in salinity tolerance in Arabidopsis ( Wang et al, 2011 ); c) Ferredoxin 3—selected as an overexpression of plant ferredoxin-like protein has been seen to promote salinity tolerance in rice ( Huang et al, 2020 ), and salinity stress has been associated with ferredoxin associated proteins ( Berteli et al, 1995 ; Zhou et al, 2009 ); and d) Acyl-CoA-binding domain-containing protein 4—selected as Acyl-CoA-binding proteins have been shown to interact with other proteins in response to abiotic stresses ( Raboanatahiry et al, 2015 ), with overexpression in Arabidopsis shown to improve drought tolerance ( Du et al, 2016 ) and expression of maize Acyl-CoA-binding proteins in Arabidopsis increasing resistance to salinity and drought stress ( Zhu et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Evaluating Variation in Germination and Growth of Landraces of Barley (Hordeum vulgare L.) Under Salinity Stress

et al. 2022

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Ongoing climate change is resulting in increasing areas of salinity affected soils, rising saline groundwater and droughts resulting in irrigation with brackish water. This leads to increased salinity stress in crops that are already grown on marginal agricultural lands, such as barley. Tolerance to salinity stress is limited in the elite barley cultivar pools, but landraces of barley hold potential sources of tolerance due to their continuous selection on marginal lands. This study analyzed 140 heritage cultivars and landrace lines of barley, including 37 Scottish Bere lines that were selected from coastal regions, to screen for tolerance to salinity stress. Tolerance to salinity stress was screened by looking at the germination speed and the early root growth during germination, and the pre-maturity biomass accumulation during early growth stages. Results showed that most lines increased germination time, and decreased shoot biomass and early root growth with greater salinity stress. Elite cultivars showed increased response to the salinity, compared to the landrace lines. Individual Bere and landrace lines showed little to no effect of increased salinity in one or more experiments, one line showed high salinity tolerance in all experiments—Bere 49 A 27 Shetland. A Genome Wide Association Screening identified a number of genomic regions associated with increased tolerance to salinity stress. Two chromosomal regions were found, one associated with shoot biomass on 5HL, and another associated with early root growth, in each of the salinities, on 3HS. Within these regions a number of promising candidate genes were identified. Further analysis of these new regions and candidate genes should be undertaken, along with field trials, to identify targets for future breeding for salinity tolerance.

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“…Like transcription factors, HMs are important regulators of many biological processes, including plant growth and development [ 1 – 3 ]. We proposed that TaHMs and ZmHMs share similar roles with known HMs .…”

Section: Discussionmentioning

confidence: 99%

“…In plants, epigenetic histone modification (HM) can activate or silence gene expression. HM genes play essential functions in various growth and development processes and stress responses, such as carotenoid biosynthesis, floral organ development, and fungal pathogen resistance [ 1 – 3 ]. In plants, HM depends on four kinds of enzymes, including histone methyltransferases (HMTs), histone demethylases (HDMs), histone acetylases (HATs), and histone deacetylases (HDACs) [ 4 – 7 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification of Gramineae histone modification genes and their potential roles in regulating wheat and maize growth and stress responses

Zheng

Shen

et al. 2021

BMC Plant Biol

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Background In plants, histone modification (HM) genes participate in various developmental and defense processes. Gramineae plants (e.g., Triticum aestivum, Hordeum vulgare, Sorghum bicolor, Setaria italica, Setaria viridis, and Zea mays) are important crop species worldwide. However, little information on HM genes is in Gramineae species. Results Here, we identified 245 TaHMs, 72 HvHMs, 84 SbHMs, 93 SvHMs, 90 SiHMs, and 90 ZmHMs in the above six Gramineae species, respectively. Detailed information on their chromosome locations, conserved domains, phylogenetic trees, synteny, promoter elements, and gene structures were determined. Among the HMs, most motifs were conserved, but several unique motifs were also identified. Our results also suggested that gene and genome duplications potentially impacted the evolution and expansion of HMs in wheat. The number of orthologous gene pairs between rice (Oryza sativa) and each Gramineae species was much greater than that between Arabidopsis and each Gramineae species, indicating that the dicotyledons shared common ancestors. Moreover, all identified HM gene pairs likely underwent purifying selection based on to their non-synonymous (Ka)/synonymous (Ks) nucleotide substitutions. Using published transcriptome data, changes in TaHM gene expression in developing wheat grains treated with brassinosteroid, brassinazole, or activated charcoal were investigated. In addition, the transcription models of ZmHMs in developing maize seeds and after gibberellin treatment were also identified. We also examined plant stress responses and found that heat, drought, salt, insect feeding, nitrogen, and cadmium stress influenced many TaHMs, and drought altered the expression of several ZmHMs. Thus, these findings indicate their important functions in plant growth and stress adaptations. Conclusions Based on a comprehensive analysis of Gramineae HMs, we found that TaHMs play potential roles in grain development, brassinosteroid- and brassinazole-mediated root growth, activated charcoal-mediated root and leaf growth, and biotic and abiotic adaptations. Furthermore, ZmHMs likely participate in seed development, gibberellin-mediated leaf growth, and drought adaptation.

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Genome-wide analysis of JMJ-C histone demethylase family involved in salt-tolerance in Gossypium hirsutum L.

Cited by 22 publications

References 44 publications

Genome-wide Characterization of the JmjC Domain-Containing Histone Demethylase Gene Family Reveals GhJMJ24 and GhJMJ49 Involving in Somatic Embryogenesis Process in Cotton

Genome-wide Characterization of the JmjC Domain-Containing Histone Demethylase Gene Family Reveals GhJMJ24 and GhJMJ49 Involving in Somatic Embryogenesis Process in Cotton

Evaluating Variation in Germination and Growth of Landraces of Barley (Hordeum vulgare L.) Under Salinity Stress

Genome-wide identification of Gramineae histone modification genes and their potential roles in regulating wheat and maize growth and stress responses

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