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Wang L, Zhao X, Zheng R, Huang Y, Zhang C, Zhang MM, Lan S, Liu ZJ. Genome-Wide Identification and Drought Stress Response Pattern of the NF-Y Gene Family in Cymbidium sinense. Int J Mol Sci 2024; 25:3031. [PMID: 38474276 DOI: 10.3390/ijms25053031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 03/14/2024] Open
Abstract
Cymbidium sinense, a type of orchid plant, is more drought-resistant and ornamental than other terrestrial orchids. Research has shown that many members of the NUCLEAR FACTOR Y (NF-Y) transcription factor family are responsive to plant growth, development, and abiotic stress. However, the mechanism of the NF-Y gene family's response to abiotic stress in orchids has not yet been reported. In this study, phylogenetic analysis allowed for 27 CsNF-Y genes to be identified (5 CsNF-YAs, 9 CsNF-YBs, and 13 CsNF-YC subunits), and the CsNF-Ys were homologous to those in Arabidopsis and Oryza. Protein structure analysis revealed that different subfamilies contained different motifs, but all of them contained Motif 2. Secondary and tertiary protein structure analysis indicated that the CsNF-YB and CsNF-YC subfamilies had a high content of alpha helix structures. Cis-element analysis showed that elements related to drought stress were mainly concentrated in the CsNF-YB and CsNF-YC subfamilies, with CsNF-YB3 and CsNF-YC12 having the highest content. The results of a transcriptome analysis showed that there was a trend of downregulation of almost all CsNF-Ys in leaves under drought stress, while in roots, most members of the CsNF-YB subfamily showed a trend of upregulation. Additionally, seven genes were selected for real-time reverse transcription quantitative PCR (qRT-PCR) experiments. The results were generally consistent with those of the transcriptome analysis. The regulatory roles of CsNF-YB 1, 2, and 4 were particularly evident in the roots. The findings of our study may make a great contribution to the understanding of the role of CsNF-Ys in stress-related metabolic processes.
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Affiliation(s)
- Linying Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuewei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ruiyue Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ye Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cuili Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meng-Meng Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Tian Y, Song K, Li B, Song Y, Zhang X, Li H, Yang L. Genome-wide identification and expression analysis of NF-Y gene family in tobacco (Nicotiana tabacum L.). Sci Rep 2024; 14:5257. [PMID: 38438470 PMCID: PMC10912202 DOI: 10.1038/s41598-024-55799-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 02/27/2024] [Indexed: 03/06/2024] Open
Abstract
Nuclear factor Y (NF-Y) gene family is an important transcription factor composed of three subfamilies of NF-YA, NF-YB and NF-YC, which is involved in plant growth, development and stress response. In this study, 63 tobacco NF-Y genes (NtNF-Ys) were identified in Nicotiana tabacum L., including 17 NtNF-YAs, 30 NtNF-YBs and 16 NtNF-YCs. Phylogenetic analysis revealed ten pairs of orthologues from tomato and tobacco and 25 pairs of paralogues from tobacco. The gene structure of NtNF-YAs exhibited similarities, whereas the gene structure of NtNF-YBs and NtNF-YCs displayed significant differences. The NtNF-Ys of the same subfamily exhibited a consistent distribution of motifs and protein 3D structure. The protein interaction network revealed that NtNF-YC12 and NtNF-YC5 exhibited the highest connectivity. Many cis-acting elements related to light, stress and hormone response were found in the promoter of NtNF-Ys. Transcriptome analysis showed that more than half of the NtNF-Y genes were expressed in all tissues, and NtNF-YB9/B14/B15/B16/B17/B29 were specifically expressed in roots. A total of 15, 12, 5, and 6 NtNF-Y genes were found to respond to cold, drought, salt, and alkali stresses, respectively. The results of this study will lay a foundation for further study of NF-Y genes in tobacco and other Solanaceae plants.
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Affiliation(s)
- Yue Tian
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Kangkang Song
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, China
- Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, College of Forestry, Shandong Agricultural University, Tai'an, China
| | - Bin Li
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Yanru Song
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiaohua Zhang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Haozhen Li
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China.
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Chen S, Wei X, Hu X, Zhang P, Chang K, Zhang D, Chen W, Tang D, Tang Q, Li P, Tan L. Genome-Wide Analysis of Nuclear factor-YC Genes in the Tea Plant ( Camellia sinensis) and Functional Identification of CsNF-YC6. Int J Mol Sci 2024; 25:836. [PMID: 38255910 PMCID: PMC10815638 DOI: 10.3390/ijms25020836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Nuclear factor Y (NF-Y) is a class of transcription factors consisting of NF-YA, NF-YB and NF-YC subunits, which are widely distributed in eukaryotes. The NF-YC subunit regulates plant growth and development and plays an important role in the response to stresses. However, there are few reports on this gene subfamily in tea plants. In this study, nine CsNF-YC genes were identified in the genome of 'Longjing 43'. Their phylogeny, gene structure, promoter cis-acting elements, motifs and chromosomal localization of these gene were analyzed. Tissue expression characterization revealed that most of the CsNF-YCs were expressed at low levels in the terminal buds and at relatively high levels in the flowers and roots. CsNF-YC genes responded significantly to gibberellic acid (GA) and abscisic acid (ABA) treatments. We further focused on CsNF-YC6 because it may be involved in the growth and development of tea plants and the regulation of response to abiotic stresses. The CsNF-YC6 protein is localized in the nucleus. Arabidopsis that overexpressed CsNF-YC6 (CsNF-YC6-OE) showed increased seed germination and increased root length under ABA and GA treatments. In addition, the number of cauline leaves, stem lengths and silique numbers were significantly higher in overexpressing Arabidopsis lines than wild type under long-day growth conditions, and CsNF-YC6 promoted primary root growth and increased flowering in Arabidopsis. qPCR analysis showed that in CsNF-YC6-OE lines, flowering pathway-related genes were transcribed at higher levels than wild type. The investigation of the CsNF-YC gene has unveiled that CsNF-YC6 plays a pivotal role in plant growth, root and flower development, as well as responses to abiotic stress.
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Affiliation(s)
- Shengxiang Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (S.C.)
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Xujiao Wei
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (S.C.)
| | - Xiaoli Hu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (S.C.)
| | - Peng Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (S.C.)
| | - Kailin Chang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (S.C.)
| | - Dongyang Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (S.C.)
| | - Wei Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (S.C.)
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Dandan Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (S.C.)
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Qian Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (S.C.)
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Pinwu Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (S.C.)
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Liqiang Tan
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (S.C.)
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Chengdu 611130, China
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Jiang L, Ren Y, Jiang Y, Hu S, Wu J, Wang G. Characterization of NF-Y gene family and their expression and interaction analysis in Phalaenopsis orchid. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108143. [PMID: 37913748 DOI: 10.1016/j.plaphy.2023.108143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/03/2023]
Abstract
The complex of Nuclear Factor Ys (NF-Ys), a family of heterotrimeric transcription factors composed of three unique subunits (NF-YA, NF-YB, and NF-YC), binds to the CCAAT box of eukaryotic promoters to activate or repress transcription of the downstream genes involved into various biological processes in plants. However, the systematic characterization of NF-Y gene family has not been elucidated in Phalaenopsis. A total of 24 NF-Y subunits (4 NF-YA, 9 NF-YB, and 11 NF-YC subunits) were identified in Phalaenopsis genome, whose exon/intron structures were highly differentiated among the PhNF-Y subunits. The distribution of motifs between coding regions of PhNF-YA and PhNF-YB/C was distinct. Segmental and tandem duplication events among paralogous PhNF-Ys were occurred. Six pairs of orthologous NF-Ys from Phalaenopsis and Arabidopsis and five pairs of orthologous NF-Ys from Phalaenopsis and rice involved in the phylogenetic gene synteny were identified. The various cis-elements being responsive to low-temperature, drought and ABA were distributed in the promoters of PhNF-Ys. qRT-PCR analysis indicated all of PhNF-Ys displayed the spatial specificity of expression in different tissues. Moreover, the expression levels of multiple PhNF-Ys significantly changed responding to low-temperature and ABA treatment. Yeast two hybrid and bimolecular fluorescence complementation assays approved the interaction of PhNF-YA1/3 with PhNF-YB6/PhNF-YC7, respectively, as well as PhNF-YB6 with PhNF-YC7. PhNF-YA1/3, PhNF-YB6, and PhNF-YC7 proteins were all localized in the nucleus. Further, transient overexpression of PhNF-YB6 and PhNF-YC7 promoted PhFT3 and repressed PhSVP expression in Phalaenopsis. These findings will facilitate to explore the role of PhNF-Ys in floral transition in Phalaenopsis orchid.
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Affiliation(s)
- Li Jiang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuepeng Ren
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yifan Jiang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shasha Hu
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiayi Wu
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangdong Wang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Siriwardana CL, Risinger JR, Carpenter EM, Holt BF. Analysis of gene duplication within the Arabidopsis NUCLEAR FACTOR Y, subunit B (NF-YB) protein family reveals domains under both purifying and diversifying selection. PLoS One 2023; 18:e0289332. [PMID: 37531316 PMCID: PMC10396019 DOI: 10.1371/journal.pone.0289332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023] Open
Abstract
Gene duplication is an evolutionary mechanism that provides new genetic material. Since gene duplication is a major driver for molecular evolution, examining the fate of duplicated genes is an area of active research. The fate of duplicated genes can include loss, subfunctionalization, and neofunctionalization. In this manuscript, we chose to experimentally study the fate of duplicated genes using the Arabidopsis NUCLEAR FACTOR Y (NF-Y) transcription factor family. NF-Y transcription factors are heterotrimeric complexes, composed of NF-YA, NF-YB, and NF-YC. NF-YA subunits are responsible for nucleotide-specific binding to a CCAAT cis-regulatory element. NF-YB and NF-YC subunits make less specific, but essential complex-stabilizing contacts with the DNA flanking the core CCAAT pentamer. While ubiquitous in eukaryotes, each NF-Y family has expanded by duplication in the plant lineage. For example, the model plant Arabidopsis contains 10 each of the NF-Y subunits. Here we examine the fate of duplicated NF-YB proteins in Arabidopsis, which are composed of central histone fold domains (HFD) and less conserved flanking regions (N- and C-termini). Specifically, the principal question we wished to address in this manuscript was to what extent can the 10 Arabidopsis NF-YB paralogs functionally substitute the genes NF-YB2 and NF-YB3 in the promotion of photoperiodic flowering? Our results demonstrate that the conserved histone fold domains (HFD) may be under pressure for purifying (negative) selection, while the non-conserved N- and C-termini may be under pressure for diversifying (positive) selection, which explained each paralog's ability to substitute. In conclusion, our data demonstrate that the N- and C-termini may have allowed the duplicated genes to undergo functional diversification, allowing the retention of the duplicated genes.
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Affiliation(s)
- Chamindika L Siriwardana
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
- Department of Science and Mathematics, Texas A&M University-Central Texas, Killeen, Texas, United States of America
| | - Jan R Risinger
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
- Myriad Genetics Corporation, Salt Lake City, Utah, United States of America
| | - Emily Mills Carpenter
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
- Aquatic Biomonitoring, Austin, Texas, United States of America
| | - Ben F Holt
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
- AgBiome, Research Triangle Park, North Carolina, United States of America
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Jiang Z, Wang Y, Li W, Wang Y, Liu X, Ou X, Su W, Song S, Chen R. Genome-Wide Identification of the NF-Y Gene Family and Their Involvement in Bolting and Flowering in Flowering Chinese Cabbage. Int J Mol Sci 2023; 24:11898. [PMID: 37569274 PMCID: PMC10418651 DOI: 10.3390/ijms241511898] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Flowering Chinese cabbage (Brassica campestris L. ssp. Chinensis var. utilis Tsen et Lee) is a widely consumed vegetable in southern China with significant economic value. Developing product organs in the flowering Chinese cabbage involves two key processes: bolting and flowering. Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor known for its crucial role in various plant developmental processes. However, there is limited information available on the involvement of this gene family during flowering during Chinese cabbage development. In this study, 49 BcNF-Y genes were identified and characterized along with their physicochemical properties, gene structure, chromosomal location, collinearity, and expression patterns. We also conducted subcellular localization, yeast two-hybrid, and transcriptional activity assays on selected BcNF-Y genes. The findings of this study revealed enhanced expression levels of specific BcNF-Y genes during the stalk development and flowering stages in flowering Chinese cabbage. Notably, BcNF-YA8, BcNF-YB14, BcNF-YB20, and BcNF-YC5 interacted with BcRGA1, a negative regulator of GA signaling, indicating their potential involvement in GA-mediated stalk development. This study provides valuable insights into the role of BcNF-Y genes in flowering Chinese cabbage development and suggests that they are potential candidates for further investigating the key regulators of cabbage bolting and flowering.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Riyuan Chen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (Z.J.); (Y.W.); (W.L.); (Y.W.); (X.L.); (X.O.); (W.S.); (S.S.)
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Cao L, Ma C, Ye F, Pang Y, Wang G, Fahim AM, Lu X. Genome-wide identification of NF-Y gene family in maize ( Zea mays L.) and the positive role of ZmNF-YC12 in drought resistance and recovery ability. FRONTIERS IN PLANT SCIENCE 2023; 14:1159955. [PMID: 37265635 PMCID: PMC10229843 DOI: 10.3389/fpls.2023.1159955] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/17/2023] [Indexed: 06/03/2023]
Abstract
Nuclear factor Y (NF-Y) genes play important roles in many biological processes, such as leaf growth, nitrogen nutrition, and drought resistance. However, the biological functions of these transcription factor family members have not been systematically analyzed in maize. In the present study, a total of 52 ZmNF-Y genes were identified and classified into three groups in the maize genome. An analysis of the evolutionary relationship, gene structure, and conserved motifs of these genes supports the evolutionary conservation of NF-Y family genes in maize. The tissue expression profiles based on RNA-seq data showed that all genes apart from ZmNF-Y16, ZmNF-YC15, and ZmNF-YC17 were expressed in different maize tissues. A weighted correlation network analysis was conducted and a gene co expression network method was used to analyze the transcriptome sequencing results; six core genes responding to drought and rewatering were identified. A real time fluorescence quantitative analysis showed that these six genes responded to high temperature, drought, high salt, and abscisic acid (ABA) treatments, and subsequent restoration to normal levels. ZmNF-YC12 was highly induced by drought and rewatering treatments. The ZmNF-YC12 protein was localized in the nucleus, and the Gal4-LexA/UAS system and a transactivation analysis demonstrated that ZmNF-YC12 in maize (Zea mays L.) is a transcriptional activator that regulates drought resistance and recovery ability. Silencing ZmNF-YC12 reduced net photosynthesis, chlorophyll content, antioxidant (superoxide dismutase, catalase, peroxidase and ascorbate peroxidase) system activation, and soluble protein and proline contents; it increased the malondialdehyde content, the relative water content, and the water loss rate, which weakened drought resistance and the recoverability of maize. These results provide insights into understanding the evolution of ZmNF-Y family genes in maize and their potential roles in genetic improvement. Our work provides a foundation for subsequent functional studies of the NF-Y gene family and provides deep insights into the role of the ZmNF-YC12 regulatory network in controlling drought resistance and the recoverability of maize.
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Affiliation(s)
- Liru Cao
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou Henan, China
| | - Chenchen Ma
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Feiyu Ye
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yunyun Pang
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Guorui Wang
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Abbas Muhammad Fahim
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Xiaomin Lu
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou Henan, China
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Deng S, Wang R, Tao C, Li L, Wang S, Jia C, Liu Y, Du R, Du L, Yang J. Genome-wide analysis of CtNF-YB and lipid synthesis regulation of CtNF-YB12 in Carthamus tinctorius L. PLANT CELL REPORTS 2023; 42:57-72. [PMID: 36309876 DOI: 10.1007/s00299-022-02936-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The nuclear Factor YB of Carthamus tinctorius L. increased the content of unsaturated fatty acids by regulating the expression of genes involved in fatty acid synthesis and oil accumulation. Safflower (Carthamus tinctorius L.) seed oil is rich in linoleic acid and is widely used in food and medicine. Therefore, key genes regulating oil synthesis were mined through genetic engineering to provide genetic resources for improving oil content. Based on the conserved domain of the NF-YB, we screened and identified 14 CtNF-YB transcription factors in the safflower genome and divided them into three subfamilies through phylogenetic analysis. Regulatory motif analysis of the CtNF-YB promoter revealed specific cis-regulatory elements related to abiotic stress, growth, and development. Expression analysis of CtNF-YB family genes showed that non-Leafy Cotyledon 1(non-LEC1) genes were highly expressed in roots, leaves, and flowers; Leafy Cotyledon 1(LEC1) genes were highly expressed during early seed development; and Dr1-like genes were highly expressed in roots, stems, and leaves. CtNF-YB12 was identified as a LEC1 transcription factor based on phylogeny and BLAST alignment. Heterologous CtNF-YB12 expression in Arabidopsis thaliana increased seed pod length and seed size. Moreover, CtNF-YB12 overexpression increased the oil content of seeds, upregulated genes involved in fatty acid biosynthesis and glycolysis, and altered the content of unsaturated fatty acids, including oleic acid (C18:1), linoleic acid (C18:2), and linolenic acid (C18:3), as well as of sucrose, fructose, and glucose. CtNF-YB12 may increase the oil content by regulating key enzyme genes of oil synthesis, so it can be used as a reliable target.
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Affiliation(s)
- Sinan Deng
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Ruinan Wang
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Chenlu Tao
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Lixia Li
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Shuai Wang
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Chang Jia
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Yilin Liu
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Ruo Du
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Linna Du
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Jing Yang
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China.
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Zhao Y, Zhang Y, Li T, Ni C, Bai X, Lin R, Xiao K. TaNF-YA7-5B, a gene encoding nuclear factor Y (NF-Y) subunit A in Triticum aestivum, confers plant tolerance to PEG-inducing dehydration simulating drought through modulating osmotic stress-associated physiological processes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 188:81-96. [PMID: 35988390 DOI: 10.1016/j.plaphy.2022.07.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/20/2022] [Accepted: 07/23/2022] [Indexed: 05/27/2023]
Abstract
Members of nuclear factor-Y (NF-Y) transcription factors play important roles in regulating physiological processes associated with abiotic stress responses. In this study, we characterized TaNF-YA7-5B, a gene encoding wheat NY-YA subunit, in mediating plant adaptation to PEG-inducing dehydration stress. TaNF-YA7-5B shares high similarities to its homologs across various plant species. The TaNF-YA7-5B protein is specified by its conserved domains as plant NF-YA members and targets onto nucleus after endoplasmic reticulum assortment. Yeast two-hybrid assays indicated that TaNF-YA7-5B interacts with TaNF-YB2 and TaNF-YC7, two members of NF-YB and NF-YC subfamilies, suggesting a heterotrimer constituted by TaNF-YA7-5B and above NF-YB and -YC partners. TaNF-YA7-5B displayed induced expression upon drought and whose PEG-inducing dehydration-elevated transcripts were restored under normal recovery condition, suggesting its involvement in plant PEG-inducing dehydration response through modifying transcription efficiency. Overexpressing TaNF-YA7-5B conferred plant improved growth under PEG-inducing dehydration, which was ascribed largely to the gene function in regulating stomata closing and leaf water retention, osmolyte biosynthesis, and cellular ROS homeostasis. The expression of P5CS gene TaP5CS2 and antioxidant enzyme (AE) genes, namely, TaSOD3, TaCAT1, and TaPOD4, was upregulated and downregulated in lines with overexpression and knockdown of TaNF-YA7-5B, respectively; transgene analysis on them validated their functions in positively regulating proline accumulation and ROS scavenging under PEG-inducing dehydration. RNA-seq analysis revealed modified transcription of numerous genes underlying TaNF-YA7-5B enriched by GO terms 'biological process', 'cellular components', and 'molecular function'. Therefore, TaNF-YA7-5B is a crucial regulator for plant drought adaptation through comprehensively integrating diverse physiological processes associated with drought acclimation.
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Affiliation(s)
- Yingjia Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, 071001, China; College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China
| | - Yanyang Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, 071001, China; College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China
| | - Tianjiao Li
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, 071001, China; College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China
| | - Chenyang Ni
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, 071001, China; College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China
| | - Xinyang Bai
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, 071001, China; College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China
| | - Ruize Lin
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, 071001, China; College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China
| | - Kai Xiao
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, 071001, China; College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China.
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Zhou J, Yang L, Chen X, Zhou M, Shi W, Deng S, Luo Z. Genome-Wide Identification and Characterization of the NF-YA Gene Family and Its Expression in Response to Different Nitrogen Forms in Populus × canescens. Int J Mol Sci 2022; 23:ijms231911217. [PMID: 36232523 PMCID: PMC9570100 DOI: 10.3390/ijms231911217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
The NF-YA gene family is a class of conserved transcription factors that play important roles in plant growth and development and the response to abiotic stress. Poplar is a model organism for studying the rapid growth of woody plants that need to consume many nutrients. However, studies on the response of the NF-YA gene family to nitrogen in woody plants are limited. In this study, we conducted a systematic and comprehensive bioinformatic analysis of the NF-YA gene family based on Populus × canescens genomic data. A total of 13 PcNF-YA genes were identified and mapped to 6 chromosomes. According to the amino acid sequence characteristics and genetic structure of the NF-YA domains, the PcNF-YAs were divided into five clades. Gene duplication analysis revealed five pairs of replicated fragments and one pair of tandem duplicates in 13 PcNF-YA genes. The PcNF-YA gene promoter region is rich in different cis-acting regulatory elements, among which MYB and MYC elements are the most abundant. Among the 13 PcNF-YA genes, 9 contained binding sites for P. × canescens miR169s. In addition, RT-qPCR data from the roots, wood, leaves and bark of P. × canescens showed different spatial expression profiles of PcNF-YA genes. Transcriptome data and RT-qPCR analysis showed that the expression of PcNF-YA genes was altered by treatment with different nitrogen forms. Furthermore, the functions of PcNF-YA genes in transgenic poplar were analyzed, and the potential roles of PcNF-YA genes in the response of poplar roots to different nitrogen forms were revealed, indicating that these genes regulate root growth and development.
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Affiliation(s)
- Jing Zhou
- Correspondence: ; Tel.: +86-10-62889368
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11
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Huang Y, Ma H, Wang X, Cui T, Han G, Zhang Y, Wang C. Expression patterns of the poplar NF-Y gene family in response to Alternaria alternata and hormone treatment and the role of PdbNF-YA11 in disease resistance. Front Bioeng Biotechnol 2022; 10:956271. [PMID: 36185440 PMCID: PMC9523018 DOI: 10.3389/fbioe.2022.956271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Plant nuclear factor-Y (NF-Y) transcription factors (TFs) are key regulators of growth and stress resistance. However, the role of NF-Y TFs in poplar in response to biotic stress is still unclear. In this study, we cloned 26 PdbNF-Y encoding genes in the hybrid poplar P. davidiana × P. bollena, including 12 PdbNF-YAs, six PdbNF-YBs, and eight PdbNF-YCs. Their physical and chemical parameters, conserved domains, and phylogeny were subsequently analyzed. The protein–protein interaction (PPI) network showed that the three PdbNF-Y subunits may interact with NF-Y proteins belonging to two other subfamilies and other TFs. Tissue expression analysis revealed that PdbNF-Ys exhibited three distinct expression patterns in three tissues. Cis-elements related to stress-responsiveness were found in the promoters of PdbNF-Ys, and most PdbNF-Ys were shown to be differentially expressed under Alternaria alternata and hormone treatments. Compared with the PdbNF-YB and PdbNF-YC subfamilies, more PdbNF-YAs were significantly induced under the two treatments. Moreover, loss- and gain-of-function analyses showed that PdbNF-YA11 plays a positive role in poplar resistance to A. alternata. Additionally, RT‒qPCR analyses showed that overexpression and silencing PdbNF-YA11 altered the transcript levels of JA-related genes, including LOX, AOS, AOC, COI, JAZ, ORCA, and MYC, suggesting that PdbNF-YA11-mediated disease resistance is related to activation of the JA pathway. Our findings will contribute to functional analysis of NF-Y genes in woody plants, especially their roles in response to biotic stress.
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Rolling WR, Senalik D, Iorizzo M, Ellison S, Van Deynze A, Simon PW. CarrotOmics: a genetics and comparative genomics database for carrot ( Daucus carota). Database (Oxford) 2022; 2022:6693759. [PMID: 36069936 PMCID: PMC9450951 DOI: 10.1093/database/baac079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 08/19/2022] [Accepted: 09/01/2022] [Indexed: 11/15/2022]
Abstract
Abstract
CarrotOmics (https://carrotomics.org/) is a comprehensive database for carrot (Daucus carota L.) breeding and research. CarrotOmics was developed using resources available at the MainLab Bioinformatics core (https://www.bioinfo.wsu.edu/) and is implemented using Tripal with Drupal modules. The database delivers access to download or visualize the carrot reference genome with gene predictions, gene annotations and sequence assembly. Other genomic resources include information for 11 224 genetic markers from 73 linkage maps or genotyping-by-sequencing and descriptions of 371 mapped loci. There are records for 1601 Apiales species (or subspecies) and descriptions of 9408 accessions from 11 germplasm collections representing more than 600 of these species. Additionally, 204 Apiales species have phenotypic information, totaling 28 517 observations from 10 041 biological samples. Resources on CarrotOmics are freely available, search functions are provided to find data of interest and video tutorials are available to describe the search functions and genomic tools. CarrotOmics is a timely resource for the Apiaceae research community and for carrot geneticists developing improved cultivars with novel traits addressing challenges including an expanding acreage in tropical climates, an evolving consumer interested in sustainably grown vegetables and a dynamic environment due to climate change. Data from CarrotOmics can be applied in genomic-assisted selection and genetic research to improve basic research and carrot breeding efficiency.
Database URL
https://carrotomics.org/
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Affiliation(s)
- William R Rolling
- Vegetable Crop Research Unit, USDA-ARS , Moore Hall, 1575 Linden Drive, Madison, WI 53706-1514, USA
- Department of Horticulture, University of Wisconsin-Madison , Moore Hall, 1575 Linden Drive, Madison, WI 53706-1514, USA
| | - Douglas Senalik
- Vegetable Crop Research Unit, USDA-ARS , Moore Hall, 1575 Linden Drive, Madison, WI 53706-1514, USA
- Department of Horticulture, University of Wisconsin-Madison , Moore Hall, 1575 Linden Drive, Madison, WI 53706-1514, USA
| | - Massimo Iorizzo
- Department of Horticultural Science and Plants for Human Health Institute, North Carolina State University , NC Research Campus, 600 Laureate Way, Kannapolis, NC 28081, USA
| | - Shelby Ellison
- Department of Horticulture, University of Wisconsin-Madison , Moore Hall, 1575 Linden Drive, Madison, WI 53706-1514, USA
| | - Allen Van Deynze
- College of Agricultural & Environmental Sciences, Seed Biotechnology Center, University of California-Davis , 150 Mrak Hall, One Shields Avenue, Davis, CA 95616, USA
| | - Philipp W Simon
- Vegetable Crop Research Unit, USDA-ARS , Moore Hall, 1575 Linden Drive, Madison, WI 53706-1514, USA
- Department of Horticulture, University of Wisconsin-Madison , Moore Hall, 1575 Linden Drive, Madison, WI 53706-1514, USA
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13
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Yu J, Yuan Y, Zhang W, Song T, Hou X, Kong L, Cui G. Overexpression of an NF-YC2 gene confers alkali tolerance to transgenic alfalfa ( Medicago sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:960160. [PMID: 35991397 PMCID: PMC9389336 DOI: 10.3389/fpls.2022.960160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Alkaline stress severely limits plant growth and yield worldwide. NF-YC transcription factors (TFs) respond to abiotic stress by activating gene expression. However, the biological function of NF-YC TFs in alfalfa (Medicago sativa L.) is not clear. In our study, an NF-YC2 gene was identified and transgenic plants were obtained by constructing overexpression vector and cotyledon node transformation system in alfalfa. The open reading frame of MsNF-YC2 is 879 bp with 32.4 kDa molecular mass. MsNF-YC2 showed tissue expression specificity and was induced by a variety of abiotic stresses including drought, salt, and alkali stress in alfalfa. Under alkali stress treatment, transgenic plants exhibited higher levels of antioxidant enzyme activities and proline (Pro), correlating with a lower levels of hydrogen peroxide (H2O2), superoxide anion (O2 -) compared with wild-type (WT) plants. Transcriptomic results showed that overexpression of MsNF-YC2 regulated the expression of phytohormone signal transduction and photosynthesis-related genes under normal and alkaline stress treatments. These results suggest that the MsNF-YC2 gene plays crucial role enhance alkali adaptation abilities in alfalfa.
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14
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Ge H, Xu J, Hua M, An W, Wu J, Wang B, Li P, Fang H. Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench. BMC Genomics 2022; 23:538. [PMID: 35879672 PMCID: PMC9310384 DOI: 10.1186/s12864-022-08776-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 07/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acyl carrier proteins (ACP) constitute a very conserved carrier protein family. Previous studies have found that ACP not only takes part in the fatty acid synthesis process of almost all organisms, but also participates in the regulation of plant growth, development, and metabolism, and makes plants adaptable to stresses. However, this gene family has not been systematically studied in sorghum. RESULTS Nine ACP family members were identified in the sorghum genome, which were located on chromosomes 1, 2, 5, 7, 8 and 9, respectively. Evolutionary analysis among different species divided the ACP family into four subfamilies, showing that the SbACPs were more closely related to maize. The prediction results of subcellular localization showed that SbACPs were mainly distributed in chloroplasts and mitochondria, while fluorescence localization showed that SbACPs were mainly localized in chloroplasts in tobacco leaf. The analysis of gene structure revealed a relatively simple genetic structure, that there were 1-3 introns in the sorghum ACP family, and the gene structure within the same subfamily had high similarity. The amplification method of SbACPs was mainly large fragment replication, and SbACPs were more closely related to ACPs in maize and rice. In addition, three-dimensional structure analysis showed that all ACP genes in sorghum contained four α helices, and the second helix structure was more conserved, implying a key role in function. Cis-acting element analysis indicated that the SbACPs might be involved in light response, plant growth and development regulation, biotic and abiotic stress response, plant hormone regulation, and other physiological processes. What's more, qRT-PCR analysis uncovered that some of SbACPs might be involved in the adaptive regulation of drought and salt stresses, indicating the close relationship between fatty acids and the resistance to abiotic stresses in sorghum. CONCLUSIONS In summary, these results showed a comprehensive overview of the SbACPs and provided a theoretical basis for further studies on the biological functions of SbACPs in sorghum growth, development and abiotic stress responses.
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Affiliation(s)
- Hanqiu Ge
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Jingjing Xu
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Mingzhu Hua
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Wenwen An
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Junping Wu
- Nantong Changjiang Seed Co., Ltd, Nantong, 226368, Jiangsu, People's Republic of China
| | - Baohua Wang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China.
| | - Ping Li
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China.
| | - Hui Fang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China.
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15
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Liu M, Pan Z, Yu J, Zhu L, Zhao M, Wang Y, Chen P, Liu C, Hu J, Liu T, Wang K, Wang Y, Zhang M. Transcriptome-wide characterization, evolutionary analysis, and expression pattern analysis of the NF-Y transcription factor gene family and salt stress response in Panax ginseng. BMC PLANT BIOLOGY 2022; 22:320. [PMID: 35787249 PMCID: PMC9252045 DOI: 10.1186/s12870-022-03687-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Jilin ginseng (Panax ginseng C. A. Meyer) has a long history of medicinal use worldwide. The quality of ginseng is governed by a variety of internal and external factors. Nuclear factor Y (NF-Y), an important transcription factor in eukaryotes, plays a crucial role in the plant response to abiotic stresses by binding to a specific promoter, the CCAAT box. However, the NF-Y gene family has not been reported in Panax ginseng. In this study, 115 PgNF-Y transcripts with 40 gene IDs were identified from the Jilin ginseng transcriptome database. These genes were classified into the PgNF-YA (13), PgNF-YB (14), and PgNF-YC (13) subgroups according to their subunit types, and their nucleotide sequence lengths, structural domain information, and amino acid sequence lengths were analyzed. The phylogenetic analysis showed that the 79 PgNF-Y transcripts with complete ORFs were divided into three subfamilies, NF-YA, NF-YB, and NF-YC. PgNF-Y was annotated to eight subclasses under three major functions (BP, MF, and CC) by GO annotation, indicating that these transcripts perform different functions in ginseng growth and development. Expression pattern analysis of the roots of 42 farm cultivars, 14 different tissues of 4-year-old ginseng plants, and the roots of 4 different-ages of ginseng plants showed that PgNF-Y gene expression differed across lineages and had spatiotemporal specificity. Coexpression network analysis showed that PgNF-Ys acted synergistically with each other in Jilin ginseng. In addition, the analysis of the response of PgNF-YB09, PgNF-YC02, and PgNF-YC07-04 genes to salt stress treatment was investigated by fluorescence quantitative PCR. The expression of these genes increased after salt stress treatment, indicating that they may be involved in the regulation of the response to salt stresses in ginseng. These results provide important functional genetic resources for the improvement and gene breeding of ginseng in the future.Conclusions: This study fills a knowledge gap regarding the NF-Y gene family in ginseng, provides systematic theoretical support for subsequent research on PgNF-Y genes, and provides data resources for resistance to salt stress in ginseng.
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Affiliation(s)
- Mingming Liu
- College of Life Science, Jilin Agricultural University, Changchun, 130118 Jilin China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, 130118 Jilin China
| | - Zhaoxi Pan
- College of Life Science, Jilin Agricultural University, Changchun, 130118 Jilin China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, 130118 Jilin China
| | - Jie Yu
- College of Life Science, Jilin Agricultural University, Changchun, 130118 Jilin China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, 130118 Jilin China
| | - Lei Zhu
- College of Life Science, Jilin Agricultural University, Changchun, 130118 Jilin China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, 130118 Jilin China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun, 130118 Jilin China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, 130118 Jilin China
| | - Yanfang Wang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118 Jilin China
| | - Ping Chen
- College of Life Science, Jilin Agricultural University, Changchun, 130118 Jilin China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, 130118 Jilin China
| | - Chang Liu
- College of Life Science, Jilin Agricultural University, Changchun, 130118 Jilin China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, 130118 Jilin China
| | - Jian Hu
- College of Life Science, Jilin Agricultural University, Changchun, 130118 Jilin China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, 130118 Jilin China
| | - Tao Liu
- College of Life Science, Jilin Agricultural University, Changchun, 130118 Jilin China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, 130118 Jilin China
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun, 130118 Jilin China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, 130118 Jilin China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun, 130118 Jilin China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, 130118 Jilin China
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun, 130118 Jilin China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, 130118 Jilin China
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16
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Panzade KP, Kale SS, Manoj ML, Kothawale SP, Damse DN. Genome-Wide Analysis and Expression Profile of Nuclear Factor Y (NF-Y) Gene Family in Z. jujuba. Appl Biochem Biotechnol 2022; 194:1373-1389. [PMID: 34731431 DOI: 10.1007/s12010-021-03730-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/21/2021] [Indexed: 10/19/2022]
Abstract
Nuclear factor-Y (NF-Y) is an important transcription factor in the plant species, which potentially provides a higher level of functional diversity including for abiotic stress tolerance. The genome-wide study and expression analysis of NF-Y gene family in Ziziphus, an elite abiotic stress-tolerant species, assist bioprospecting of genes. Here, a total of 32 NF-Y (8 NF-YA, 15 NF-YB, and 9 NF-YC) genes were identified in genome-wide search of Z. jujuba genome. Physicochemical properties, cellular localization, gene structure, chromosomal location, and protein motifs were analyzed for structural and functional understanding. Identified 12 NF-Ys were responsible for the expansion of NF-Y gene family by tandem duplication in Z. jujuba. Phylogenetic and comparative physical mapping of Z. jujuba NF-Ys with its orthologs illustrated evolutionary and functional insights into NF-Y gene family. A total of 45 perfect microsatellites (20bp to 40bp) were extracted across the ZjNF-Y genes. The promoter and gene ontology study suggested that Z. jujuba NF-Y gene family is functionally diverse and could play a wide-ranging role in plant abiotic stress, development, and cellular processes. An expression study revealed that large numbers of the NF-Ys are differentially expressed in response to drought and salinity. The total 15 and 18 ZjNF-Y genes that are upregulated under drought and salinity stress, respectively, are the potential candidates for further functional analysis for development of climate-resilient crops. The present study established a base for understanding the role of NF-Ys in Z. jujuba under abiotic stress conditions and paved a way for further research.
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Affiliation(s)
- Kishor Prabhakar Panzade
- Department of Plant Biotechnology, SDMVM College of Agricultural Biotechnology, Georai Tanda, Maharashtra, 431002, India.
| | - Sonam S Kale
- Department of Plant Biotechnology, MGM College of Agricultural Biotechnology, Aurangabad, Maharashtra, 431007, India
| | | | | | - Dipak N Damse
- Central Sugarcane Research Station, Padegaon, Mahatma Phule Agriculture University, Rahuri, Maharashtra, 415521, India
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17
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Genome-wide screening and identification of nuclear Factor-Y family genes and exploration their function on regulating abiotic and biotic stress in potato (Solanum tuberosum L.). Gene 2021; 812:146089. [PMID: 34896520 DOI: 10.1016/j.gene.2021.146089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/21/2021] [Accepted: 11/16/2021] [Indexed: 12/30/2022]
Abstract
The Nuclear Factor-Y (NF-Y) transcription factor (TF), which includes three distinct subunits (NF-YA, NF-YB and NF-YC), is known to manipulate various aspects of plant growth, development, and stress responses. Although the NF-Y gene family was well studied in many species, little is known about their functions in potato. In this study, a total of 37 potato NF-Y genes were identified, including 11 StNF-YAs, 20 StNF-YBs, and 6 StNF-YCs. The genetic features of these StNF-Y genes were investigated by comparing their evolutionary relationship, intron/exon organization and motif distribution pattern. Multiple alignments showed that all StNF-Y proteins possessed clearly conserved core regions that were flanked by non-conserved sequences. Gene duplication analysis indicated that nine StNF-Y genes were subjected to tandem duplication and eight StNF-Ys arose from segmental duplication events. Synteny analysis suggested that most StNF-Y genes (33 of 37) were orthologous to potato's close relative tomato (Solanum lycopersicum L.). Tissue-specific expression of the StNF-Y genes suggested their potential roles in controlling potato growth and development. The role of StNF-Ys in regulating potato responses to abiotic stress (ABA, drought and salinity) was also confirmed: twelve StNF-Y genes were up-regulated and another two were down-regulated under different abiotic treatments. In addition, genes responded differently to pathogen challenges, suggesting that StNF-Y genes may play distinct roles under certain biotic stress. In summary, insights into the evolution of NF-Y family members and their functions in potato development and stress responses are provided.
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Genome-wide analysis of the NF-Y gene family and their roles in relation to fruit development in Tartary buckwheat (Fagopyrum tataricum). Int J Biol Macromol 2021; 190:487-498. [PMID: 34508718 DOI: 10.1016/j.ijbiomac.2021.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/20/2022]
Abstract
Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor playing crucial roles in various biological process in plant. However, thorough research on NF-Y gene family of Tartary buckwheat (Fagopyrum tataricum) is little. In this study, 38 FtNF-Y genes (12 FtNF-YAs, 17 FtNF-YBs, and 9 FtNF-YCs) were identified and renamed on the basis of their subfamily and chromosomal location. Their gene structure, genomic mapping, motif composition, conserved domain, phylogenetic relationships, cis-acting elements and gene expression were investigated. Illustration of gene structures and conserved domains of FtNF-Ys revealed their functional conservation and specificity. Construction of phylogenetic trees of NF-Ys in Tartary buckwheat, Arabidopsis, tomato, rice and banana, allowed us to predict functional similarities among NF-Ys from different species. Gene expression analysis displayed that twenty-four FtNF-Ys were expressed in all the tissues and the transcript levels of them were different, suggesting their function varieties. Moreover, expression profiles of twenty FtNF-Ys along five different fruit development stages acquired by real-time quantitative PCR (RT-qPCR) demonstrated distinct abundance diversity at different stages, providing some clues of potential fruit development regulators. Our study could provide helpful reference information for further function characterization of FtNF-Ys and for the fruit quality enhancement of Tartary buckwheat.
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Expression of the Malus sieversii NF-YB21 Encoded Gene Confers Tolerance to Osmotic Stresses in Arabidopsis thaliana. Int J Mol Sci 2021; 22:ijms22189777. [PMID: 34575941 PMCID: PMC8467963 DOI: 10.3390/ijms22189777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/30/2021] [Accepted: 09/08/2021] [Indexed: 11/23/2022] Open
Abstract
Drought is the main environmental factor that limits the yield and quality of apples (Malus × domestica) grown in arid and semi-arid regions. Nuclear factor Ys (NF-Ys) are important transcription factors involved in the regulation of plant growth, development, and various stress responses. However, the function of NF-Y genes is poorly understood in apples. Here, we identified 43 NF-Y genes in the genome of apples and conducted an initial functional characterization of the apple NF-Y. Expression analysis of NF-Y members in M. sieversii revealed that a large number of NF-Ys were highly expressed in the roots compared with the leaves, and a large proportion of NF-Y genes responded to drought treatment. Furthermore, heterologous expression of MsNF-YB21, which was significantly upregulated by drought, led to a longer root length and, thus, conferred improved osmotic and salt tolerance in Arabidopsis. Moreover, the physiological analysis of MsNF-YB21 overexpression revealed enhanced antioxidant systems, including antioxidant enzymes and compatible solutes. In addition, genes encoding catalase (AtCAT2, AtCAT3), superoxide dismutase (AtFSD1, AtFSD3, AtCSD1), and peroxidase (AtPER12, AtPER42, AtPER47, AtPER51) showed upregulated expression in the MsNF-YB21 overexpression lines. These results for the MsNF-Y gene family provide useful information for future studies on NF-Ys in apples, and the functional analysis of MsNF-YB21 supports it as a potential target in the improvement of apple drought tolerance via biotechnological strategies.
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Qu Y, Wang Y, Zhu J, Zhang Y, Hou H. Genomic Organization, Phylogenetic Comparison, and Differential Expression of the Nuclear Factor-Y Gene Family in Apple ( Malus Domestica). PLANTS 2020; 10:plants10010016. [PMID: 33374140 PMCID: PMC7824617 DOI: 10.3390/plants10010016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 01/23/2023]
Abstract
The nuclear factor Y (NF-Y) as a transcription factor plays an important role in plants growth and development, and response to stress. However, few genome-wide analyzes and functional research of the NF-Y family has been undertaken in apple (Malus domestica Borkh.) so far. In this study, we comprehensively identified the 43 MdNF-Y genes in apple, which dispersedly distributed among the three subgroups based on their sequence alignment analysis, including 11 MdNF-YAs, 22 MdNF-YBs and 10 MdNF-YCs. The members in the same subgroups had similar evolution relationships, gene structures, and conserved motifs. The gene duplication analysis suggested that all the genes were dispersed followed by 27 segmental duplication. Moreover, based on synteny analysis of MdNF-Ys with eight plant species results suggested that some ortholog genes were preserved during the evolution of these species. Cis-element analysis showed potential functions of MdNF-Ys in apple growth and development and responded to abiotic stress. Furthermore, the interaction among MdNF-Ys protein were investigated in yeast two-hybrid assays. The expression patterns of MdNF-Ys in tissue-specific response reveled divergence and might play important role in apple growth and development. Subsequently, whole MdNF-Y genes family was carried out for RT-PCR in response to five abiotic stress (ABA, drought, heat, cold, and salinity) to identify their expression patterns. Taken together, our study will provide a foundation for the further study to the molecular mechanism of apple in growing development and response to abiotic stresses.
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Affiliation(s)
- Yanjie Qu
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, Shandong, China; (Y.Q.); (Y.W.); (J.Z.); (Y.Z.)
- Qingdao Key Laboratory of Genetic Development and Breeding in Horticultural Plants, Qingdao Agricultural University, Qingdao 266109, Shandong, China
| | - Yaping Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, Shandong, China; (Y.Q.); (Y.W.); (J.Z.); (Y.Z.)
- Qingdao Key Laboratory of Genetic Development and Breeding in Horticultural Plants, Qingdao Agricultural University, Qingdao 266109, Shandong, China
| | - Jun Zhu
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, Shandong, China; (Y.Q.); (Y.W.); (J.Z.); (Y.Z.)
- Qingdao Key Laboratory of Genetic Development and Breeding in Horticultural Plants, Qingdao Agricultural University, Qingdao 266109, Shandong, China
| | - Yugang Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, Shandong, China; (Y.Q.); (Y.W.); (J.Z.); (Y.Z.)
- Qingdao Key Laboratory of Genetic Development and Breeding in Horticultural Plants, Qingdao Agricultural University, Qingdao 266109, Shandong, China
| | - Hongmin Hou
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, Shandong, China; (Y.Q.); (Y.W.); (J.Z.); (Y.Z.)
- Qingdao Key Laboratory of Genetic Development and Breeding in Horticultural Plants, Qingdao Agricultural University, Qingdao 266109, Shandong, China
- Correspondence: ; Tel.: +86-0532-860-80752
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Valandro F, Menguer PK, Cabreira-Cagliari C, Margis-Pinheiro M, Cagliari A. Programmed cell death (PCD) control in plants: New insights from the Arabidopsis thaliana deathosome. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110603. [PMID: 32900441 DOI: 10.1016/j.plantsci.2020.110603] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/28/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Programmed cell death (PCD) is a genetically controlled process that leads to cell suicide in both eukaryotic and prokaryotic organisms. In plants PCD occurs during development, defence response and when exposed to adverse conditions. PCD acts controlling the number of cells by eliminating damaged, old, or unnecessary cells to maintain cellular homeostasis. Unlike in animals, the knowledge about PCD in plants is limited. The molecular network that controls plant PCD is poorly understood. Here we present a review of the current mechanisms involved with the genetic control of PCD in plants. We also present an updated version of the AtLSD1 deathosome, which was previously proposed as a network controlling HR-mediated cell death in Arabidopsis thaliana. Finally, we discuss the unclear points and open questions related to the AtLSD1 deathosome.
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Affiliation(s)
- Fernanda Valandro
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Universidade Federal do Rio Grande do Sul (UFRGS), RS, Brazil.
| | - Paloma Koprovski Menguer
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Universidade Federal do Rio Grande do Sul (UFRGS), RS, Brazil.
| | | | - Márcia Margis-Pinheiro
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Universidade Federal do Rio Grande do Sul (UFRGS), RS, Brazil.
| | - Alexandro Cagliari
- Programa de Pós-Graduação em Ambiente e Sustentabilidade, Universidade Estadual do Rio Grande do Sul, RS, Brazil; Universidade Estadual do Rio Grande do Sul (UERGS), RS, Brazil.
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Wei Q, Wen S, Lan C, Yu Y, Chen G. Genome-Wide Identification and Expression Profile Analysis of the NF-Y Transcription Factor Gene Family in Petunia hybrida. PLANTS (BASEL, SWITZERLAND) 2020; 9:E336. [PMID: 32155874 PMCID: PMC7154908 DOI: 10.3390/plants9030336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 11/17/2022]
Abstract
Nuclear Factor Ys (NF-Ys) are a class of heterotrimeric transcription factors that play key roles in many biological processes, such as abiotic stress responses, flowering time, and root development. The petunia (Petunia hybrida) is a model ornamental plant, and its draft genome has been published. However, no details regarding the NF-Y gene family in petunias are available. Here, 27 NF-Y members from the petunia genome were identified, including 10 PhNF-YAs, 13 PhNF-YBs, and 4 PhNF-YCs. Multiple alignments showed that all PhNF-Y proteins had clear conserved core regions flanked by non-conserved sequences. Phylogenetic analyses identified five pairs of orthologues NF-YB proteins from Petunia and Arabidopsis, and six pairs of paralogues NF-Y proteins in Petunia. Analysis of the gene structure and conserved motifs further confirmed the closer relationship in each subfamily. Bioinformatics analysis revealed that 16 PhNF-Ys could be targeted by 18 miRNA families. RNA-seq results showed that expression patterns of PhNF-Ys among four major organs (leaf, stem, flower, and root) were clustered into six major groups. The stress response pattern of PhNF-Ys was identified under cold, heat, drought, and salinity treatments. Based on the RNA-seq data, we found that 3 genes responded to drought, 4 genes responded to salt, 10 genes responded to cold, and 9 genes responded to hot. In conclusion, this study provides useful information for further studying the functions of NF-Ys in stress response.
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Affiliation(s)
- Qian Wei
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Q.W.); (S.W.); (C.L.); (Y.Y.)
| | - Shiyun Wen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Q.W.); (S.W.); (C.L.); (Y.Y.)
| | - Chuying Lan
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Q.W.); (S.W.); (C.L.); (Y.Y.)
| | - Yixun Yu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Q.W.); (S.W.); (C.L.); (Y.Y.)
| | - Guoju Chen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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Liu J, Wang Z, Li J, Li H, Yang L. Genome-wide identification of Diacylglycerol Acyltransferases (DGAT) family genes influencing Milk production in Buffalo. BMC Genet 2020; 21:26. [PMID: 32138658 PMCID: PMC7059399 DOI: 10.1186/s12863-020-0832-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/25/2020] [Indexed: 12/24/2022] Open
Abstract
Background The diacylglycerol acyltransferases (DGAT) are a vital group of enzymes in catalyzing triacylglycerol biosynthesis. DGAT genes like DGAT1 and DGAT2, have been identified as two functional candidate genes affecting milk production traits, especially for fat content in milk. Buffalo milk is famous for its excellent quality, which is rich in fat and protein content. Therefore, this study aimed to characterize DGAT family genes in buffalo and to find candidate markers or DGAT genes influencing lactation performance. Results We performed a genome-wide study and identified eight DGAT genes in buffalo. All the DGAT genes classified into two distinct clades (DGAT1 and DGAT2 subfamily) based on their phylogenetic relationships and structural features. Chromosome localization displayed eight buffalo DGAT genes distributed on five chromosomes. Collinearity analysis revealed that the DGAT family genes were extensive homologous between buffalo and cattle. Afterward, we discovered genetic variants loci within the genomic regions that DGAT genes located in buffalo. Seven haplotype blocks were constructed and were associated with buffalo milk production traits. Single marker association analyses revealed four most significant single nucleotide polymorphisms (SNPs) mainly affecting milk protein percentage or milk fat yield in buffalo. Genes functional analysis indicated that these DGAT family genes could influence lactation performance in the mammal through regulating lipid metabolism. Conclusion In the present study, we performed a comprehensive analysis for the DGAT family genes in buffalo, which including identification, structural characterization, phylogenetic classification, chromosomal distribution, collinearity analysis, association analysis, and functional analysis. These findings provide useful information for an in-depth study to determine the role of DGAT family gens play in the regulation of milk production and milk quality improvement in buffalo.
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Affiliation(s)
- Jiajia Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan, China.,School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Zhiquan Wang
- Department of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, Canada
| | - Jun Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan, China.,Department of Immunology, Zunyi Medical College, Zunyi, China
| | - Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan, China.
| | - Liguo Yang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan, China.
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