Genome-Wide Identification and Expression Profiling of the<i>ERF</i>Gene Family in<i>Medicago sativa</i>L. Under Various Abiotic Stresses

Jin, Xiaoyu; Yin, Xiaofan; Ndayambaza, Boniface; Zhang, Zhengshe; Min, Xueyang; Lin, Xiaoshan; Wang, Yanrong; Liu, Wenxian

doi:10.1089/dna.2019.4881

Cited by 34 publications

(21 citation statements)

References 64 publications

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“…Alfalfa genome encoded 11 ACS homologs and 48 ACO homologs, and we did phylogenetic analysis to indicate their evolutionary relationships ( Supplementary Figures 13A, B). We found 159 ERF homologs in alfalfa (Jin et al, 2019), and we classified them to 10 subfamilies (Supplementary Figure 13C). We selected MsERF8 and MsERF11 for expression analysis as they were reported to be involved in NaCl and ethylene responses in alfalfa (Chen et al, 2012a;Chen et al, 2012b).…”

Section: Ethylene Related Genes Are Involved In Alfalfa Responses Towmentioning

confidence: 99%

Ethylene Enhances Seed Germination and Seedling Growth Under Salinity by Reducing Oxidative Stress and Promoting Chlorophyll Content via ETR2 Pathway

et al. 2020

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Alfalfa (Medicago sativa L.) is an important forage, and salinity is a major stress factor on its yield. In this study, we show that osmotic stress retards alfalfa seedling growth, while ionic/oxidative stress reduces its seed germination. Ethylene treatment can recover the germination rate of alfalfa seeds under salt stress, while ethylene inhibitor silver thiosulfate exacerbates salt effects. ETH reduces the accumulation of MDA and H 2 O 2 and increases POD activity. ETH and ACC improve the salt tolerance of alfalfa by increasing proline content under salt stress. In contrast, STS inhibits alfalfa seed germination by reducing POD activity. NaCl treatment reduces chlorophyll content in alfalfa leaves, while ETH and ACC can increase the chlorophyll content and promote seedling growth. ETH promotes the growth of alfalfa in saline condition by reducing the expression of MsACO and MsERF8 genes, while increases its germination rate by upregulating MsERF11 gene. Silencing of MsETR2, a putative ethylene receptor gene in alfalfa, abolishes ethylene triggered tolerance to salt stress. In summary, we show that ethylene improves salt tolerance in alfalfa via MsETR2 dependent manner, and we also analyze the regulatory mechanism of ethylene during germination of alfalfa seeds under salt stress.

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Section: Ethylene Related Genes Are Involved In Alfalfa Responses Towmentioning

confidence: 99%

Ethylene Enhances Seed Germination and Seedling Growth Under Salinity by Reducing Oxidative Stress and Promoting Chlorophyll Content via ETR2 Pathway

et al. 2020

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“…Systematic evaluation of the diverse gene/protein families involved in the regulation of multiple developmental processes and stimuli can provide insights into the critical regulatory mechanisms of different plant genomes. A vast number of previously published reports have shown extensive involvement of AP2/ERF transcription factors in plant growth and development and critical cellular metabolism processes [15,68,69]. In the present study, 271 AP2/ERF genes were identified in the durum wheat genome, the number of which was lower than that reported in Brassica napus [14], with 321 members; however, 271 was greater than the 171 AP2/ERF genes in Setaria italica [19], the 141 genes identified in B. distachyon [34], the 122 genes in Arabidopsis [67], the 139 genes in rice [67], and the 117 genes in bread wheat [12].…”

Section: Discussionmentioning

confidence: 99%

“…AP2/ERF family-related proteins, which compose a large family, play essential roles in plant growth, enlargement, and coping with different stresses such as extreme chilling/heat, drought, and high-salinity conditions as well as infection by viral and microbial pathogens [8][9][10]. A large number of AP2/ERF genes have been recognized in various plant species, such as Arabidopsis [11], bread wheat [12], soybean [13], rice [9], Brassica napus [14], Medicago sativa [15], pineapple [16], Camptotheca acuminata [17], orchardgrass [18], foxtail millet [19], sorghum [20], ginseng [21], and Gynostemma pentaphyllum [22]. Three main clades of AP2/ERF family members have been determined based on the domain number: the ERF subfamily, whose members contain a single AP2 domain; the AP2 subfamily, whose members contain two AP2 domains connected by a 25 amino acid linker; and the RAV subfamily, whose members have a single AP2 domain and an additional B3 DNA-binding motif [19].…”

Section: Introductionmentioning

confidence: 99%

The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses

Faraji

Filiz

Kazemitabar

et al. 2020

Genes

100

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Members of the AP2/ERF transcription factor family play critical roles in plant development, biosynthesis of key metabolites, and stress response. A detailed study was performed to identify TtAP2s/ERFs in the durum wheat (Triticum turgidum ssp. durum) genome, which resulted in the identification of 271 genes distributed on chromosomes 1A-7B. By carrying 27 genes, chromosome 6A had the highest number of TtAP2s/ERFs. Furthermore, a duplication assay of TtAP2s/ERFs demonstrated that 70 duplicated gene pairs had undergone purifying selection. According to RNA-seq analysis, the highest expression levels in all tissues and in response to stimuli were associated with DRF and ERF subfamily genes. In addition, the results revealed that TtAP2/ERF genes have tissue-specific expression patterns, and most TtAP2/ERF genes were significantly induced in the root tissue. Additionally, 13 TtAP2/ERF genes (six ERFs, three DREBs, two DRFs, one AP2, and one RAV) were selected for further analysis via qRT-PCR of their potential in coping with drought and salinity stresses. The TtAP2/ERF genes belonging to the DREB subfamily were markedly induced under both drought-stress and salinity-stress conditions. Furthermore, docking simulations revealed several residues in the pocket sites of the proteins associated with the stress response, which may be useful in future site-directed mutagenesis studies to increase the stress tolerance of durum wheat. This study could provide valuable insights for further evolutionary and functional assays of this important gene family in durum wheat.

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“…In addition, the AP2/ERF TF family had the greatest number in our rhizome (Fig.4a), among which ethylene response factors, such as BBM/PLT4 and PLT1-3, have been described as master regulators of root meristem initiation and maintenance in Arabidopsis thaliana [44,45]. In Raphanus sativus and alfalfa [46,47], the abiotic stress response mechanism regulated by AP2/ERF has been carefully studied. The Arabidopsis NAC family member NAC1 transduces auxin signals downstream of TIR1 to promote lateral root development [48].…”

Section: Discussionmentioning

confidence: 99%

Revealing the full-length transcriptome of caucasian clover rhizome development

Yin

Zhao

et al. 2020

Preprint

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Background: Caucasian clover (Trifolium ambiguum M.Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. Result: We adopted PacBio Sequencing and Illumina Sequencing to identify differentially expressed transcripts in five tissues taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) of the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analyzed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6,821 alternative splicing (AS) sites, 24,29 long noncoding RNAs (lncRNAs) and 4,501 putative transcription factors (TFs)from 64 different families. Compared with other tissues, T5 exhibited more differentially expressed genes, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene specific to T5. WGCNA cluster analysis of transcription factors and physiological indicators were combined to reveal 11 candidate genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analyzed 276 differential transcripts involved in hormone signaling and transduction, and the largest number of transcripts are associated with the IAA signaling pathway, with significant upregulation in T2 and T5. Conclusions: Taken together, this study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.

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Genome-Wide Identification and Expression Profiling of theERFGene Family inMedicago sativaL. Under Various Abiotic Stresses

Cited by 34 publications

References 64 publications

Ethylene Enhances Seed Germination and Seedling Growth Under Salinity by Reducing Oxidative Stress and Promoting Chlorophyll Content via ETR2 Pathway

Ethylene Enhances Seed Germination and Seedling Growth Under Salinity by Reducing Oxidative Stress and Promoting Chlorophyll Content via ETR2 Pathway

The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses

Revealing the full-length transcriptome of caucasian clover rhizome development

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