Identification, Characterization, and Expression Profile Analysis of the mTERF Gene Family and Its Role in the Response to Abiotic Stress in Barley (Hordeum vulgare L.)

Li, Tingting; Pan, Wenqiu; Yuan, Yiyuan; Liu, Ying; Li, Yihan; Wu, Xiaoyu; Wang, Fei; Cui, Licao

doi:10.3389/fpls.2021.684619

Cited by 6 publications

(7 citation statements)

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“…The genetic divergence of the HvC3H genes between wild and domesticated barley populations was characterized using publicly released exome capture datasets [ 47 ]. Two genetically divergent populations associated with domestic vs. wild barley rather than barley populations with different geographic origins were observed, which was consistent with the deep phylogenetic split between wild and domesticated barley of HvmTERF s [ 48 ]. The greater effect of human-driven selection on the genomic regions of HvC3H s relative to natural selection was confirmed by the genetic diversity analysis.…”

Section: Discussionsupporting

confidence: 68%

CCCH Zinc finger genes in Barley: genome-wide identification, evolution, expression and haplotype analysis

Pan

Zeng

et al. 2022

BMC Plant Biol

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Background CCCH transcription factors are important zinc finger transcription factors involved in the response to biotic and abiotic stress and physiological and developmental processes. Barley (Hordeum vulgare) is an agriculturally important cereal crop with multiple uses, such as brewing production, animal feed, and human food. The identification and assessment of new functional genes are important for the molecular breeding of barley. Results In this study, a total of 53 protein-encoding CCCH genes unevenly dispersed on seven different chromosomes were identified in barley. Phylogenetic analysis categorized the barley CCCH genes (HvC3Hs) into eleven subfamilies according to their distinct features, and this classification was supported by intron–exon structure and conserved motif analysis. Both segmental and tandem duplication contributed to the expansion of CCCH gene family in barley. Genetic variation of HvC3Hs was characterized using publicly available exome-capture sequencing datasets. Clear genetic divergence was observed between wild and landrace barley populations in HvC3H genes. For most HvC3Hs, nucleotide diversity and the number of haplotype polymorphisms decreased during barley domestication. Furthermore, the HvC3H genes displayed distinct expression profiles for different developmental processes and in response to various types of stresses. The HvC3H1, HvC3H2 and HvC3H13 of arginine-rich tandem CCCH zinc finger (RR-TZF) genes were significantly induced by multiple types of abiotic stress and/or phytohormone treatment, which might make them as excellent targets for the molecular breeding of barley. Conclusions Overall, our study provides a comprehensive characterization of barley CCCH transcription factors, their diversity, and their biological functions.

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Section: Discussionsupporting

confidence: 68%

CCCH Zinc finger genes in Barley: genome-wide identification, evolution, expression and haplotype analysis

Pan

Zeng

et al. 2022

BMC Plant Biol

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“…The seeds of barley cv. Morex, which is stored by the Wheat Genomics Lab in Northwest A&F University (Central Shaanxi Province, China; 34 26′ N latitude, 108 07′ E longitude, altitude: 458 m), were sterilized by 5% ( w/v ) sodium hypochlorite (NaClO) (Xinyicheng, Shaanxi, China) for 5 min, and then rinsed using distilled water for 3 min, and finally incubated on wet filter paper in a petri dish at 25 °C for 5 days [ 51 ]. This experiment was conducted from 10 to 30 March 2022 in NWSUAF.…”

Section: Methodsmentioning

confidence: 99%

“…When the seedlings had grown to 4–5 cm, they were transplanted to hydroponic colonization plates, and put in culture medium (aqueous solution with 1/2 Hogeland nutrient) to reach the trifoliate leaf stage in a growth chamber under 20 °C /15 °C day/night, 16 h light/8 h dark cycle, and 50% relative humidity. Hydraulically cultured trifoliate leaf stage seedlings were exposed to culture medium, adding 150 mM NaCl, 20% PEG, 4 °C, or 100 µM ABA, and the roots and leaves were sampled at 0, 6 h, 12 h and 24 h as the stressed treatments [ 51 , 52 ]. The seedlings grown in the culture medium without any treatment were sampled simultaneously at the corresponding time point as the control.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification, Evolution and Expressional Analysis of OSCA Gene Family in Barley (Hordeum vulgare L.)

Kuijun

Pan

Yan

et al. 2022

IJMS

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The hyperosmolality-gated calcium-permeable channel gene family (OSCA) is one kind of conserved osmosensors, playing a crucial role in maintaining ion and water homeostasis and protecting cellular stability from the damage of hypertonic stress. Although it has been systematically characterized in diverse plants, it is necessary to explore the role of the OSCA family in barley, especially its importance in regulating abiotic stress response. In this study, a total of 13 OSCA genes (HvOSCAs) were identified in barley through an in silico genome search method, which were clustered into 4 clades based on phylogenetic relationships with members in the same clade showing similar protein structures and conserved motif compositions. These HvOSCAs had many cis-regulatory elements related to various abiotic stress, such as MBS and ARE, indicating their potential roles in abiotic stress regulation. Furthermore, their expression patterns were systematically detected under diverse stresses using RNA-seq data and qRT-PCR methods. All of these 13 HvOSCAs were significantly induced by drought, cold, salt and ABA treatment, demonstrating their functions in osmotic regulation. Finally, the genetic variations of the HvOSCAs were investigated using the re-sequencing data, and their nucleotide diversity in wild barley and landrace populations were 0.4966 × 10−3 and 0.391 × 10−3, respectively, indicating that a genetic bottleneck has occurred in the OSCA family during the barley evolution process. This study evaluated the genomic organization, evolutionary relationship and genetic expression of the OSCA family in barley, which not only provides potential candidates for further functional genomic study, but also contributes to genetically improving stress tolerance in barley and other crops.

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“…In the barley genome, segmental, and tandem duplication events are largely responsible for the expansion of gene families. Ten and thirteen HvmTERFs have undergone tandem and segmental duplications, respectively, accounting for about 38.33% of the total size of barley mTERFs (Li et al, 2021b). Tandem duplication was the main force driving the expansion of HvNRT2.1 (80.00%) (Guo et al, 2020), whereas segmental Frontiers in Genetics frontiersin.org duplication contributed greatly for the expansion of HvbHLH (42.55%) (Ke et al, 2020).…”

Section: Tandem Duplication Contributes Greatly To the Expansion Of H...mentioning

confidence: 99%

The barley DIR gene family: An expanded gene family that is involved in stress responses

Luo

Pan²,

Liu³

et al. 2022

Front. Genet.

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Gene family expansion plays a central role in adaptive divergence and, ultimately, speciation is influenced by phenotypic diversity in different environments. Barley (Hordeum vulgare) is the fourth most important cereal crop in the world and is used for brewing purposes, animal feed, and human food. Systematic characterization of expanded gene families is instrumental in the research of the evolutionary history of barley and understanding of the molecular function of their gene products. A total of 31,750 conserved orthologous groups (OGs) were identified using eight genomes/subgenomes, of which 1,113 and 6,739 were rapidly expanded and contracted OGs in barley, respectively. Five expanded OGs containing 20 barley dirigent genes (HvDIRs) were identified. HvDIRs from the same OG were phylogenetically clustered with similar gene structure and domain organization. In particular, 7 and 5 HvDIRs from OG0000960 and OG0001516, respectively, contributed greatly to the expansion of the DIR-c subfamily. Tandem duplication was the driving force for the expansion of the barley DIR gene family. Nucleotide diversity and haplotype network analysis revealed that the expanded HvDIRs experienced severe bottleneck events during barley domestication, and can thus be considered as potential domestication-related candidate genes. The expression profile and co-expression network analysis revealed the critical roles of the expanded HvDIRs in various biological processes, especially in stress responses. HvDIR18, HvDIR19, and HvDIR63 could serve as excellent candidates for further functional genomics studies to improve the production of barley products. Our study revealed that the HvDIR family was significantly expanded in barley and might be involved in different developmental processes and stress responses. Thus, besides providing a framework for future functional genomics and metabolomics studies, this study also identified HvDIRs as candidates for use in improving barley crop resistance to biotic and abiotic stresses.

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Identification, Characterization, and Expression Profile Analysis of the mTERF Gene Family and Its Role in the Response to Abiotic Stress in Barley (Hordeum vulgare L.)

Cited by 6 publications

References 84 publications

CCCH Zinc finger genes in Barley: genome-wide identification, evolution, expression and haplotype analysis

CCCH Zinc finger genes in Barley: genome-wide identification, evolution, expression and haplotype analysis

Genome-Wide Identification, Evolution and Expressional Analysis of OSCA Gene Family in Barley (Hordeum vulgare L.)

The barley DIR gene family: An expanded gene family that is involved in stress responses

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