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Yin L, Wu R, An R, Feng Y, Qiu Y, Zhang M. Genome-wide identification, molecular evolution and expression analysis of the B-box gene family in mung bean (Vigna radiata L.). BMC PLANT BIOLOGY 2024; 24:532. [PMID: 38862892 PMCID: PMC11167828 DOI: 10.1186/s12870-024-05236-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 06/03/2024] [Indexed: 06/13/2024]
Abstract
BACKGROUND Mung bean (Vigna radiata L.) is an important warm-season grain legume. Adaptation to extreme environmental conditions, supported by evolution, makes mung bean a rich gene pool for stress tolerance traits. The exploration of resistance genes will provide important genetic resources and a theoretical basis for strengthening mung bean breeding. B-box (BBX) proteins play a major role in developmental processes and stress responses. However, the identification and analysis of the mung bean BBX gene family are still lacking. RESULTS In this study, 23 VrBBX genes were identified through comprehensive bioinformatics analysis and named based on their physical locations on chromosomes. All the VrBBXs were divided into five groups based on their phylogenetic relationships, the number of B-box they contained and whether there was an additional CONSTANS, CO-like and TOC1 (CCT) domain. Homology and collinearity analysis indicated that the BBX genes in mung bean and other species had undergone a relatively conservative evolution. Gene duplication analysis showed that only chromosomal segmental duplication contributed to the expansion of VrBBX genes and that most of the duplicated gene pairs experienced purifying selection pressure during evolution. Gene structure and motif analysis revealed that VrBBX genes clustered in the same group shared similar structural characteristics. An analysis of cis-acting elements indicated that elements related to stress and hormone responses were prevalent in the promoters of most VrBBXs. The RNA-seq data analysis and qRT-PCR of nine VrBBX genes demonstrated that VrBBX genes may play a role in response to environmental stress. Moreover, VrBBX5, VrBBX10 and VrBBX12 are important candidate genes for plant stress response. CONCLUSIONS In this study, we systematically analyzed the genomic characteristics and expression patterns of the BBX gene family under ABA, PEG and NaCl treatments. The results will help us better understand the complexity of the BBX gene family and provide valuable information for future functional characteristics of specific genes in this family.
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Affiliation(s)
- Lili Yin
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Ruigang Wu
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038, People's Republic of China
| | - Ruilan An
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Yaxin Feng
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Yaqi Qiu
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Meiling Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, People's Republic of China.
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Xu Y, Cheng J, Hu H, Yan L, Jia J, Wu B. Genome-Wide Identification of NAC Family Genes in Oat and Functional Characterization of AsNAC109 in Abiotic Stress Tolerance. PLANTS (BASEL, SWITZERLAND) 2024; 13:1017. [PMID: 38611546 PMCID: PMC11013824 DOI: 10.3390/plants13071017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024]
Abstract
The plant-specific NAC gene family is one of the largest transcription factor families, participating in plant growth regulation and stress response. Despite extensive characterization in various plants, our knowledge of the NAC family in oat is lacking. Herein, we identified 333 NAC genes from the latest release of the common oat genome. We provide a comprehensive overview of the oat NAC gene family, covering gene structure, chromosomal localization, phylogenetic characteristics, conserved motif compositions, and gene duplications. AsNAC gene expression in different tissues and the response to various abiotic stresses were characterized using RT-qPCR. The main driver of oat NAC gene family expansion was identified as segmental duplication using collinearity analysis. In addition, the functions of AsNAC109 in regulating abiotic stress tolerance in Arabidopsis were clarified. This is the first genome-wide investigation of the NAC gene family in cultivated oat, which provided a unique resource for subsequent research to elucidate the mechanisms responsible for oat stress tolerance and provides valuable clues for the improvement of stress resistance in cultivated oat.
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Affiliation(s)
- Yahui Xu
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.X.); (J.C.)
| | - Jialong Cheng
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.X.); (J.C.)
| | - Haibin Hu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- State Key Laboratory of Crop Gene Resources and Breeding, Beijing 100081, China
| | - Lin Yan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- State Key Laboratory of Crop Gene Resources and Breeding, Beijing 100081, China
| | - Juqing Jia
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.X.); (J.C.)
| | - Bin Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- State Key Laboratory of Crop Gene Resources and Breeding, Beijing 100081, China
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Ricciardi V, Crespan M, Maddalena G, Migliaro D, Brancadoro L, Maghradze D, Failla O, Toffolatti SL, De Lorenzis G. Novel loci associated with resistance to downy and powdery mildew in grapevine. FRONTIERS IN PLANT SCIENCE 2024; 15:1386225. [PMID: 38584944 PMCID: PMC10998452 DOI: 10.3389/fpls.2024.1386225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/06/2024] [Indexed: 04/09/2024]
Abstract
Among the main challenges in current viticulture, there is the increasing demand for sustainability in the protection from fungal diseases, such as downy mildew (DM) and powdery mildew (PM). Breeding disease-resistant grapevine varieties is a key strategy for better managing fungicide inputs. This study explores the diversity of grapevine germplasm (cultivated and wild) from Caucasus and neighboring areas to identify genotypes resistant to DM and PM, based on 13 Simple Sequence Repeat (SSR) loci and phenotypical (artificial pathogen inoculation) analysis, and to identify loci associated with DM and PM resistance, via Genome-Wide Association Analysis (GWAS) on Single Nucleotide Polymorphism (SNP) profiles. SSR analysis revealed resistant alleles for 16 out of 88 genotypes. Phenotypic data identified seven DM and 31 PM resistant genotypes. GWAS identified two new loci associated with DM resistance, located on chromosome 15 and 16 (designated as Rpv36 and Rpv37), and two with PM resistance, located on chromosome 6 and 17 (designated as Ren14 and Ren15). The four novel loci identified genomic regions rich in genes related to biotic stress response, such as genes involved in pathogen recognition, signal transduction and resistance response. This study highlights potential candidate genes associated with resistance to DM and PM, providing valuable insights for breeding programs for resistant varieties. To optimize their utilization, further functional characterization studies are recommended.
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Affiliation(s)
- Valentina Ricciardi
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Manna Crespan
- Centro di Ricerca per la Viticoltura e l'Enologia, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Conegliano, Italy
| | - Giuliana Maddalena
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Daniele Migliaro
- Centro di Ricerca per la Viticoltura e l'Enologia, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Conegliano, Italy
| | - Lucio Brancadoro
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
| | - David Maghradze
- Faculty of Viticulture-Winemaking, Caucasus International University, Tbilisi, Georgia
- Faculty of Agricultural Sciences and Biosystems Engineering, Georgian Technical University, Tbilisi, Georgia
| | - Osvaldo Failla
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Silvia Laura Toffolatti
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Gabriella De Lorenzis
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milano, Italy
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Dorjee T, Cui Y, Zhang Y, Liu Q, Li X, Sumbur B, Yan H, Bing J, Geng Y, Zhou Y, Gao F. Characterization of NAC Gene Family in Ammopiptanthus mongolicus and Functional Analysis of AmNAC24, an Osmotic and Cold-Stress-Induced NAC Gene. Biomolecules 2024; 14:182. [PMID: 38397419 PMCID: PMC10886826 DOI: 10.3390/biom14020182] [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: 12/27/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
The NAC family of transcription factors (TFs) is recognized as a significant group within the plant kingdom, contributing crucially to managing growth and development processes in plants, as well as to their response and adaptation to various environmental stressors. Ammopiptanthus mongolicus, a temperate evergreen shrub renowned for its remarkable resilience to low temperatures and drought stress, presents an ideal subject for investigating the potential involvement of NAC TFs in stress response mechanisms. Here, the structure, evolution, and expression profiles of NAC family TFs were analyzed systematically, and a cold and osmotic stress-induced member, AmNAC24, was selected and functionally characterized. A total of 86 NAC genes were identified in A. mongolicus, and these were divided into 15 groups. Up to 48 and 8 NAC genes were generated by segmental duplication and tandem duplication, respectively, indicating that segmental duplication is a predominant mechanism in the expansion of the NAC gene family in A. mongolicus. A considerable amount of NAC genes, including AmNAC24, exhibited upregulation in response to cold and osmotic stress. This observation is in line with the detection of numerous cis-acting elements linked to abiotic stress response in the promoters of A. mongolicus NAC genes. Subcellular localization revealed the nuclear residence of the AmNAC24 protein, coupled with demonstrable transcriptional activation activity. AmNAC24 overexpression enhanced the tolerance of cold and osmotic stresses in Arabidopsis thaliana, possibly by maintaining ROS homeostasis. The present study provided essential data for understanding the biological functions of NAC TFs in plants.
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Affiliation(s)
- Tashi Dorjee
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yican Cui
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yuxin Zhang
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Qi Liu
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Xuting Li
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Batu Sumbur
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Hongxi Yan
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Jie Bing
- College of Life Sciences, Beijing Normal University, Beijing 100080, China;
| | - Yuke Geng
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yijun Zhou
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Fei Gao
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (T.D.); (Y.C.); (Y.Z.); (Q.L.); (X.L.); (B.S.); (H.Y.); (Y.G.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
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5
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Wang Z, Chen Z, Wu Y, Mu M, Jiang J, Nie W, Zhao S, Cui G, Yin X. Genome-wide identification and characterization of NAC transcription factor family members in Trifolium pratense and expression analysis under lead stress. BMC Genomics 2024; 25:128. [PMID: 38297198 PMCID: PMC10829316 DOI: 10.1186/s12864-023-09944-8] [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: 10/11/2023] [Accepted: 12/26/2023] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND The NAC TF family is widely involved in plant responses to various types of stress. Red clover (Trifolium pratense) is a high-quality legume, and the study of NAC genes in red clover has not been comprehensive. The aim of this study was to analyze the NAC gene family of red clover at the whole-genome level and explore its potential role in the Pb stress response. RESULTS In this study, 72 TpNAC genes were identified from red clover; collinearity analysis showed that there were 5 pairs of large fragment replicators of TpNAC genes, and red clover was found to be closely related to Medicago truncatula. Interestingly, the TpNAC genes have more homologs in Arabidopsis thaliana than in soybean (Glycine max). There are many elements in the TpNAC genes promoters that respond to stress. Gene expression analysis showed that all the TpNAC genes responded to Pb stress. qRT-PCR showed that the expression levels of TpNAC29 and TpNAC42 were significantly decreased after Pb stress. Protein interaction network analysis showed that 21 TpNACs and 23 other genes participated in the interaction. In addition, the TpNAC proteins had three possible 3D structures, and the secondary structure of these proteins were mainly of other types. These results indicated that most TpNAC members were involved in the regulation of Pb stress in red clover. CONCLUSION These results suggest that most TpNAC members are involved in the regulation of Pb stress in red clover. TpNAC members play an important role in the response of red clover to Pb stress.
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Affiliation(s)
- Zicheng Wang
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Zirui Chen
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Yuchen Wu
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Meiqi Mu
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Jingwen Jiang
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Wanting Nie
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Siwen Zhao
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Guowen Cui
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Xiujie Yin
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China.
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Zou X, Zhang J, Cheng T, Guo Y, Zhang L, Han X, Liu C, Wan Y, Ye X, Cao X, Song C, Zhao G, Xiang D. New strategies to address world food security and elimination of malnutrition: future role of coarse cereals in human health. FRONTIERS IN PLANT SCIENCE 2023; 14:1301445. [PMID: 38107010 PMCID: PMC10722300 DOI: 10.3389/fpls.2023.1301445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 12/19/2023]
Abstract
As we face increasing challenges of world food security and malnutrition, coarse cereals are coming into favor as an important supplement to human staple foods due to their high nutritional value. In addition, their functional components, such as flavonoids and polyphenols, make them an important food source for healthy diets. However, we lack a systematic understanding of the importance of coarse cereals for world food security and nutritional goals. This review summarizes the worldwide cultivation and distribution of coarse cereals, indicating that the global area for coarse cereal cultivation is steadily increasing. This paper also focuses on the special adaptive mechanisms of coarse cereals to drought and discusses the strategies to improve coarse cereal crop yields from the perspective of agricultural production systems. The future possibilities, challenges, and opportunities for coarse cereal production are summarized in the face of food security challenges, and new ideas for world coarse cereal production are suggested.
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Affiliation(s)
- Xin Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Jieyu Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Ting Cheng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yangyang Guo
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Li Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Xiao Han
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Changying Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yan Wan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Xueling Ye
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Xiaoning Cao
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Chao Song
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Dabing Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
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Liu S, Lei C, Zhu Z, Li M, Chen Z, He W, Liu B, Chen L, Li X, Xie Y. Genome-Wide Analysis and Identification of 1-Aminocyclopropane-1-Carboxylate Synthase ( ACS) Gene Family in Wheat ( Triticum aestivum L.). Int J Mol Sci 2023; 24:11158. [PMID: 37446336 DOI: 10.3390/ijms241311158] [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: 05/30/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Ethylene has an important role in regulating plant growth and development as well as responding to adversity stresses. The 1-aminocyclopropane-1-carboxylate synthase (ACS) is the rate-limiting enzyme for ethylene biosynthesis. However, the role of the ACS gene family in wheat has not been examined. In this study, we identified 12 ACS members in wheat. According to their position on the chromosome, we named them TaACS1-TaACS12, which were divided into four subfamilies, and members of the same subfamilies had similar gene structures and protein-conserved motifs. Evolutionary analysis showed that fragment replication was the main reason for the expansion of the TaACS gene family. The spatiotemporal expression specificity showed that most of the members had the highest expression in roots, and all ACS genes contained W box elements that were related to root development, which suggested that the ACS gene family might play an important role in root development. The results of the gene expression profile analysis under stress showed that ACS members could respond to a variety of stresses. Protein interaction prediction showed that there were four types of proteins that could interact with TaACS. We also obtained the targeting relationship between TaACS family members and miRNA. These results provided valuable information for determining the function of the wheat ACS gene, especially under stress.
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Affiliation(s)
- Shuqing Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Chao Lei
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Zhanhua Zhu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Mingzhen Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Zhaopeng Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Wei He
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Bin Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Liuping Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Xuejun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Yanzhou Xie
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
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8
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He H, Li Q, Fang L, Yang W, Xu F, Yan Y, Mao R. Comprehensive analysis of NAC transcription factors in Scutellaria baicalensis and their response to exogenous ABA and GA 3. Int J Biol Macromol 2023:125290. [PMID: 37302633 DOI: 10.1016/j.ijbiomac.2023.125290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/04/2023] [Accepted: 06/07/2023] [Indexed: 06/13/2023]
Abstract
The NAC is a plant-specific family of transcription factor that plays important roles in various biological processes. Scutellaria baicalensis Georgi, belongs to the Lamiaceae family and has been widely used as a traditional herb with a wide range of pharmacological activities, including antitumor, heat-clearing, and detoxifying functions. However, no study on the NAC family in S. baicalensis has been conducted to date. In the present study, we identified 56 SbNAC genes using genomic and transcriptome analyses. These 56 SbNACs were unevenly distributed across nine chromosomes and were phylogenetically divided into six clusters. Cis-element analysis identified plant growth and development-, phytohormone-, light-, and stress-responsive elements were present in SbNAC genes promoter regions. Protein-protein interaction analysis was performed using Arabidopsis homologous proteins. Potential transcription factors, including bHLH, ERF, MYB, WRKY, and bZIP, were identified and constructed a regulatory network with SbNAC genes. The expression of 12 flavonoid biosynthetic genes was significantly upregulated with abscisic acid (ABA) and gibberellin (GA3) treatments. Eight SbNAC genes (SbNAC9/32/33/40/42/43/48/50) also exhibited notable variation with two phytohormone treatments, among which SbNAC9 and SbNAC43 showed the most significant variation and deserved further study. Additionally, SbNAC44 displayed a positive correlation with C4H3, PAL5, OMT3, and OMT6, while SbNAC25 had negatively correlated with OMT2, CHI, F6H2, and FNSII-2. This study constitutes the first analysis of SbNAC genes and lays the basis foundation for further functional studies of SbNAC genes family members, while it may also facilitate the genetic improvement of plants and breeding of elite S. baicalensis varieties.
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Affiliation(s)
- Huan He
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China
| | - Qiuyue Li
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China
| | - Liang Fang
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China
| | - Wen Yang
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China
| | - Feican Xu
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China
| | - Yan Yan
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China; Shaanxi Key Laboratory of Chinese Jujube, Yan'an 716000, Shaanxi, China
| | - Renjun Mao
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China; Shaanxi Key Laboratory of Chinese Jujube, Yan'an 716000, Shaanxi, China.
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Liu H, Chen S, Wu X, Li J, Xu C, Huang M, Wang H, Liu H, Zhao Z. Identification of the NAC Transcription Factor Family during Early Seed Development in Akebia trifoliata ( Thunb.) Koidz. PLANTS (BASEL, SWITZERLAND) 2023; 12:1518. [PMID: 37050144 PMCID: PMC10096588 DOI: 10.3390/plants12071518] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
This study aimed to gain an understanding of the possible function of NACs by examining their physicochemical properties, structure, chromosomal location, and expression. Being a family of plant-specific transcription factors, NAC (petunia no apical meristem and Arabidopsis thaliana ATAF1, ATAF2, and CUC2) is involved in plant growth and development. None of the NAC genes has been reported in Akebia trifoliata (Thunb.) Koidz (A. trifoliata). In this study, we identified 101 NAC proteins (AktNACs) in the A. trifoliata genome by bioinformatic analysis. One hundred one AktNACs were classified into the following twelve categories based on the phylogenetic analysis of NAC protein: NAC-a, NAC-b, NAC-c, NAC-d, NAC-e, NAC-f, NAC-g, NAC-h, NAC-i, NAC-j, NAC-k, and NAC-l. The accuracy of the clustering results was demonstrated based on the gene structure and conserved motif analysis of AktNACs. In addition, we identified 44 pairs of duplication genes, confirming the importance of purifying selection in the evolution of AktNACs. The morphology and microstructure of early A. trifoliata seed development showed that it mainly underwent rapid cell division, seed enlargement, embryo formation and endosperm development. We constructed AktNACs co-expression network and metabolite correlation network based on transcriptomic and metabolomic data of A. trifoliata seeds. The results of the co-expression network showed that 25 AtNAC genes were co-expressed with 233 transcription factors. Metabolite correlation analysis showed that 23 AktNACs were highly correlated with 28 upregulated metabolites. Additionally, 25 AktNACs and 235 transcription factors formed co-expression networks with 141 metabolites, based on correlation analysis involving AktNACs, transcription factors, and metabolites. Notably, AktNAC095 participates in the synthesis of 35 distinct metabolites. Eight of these metabolites, strongly correlated with AktNAC095, were upregulated during early seed development. These studies may provide insight into the evolution, possible function, and expression of AktNACs genes.
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Affiliation(s)
- Huijuan Liu
- College of Life Sciences, Guizhou University, Guiyang 550025, China
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Songshu Chen
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Xiaomao Wu
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Jinling Li
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Cunbin Xu
- College of Life Sciences, Guizhou University, Guiyang 550025, China
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Mingjin Huang
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Hualei Wang
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Hongchang Liu
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Zhi Zhao
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
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Huang X, Qiu X, Wang Y, Abubakar AS, Chen P, Chen J, Chen K, Yu C, Wang X, Gao G, Zhu A. Genome-Wide Investigation of the NAC Transcription Factor Family in Apocynum venetum Revealed Their Synergistic Roles in Abiotic Stress Response and Trehalose Metabolism. Int J Mol Sci 2023; 24:ijms24054578. [PMID: 36902009 PMCID: PMC10003206 DOI: 10.3390/ijms24054578] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs) are one of the most prominent plant-specific TF families and play essential roles in plant growth, development and adaptation to abiotic stress. Although the NAC gene family has been extensively characterized in many species, systematic analysis is still relatively lacking in Apocynum venetum (A. venetum). In this study, 74 AvNAC proteins were identified from the A. venetum genome and were classified into 16 subgroups. This classification was consistently supported by their gene structures, conserved motifs and subcellular localizations. Nucleotide substitution analysis (Ka/Ks) showed the AvNACs to be under the influence of strong purifying selection, and segmental duplication events were found to play the dominant roles in the AvNAC TF family expansion. Cis-elements analysis demonstrated that the light-, stress-, and phytohormone-responsive elements being dominant in the AvNAC promoters, and potential TFs including Dof, BBR-BPC, ERF and MIKC_MADS were visualized in the TF regulatory network. Among these AvNACs, AvNAC58 and AvNAC69 exhibited significant differential expression in response to drought and salt stresses. The protein interaction prediction further confirmed their potential roles in the trehalose metabolism pathway with respect to drought and salt resistance. This study provides a reference for further understanding the functional characteristics of NAC genes in the stress-response mechanism and development of A. venetum.
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Affiliation(s)
- Xiaoyu Huang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Xiaojun Qiu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Yue Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Aminu Shehu Abubakar
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
- Department of Agronomy, Bayero University Kano, Kano PMB 3011, Nigeria
| | - Ping Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Jikang Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Kunmei Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Chunming Yu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Xiaofei Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Gang Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
- National Breeding Center for Bast Fiber Crops, Changsha 410221, China
- Key Laboratory of Genetic Breeding and Microbial Processing for Bast Fiber Product of Hunan Province, Changsha 410221, China
- Correspondence: (G.G.); (A.Z.); Tel.: +86-0731-8899-8511 (G.G.); +86-0731-8899-8586 (A.Z.)
| | - Aiguo Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
- National Breeding Center for Bast Fiber Crops, Changsha 410221, China
- Key Laboratory of Genetic Breeding and Microbial Processing for Bast Fiber Product of Hunan Province, Changsha 410221, China
- Correspondence: (G.G.); (A.Z.); Tel.: +86-0731-8899-8511 (G.G.); +86-0731-8899-8586 (A.Z.)
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Guo Y, Zhang S, Ai J, Zhang P, Yao H, Liu Y, Zhang X. Transcriptomic and biochemical analyses of drought response mechanism in mung bean (Vignaradiata (L.) Wilczek) leaves. PLoS One 2023; 18:e0285400. [PMID: 37163521 PMCID: PMC10171660 DOI: 10.1371/journal.pone.0285400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/23/2023] [Indexed: 05/12/2023] Open
Abstract
Drought is a major factor that limiting mung bean development. To clarify the molecular mechanism of mung bean in response to drought stress, 2 mung bean groups were established, the experimental group (drought-treated) and the control group (normal water management). With prominent difference of 2 groups in stomatal conductance, relative water content and phenotype, leaf samples were collected at 4 stages, and the physiological index of MDA, POD, chlorophyll, and soluble proteins were estimated. RNA-seq was used to obtain high quality data of samples, and differentially expressed genes were identified by DESeq2. With GO and KEGG analysis, DEGs were enriched into different classifications and pathways. WGCNA was used to detect the relationship between physiological traits and genes, and qPCR was performed to confirm the accuracy of the data. We obtained 169.49 Gb of clean data from 24 samples, and the Q30 of each date all exceeded 94%. In total, 8963 DEGs were identified at 4 stages between the control and treated samples, and the DEGs were involved in most biological processes. 1270 TFs screened from DEGs were clustered into 158 TF families, such as AP2, RLK-Pelle-DLSVA, and NAC TF families. Genes related to physiological traits were closely related to plant hormone signaling, carotenoid biosynthesis, chlorophyll metabolism, and protein processing. This paper provides a large amount of data for drought research in mung bean.
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Affiliation(s)
- Yaning Guo
- College of Life Science, Yulin University, Yulin, Shannxi Province, China
| | - Siyu Zhang
- College of Life Science, Yulin University, Yulin, Shannxi Province, China
| | - Jing Ai
- College of Life Science, Yulin University, Yulin, Shannxi Province, China
| | - Panpan Zhang
- College of Life Science, Yulin University, Yulin, Shannxi Province, China
| | - Han Yao
- College of Life Science, Yulin University, Yulin, Shannxi Province, China
| | - Yunfei Liu
- College of Life Science, Yulin University, Yulin, Shannxi Province, China
| | - Xiong Zhang
- College of Life Science, Yulin University, Yulin, Shannxi Province, China
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Wang GL, An YH, Zhou CL, Hu ZZ, Ren XQ, Xiong AS. Transcriptome-wide identification of NAC (no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon) transcription factors potentially involved in salt stress response in garlic. PeerJ 2022; 10:e14602. [PMID: 36570011 PMCID: PMC9774012 DOI: 10.7717/peerj.14602] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Soil salinity has been an increasing problem worldwide endangering crop production and human food security. It is an ideal strategy to excavate stress resistant genes and develop salt tolerant crops. NAC (no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon) transcription factors have been demonstrated to be involved in salt stress response. However, relevant studies have not been observed in garlic, an important vegetable consumed in the world. In this study, a total of 46 AsNAC genes encoding NAC proteins were identified in garlic plant by transcriptome data. Phylogenetic analysis showed that the examined AsNAC proteins were clustered into 14 subgroups. Motif discovery revealed that the conserved domain region was mainly composed of five conserved subdomains. Most of the genes selected could be induced by salt stress in different tissues, indicating a potential role in salt stress response. Further studies may focus on the molecular mechanisms of the AsNAC genes in salt stress response. The results of the current work provided valuable resources for researchers aimed at developing salt tolerant crops.
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Affiliation(s)
- Guang-Long Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Ya-Hong An
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Cheng-Ling Zhou
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Zhen-Zhu Hu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Xu-Qin Ren
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Du Z, You S, Yang D, Tao Y, Zhu Y, Sun W, Chen Z, Li J. Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:1048822. [PMID: 36466244 PMCID: PMC9714628 DOI: 10.3389/fpls.2022.1048822] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Kandelia obovata is an important mangrove species extensively distributed in Eastern Asia that is susceptible to low-temperature stress. NAC (NAM, ATAF1/2 and CUC2) domain proteins are transcription factors (TFs) that play various roles in plant growth and development and in the plant response to environmental stresses. Nevertheless, genome-wide analyses of K. obovata NAC genes (KoNACs) and their responses to chilling stress have rarely been studied. METHODS The KoNAC gene family was identified and characterized using bioinformatic analysis, the subcellular location of some NAC proteins was confirmed using confocal microscopy analysis, and the KoNACs that responded to chilling stress were screened using RNA-seq and qRT-PCR analysis. RESULTS A total of 79 KoNACs were identified, and they were unequally distributed across all 18 chromosomes of K. obovata. The KoNAC proteins could be divided into 16 subgroups according to the phylogenetic tree based on NAC family members of Arabidopsis thaliana. The KoNACs exhibited greater synteny with A. thaliana sequences than with Oryza sativa sequences, indicating that KoNACs underwent extensive evolution after the divergence of dicotyledons and monocotyledons. Segmental duplication was the main driving force of the expansions of KoNAC genes. Confocal microscopy analysis verified that the four randomly selected KoNACs localized to the nucleus, indicating the accuracy of the bioinformatic predictions. Tissue expression pattern analysis demonstrated that some KoNAC genes showed tissue-specific expression, suggesting that these KoNACs might be important for plant development and growth. Additionally, the expression levels of 19 KoNACs were significantly (15 positively and 4 negatively) induced by cold treatment, demonstrating that these KoNACs might play important roles during cold stress responses and might be candidate genes for the genetic engineering of K. obovata with enhanced chilling stress tolerance. Coexpression network analysis revealed that 381 coexpressed pairs (between 13 KoNACs and 284 other genes) were significantly correlated. CONCLUSIONS Seventy-nine KoNACs were identified in K. obovata, nineteen of which displayed chilling-induced expression patterns. These genes may serve as candidates for functional analyses of KoNACs engaged in chilling stress. Our results lay the foundation for evolutionary analyses of KoNACs and their molecular mechanisms in response to environmental stress.
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Affiliation(s)
- Zhaokui Du
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Shixian You
- Section of Maritime Space and Island Management, Yuhuan Municipal Bureau of Natural Resources and Planning, Yuhuan, China
| | - Dang Yang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Yutian Tao
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Yunxiao Zhu
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Wen Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Zhengman Chen
- Department of Security Production Management, Taizhou Circular Economy Development Co., Ltd., Taizhou, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
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