Genome-Wide Analysis of C2H2 Zinc Finger Gene Family and Its Response to Cold and Drought Stress in Sorghum [Sorghum bicolor (L.) Moench]

Cui, Huiying; Chen, Jiaqi; Liu, Mengjiao; Zhang, Hongzhi; Zhang, Shuangxi; Liú, Dan; Chen, Shaolin

doi:10.3390/ijms23105571

Cited by 17 publications

(13 citation statements)

References 66 publications

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“…There were 218 C2H2 members in alfalfa, and these members had 337 individual C2H2 motifs ( Medicago truncatula ); 134 C2H2 members were identified in Camellia sinensis, which were distributed on 15 chromosomes randomly [ 48 , 50 ]; 79 C2H2 proteins were identified in potato ( Solanum tuberosum ) through hmmsearch and BLASTP in the genome database [ 47 ]. In sorghum ( Sorghum bicolor ), 145 members were identified and distributed on 10 chromosomes [ 30 ]. In this study, 150 members were used as the C2H2 members in maize ( Zea mays ), which covered all of the chromosomes of the reference genome and the splice “B73V4_ctg40”.…”

Section: Discussionmentioning

confidence: 99%

“…As an important transcription factor, C2H2 members have been identified in Arabidopsis [ 5 ], rice ( Oryza sativa ), durum wheat ( Triticum turgidum Durum ), soybean ( Glycine max ), potato ( Solanum tuberosum ), and sorghum ( Sorghum bicolor ) [ 28 , 29 , 30 ], but few studies have identified it in maize ( Zea mays ). Maize is an important crop that is domesticated from wild grass ( Z. mays subsp.…”

Section: Introductionmentioning

confidence: 99%

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Analysis of the C2H2 Gene Family in Maize (Zea mays L.) under Cold Stress: Identification and Expression

Li¹,

Li²,

Cai³

et al. 2022

Life

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The C2H2 zinc finger protein is one of the most common zinc finger proteins, widely exists in eukaryotes, and plays an important role in plant growth and development, as well as in salt, low-temperature, and drought stress and other abiotic stress responses. In this study, C2H2 members were identified and analyzed from the low-temperature tolerant transcriptome sequencing data of maize seedlings. The chromosome position, physical and chemical properties, evolution analysis, gene structure, conservative motifs, promoter cis elements and collinearity relationships of gene the family members were analyzed using bioinformatics, and the expression of the ZmC2H2 gene family under cold stress was analyzed by fluorescent quantitative PCR. The results showed that 150 members of the C2H2 zinc finger protein family were identified, and their protein lengths ranged from 102 to 1223 bp. The maximum molecular weight of the ZmC2H2s was 135196.34, and the minimum was 10823.86. The isoelectric point of the ZmC2H2s was between 33.21 and 94.1, and the aliphatic index was 42.07–87.62. The promoter cis element analysis showed that the ZmC2H2 family contains many light-response elements, plant hormone-response elements, and stress-response elements. The analysis of the transcriptome data showed that most of the ZmC2H2 genes responded to cold stress, and most of the ZmC2H2 genes were highly expressed in cold-tolerant materials and lowly expressed in cold-sensitive materials. The real-time quantitative PCR (qRT-PCR) analysis showed that ZmC2H2-69, ZmC2H2-130, and ZmC2H2-76 were significantly upregulated, and that ZmC2H2-149, ZmC2H2-33, and ZmC2H2-38 were significantly downregulated. It is hypothesized that these genes, which function in different metabolic pathways, may play a key role in the maize cold response. These genes could be further studied as candidate genes. This study provides a theoretical reference for further study on the function analysis of the maize C2H2 gene family.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Analysis of the C2H2 Gene Family in Maize (Zea mays L.) under Cold Stress: Identification and Expression

Li¹,

Li²,

Cai³

et al. 2022

Life

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“…The EPF1 gene of Petunia is the earliest zinc finger protein found in plants with a C2H2 zinc finger structure ( Takatsuji et al., 1992 ). Numerous C2H2-ZFPs have so far been found in plants, including Arabidopsis thaliana 176 ( Englbrecht et al., 2004 ), Sorghum bicolor 145 ( Cui et al., 2022 ), Vitis vinifera 98 ( Arrey-Salas et al., 2021 ), and Panax ginseng 115 ( Jiang et al., 2022 ). The length of the long spacer between the two zinc fingers in plant-specific C2H2-ZFP (Q-type C2H2-ZFP) is different from that of other eukaryotes ( Ciftci-Yilmaz and Mittler, 2008 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification of the C2H2 zinc finger gene family and expression analysis under salt stress in sweetpotato

Du,

Zhou,

Qin

et al. 2023

Front. Plant Sci.

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IntroductionThe higher plant transcription factor C2H2 zinc finger protein (C2H2-ZFP) is essential for plant growth, development, and stress response. There are limited studies on C2H2-ZFP genes in sweetpotato, despite a substantial number of C2H2-ZFP genes having been systematically found in plants.MethodsIn this work, 178 C2H2-ZFP genes were found in sweetpotato, distributed randomly on 15 chromosomes, and given new names according to where they were located. These members of the zinc finger gene family are separated into six branches, as shown by the phylogenetic tree. 24 tandem repeats of IbZFP genes and 46 fragment repeats were identified, and a homology study revealed that IbZFP genes linked more regions with wild relative species of sweetpotato as well as rhizome plants like potato and cassava. And we analyzed the expression patterns of IbZFP genes during the early development of sweetpotato storage roots (SRs) and salt stress using transcriptome data, and identified 44 IbZFP genes that exhibited differences in expression levels during the early expansion of sweetpotato SRs in different varieties, and 92 IbZFP genes that exhibited differences in expression levels under salt stress in salt tolerant and salt sensitive sweetpotato varieties. Additionally, we cloned six IbZFP genes in sweetpotato and analyzed their expression patterns in different tissues, their expression patterns under abiotic stress and hormone treatment, and subcellular localization.Results and discussionThe results showed that the IbZFP genes had tissue specificity in sweetpotato and were induced to varying degrees by drought and salt stress. ABA and GA3 treatments also affected the expression of the IbZFP genes. We selected IbZFP105, which showed significant differences in expression levels under salt stress and ABA treatment, to be heterologously expressed in Arabidopsis thaliana. We found that IbZFP105 OE lines exhibited higher tolerance to salt stress and ABA stress. This indicates that IbZFP105 can enhance the salt tolerance of plants. These results systematically identified the evolution and expression patterns of members of the C2H2-ZFP gene family in sweetpotato, providing a theoretical basis for studying the role of IbZFP genes in the development of sweetpotato SRs and in resistance to stress.

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“…The C2H2-type proteins ZFP245 and ZFP179 in Oryza sativa promoted the amount of free proline and soluble sugars, elevated the expression of stress-responsive genes, and enhanced their tolerance to salt and drought stresses [ 15 ]. Under cold environments, ZFP C2H2 directly regulates downstream genes to enhance cold resistance in Sorghum bicolor [ 16 ]. Additionally, ZFP in Glycine soja enhances salt tolerance by maintaining ion homeostasis and removing peroxides [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of the Zinc Finger Protein Gene Subfamilies under Drought Stress in Triticum aestivum

Shen

Wang

et al. 2022

Plants

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The zinc finger protein (ZFP) family is one of plants’ most diverse family of transcription factors. These proteins with finger-like structural domains have been shown to play a critical role in plant responses to abiotic stresses such as drought. This study aimed to systematically characterize Triticum aestivum ZFPs (TaZFPs) and understand their roles under drought stress. A total of 9 TaC2H2, 38 TaC3HC4, 79 TaCCCH, and 143 TaPHD were identified, which were divided into 4, 7, 12, and 14 distinct subgroups based on their phylogenetic relationships, respectively. Segmental duplication dominated the evolution of four subfamilies and made important contributions to the large-scale amplification of gene families. Syntenic relationships, gene duplications, and Ka/Ks result consistently indicate a potential strong purifying selection on TaZFPs. Additionally, TaZFPs have various abiotic stress-associated cis-acting regulatory elements and have tissue-specific expression patterns showing different responses to drought and heat stress. Therefore, these genes may play multiple functions in plant growth and stress resistance responses. This is the first comprehensive genome-wide analysis of ZFP gene families in T. aestivum to elucidate the basis of their function and resistance mechanisms, providing a reference for precise manipulation of genetic engineering for drought resistance in T. aestivum.

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Genome-Wide Analysis of C2H2 Zinc Finger Gene Family and Its Response to Cold and Drought Stress in Sorghum [Sorghum bicolor (L.) Moench]

Cited by 17 publications

References 66 publications

Analysis of the C2H2 Gene Family in Maize (Zea mays L.) under Cold Stress: Identification and Expression

Analysis of the C2H2 Gene Family in Maize (Zea mays L.) under Cold Stress: Identification and Expression

Genome-wide identification of the C2H2 zinc finger gene family and expression analysis under salt stress in sweetpotato

Genome-Wide Identification and Expression Analysis of the Zinc Finger Protein Gene Subfamilies under Drought Stress in Triticum aestivum

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