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Jiang D, Xia M, Xing H, Gong M, Jiang Y, Liu H, Li HL. Exploring the Heat Shock Transcription Factor ( HSF) Gene Family in Ginger: A Genome-Wide Investigation on Evolution, Expression Profiling, and Response to Developmental and Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:2999. [PMID: 37631210 PMCID: PMC10459109 DOI: 10.3390/plants12162999] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023]
Abstract
Ginger is a valuable crop known for its nutritional, seasoning, and health benefits. However, abiotic stresses, such as high temperature and drought, can adversely affect its growth and development. Heat shock transcription factors (HSFs) have been recognized as crucial elements for enhancing heat and drought resistance in plants. Nevertheless, no previous study has investigated the HSF gene family in ginger. In this research, a total of 25 ZoHSF members were identified in the ginger genome, which were unevenly distributed across ten chromosomes. The ZoHSF members were divided into three groups (HSFA, HSFB, and HSFC) based on their gene structure, protein motifs, and phylogenetic relationships with Arabidopsis. Interestingly, we found more collinear gene pairs between ZoHSF and HSF genes from monocots, such as rice, wheat, and banana, than dicots like Arabidopsis thaliana. Additionally, we identified 12 ZoHSF genes that likely arose from duplication events. Promoter analysis revealed that the hormone response elements (MEJA-responsiveness and abscisic acid responsiveness) were dominant among the various cis-elements related to the abiotic stress response in ZoHSF promoters. Expression pattern analysis confirmed differential expression of ZoHSF members across different tissues, with most showing responsiveness to heat and drought stress. This study lays the foundation for further investigations into the functional role of ZoHSFs in regulating abiotic stress responses in ginger.
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Affiliation(s)
- Dongzhu Jiang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (D.J.); (M.X.); (H.X.); (Y.J.)
- College of Horticulture and Gardening, Yangtze University, Jingzhou 433200, China
| | - Maoqin Xia
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (D.J.); (M.X.); (H.X.); (Y.J.)
| | - Haitao Xing
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (D.J.); (M.X.); (H.X.); (Y.J.)
| | - Min Gong
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China;
| | - Yajun Jiang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (D.J.); (M.X.); (H.X.); (Y.J.)
| | - Huanfang Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (D.J.); (M.X.); (H.X.); (Y.J.)
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Mangal V, Lal MK, Tiwari RK, Altaf MA, Sood S, Gahlaut V, Bhatt A, Thakur AK, Kumar R, Bhardwaj V, Kumar V, Singh B, Singh R, Kumar D. A comprehensive and conceptual overview of omics-based approaches for enhancing the resilience of vegetable crops against abiotic stresses. PLANTA 2023; 257:80. [PMID: 36913037 DOI: 10.1007/s00425-023-04111-5] [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: 12/27/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Abiotic stresses adversely affect the productivity and production of vegetable crops. The increasing number of crop genomes that have been sequenced or re-sequenced provides a set of computationally anticipated abiotic stress-related responsive genes on which further research may be focused. Knowledge of omics approaches and other advanced molecular tools have all been employed to understand the complex biology of these abiotic stresses. A vegetable can be defined as any component of a plant that is eaten for food. These plant parts may be celery stems, spinach leaves, radish roots, potato tubers, garlic bulbs, immature cauliflower flowers, cucumber fruits, and pea seeds. Abiotic stresses, such as deficient or excessive water, high temperature, cold, salinity, oxidative, heavy metals, and osmotic stress, are responsible for the adverse activity in plants and, ultimately major concern for decreasing yield in many vegetable crops. At the morphological level, altered leaf, shoot and root growth, altered life cycle duration and fewer or smaller organs can be observed. Likewise different physiological and biochemical/molecular processes are also affected in response to these abiotic stresses. In order to adapt and survive in a variety of stressful situations, plants have evolved physiological, biochemical, and molecular response mechanisms. A comprehensive understanding of the vegetable's response to different abiotic stresses and the identification of tolerant genotypes are essential to strengthening each vegetable's breeding program. The advances in genomics and next-generation sequencing have enabled the sequencing of many plant genomes over the last twenty years. A combination of modern genomics (MAS, GWAS, genomic selection, transgenic breeding, and gene editing), transcriptomics, and proteomics along with next-generation sequencing provides an array of new powerful approaches to the study of vegetable crops. This review examines the overall impact of major abiotic stresses on vegetables, adaptive mechanisms and functional genomic, transcriptomic, and proteomic processes used by researchers to minimize these challenges. The current status of genomics technologies for developing adaptable vegetable cultivars that will perform better in future climates is also examined.
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Affiliation(s)
- Vikas Mangal
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
| | - Milan Kumar Lal
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
| | - Rahul Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
| | | | - Salej Sood
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vijay Gahlaut
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Department of Biotechnology and University Center for Research and Development, Chandigarh University, Mohali, Punjab, India
| | | | - Ajay Kumar Thakur
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ravinder Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Brajesh Singh
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rajender Singh
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Devendra Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
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Gaccione L, Martina M, Barchi L, Portis E. A Compendium for Novel Marker-Based Breeding Strategies in Eggplant. PLANTS (BASEL, SWITZERLAND) 2023; 12:1016. [PMID: 36903876 PMCID: PMC10005326 DOI: 10.3390/plants12051016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in the fruit rather than decreasing the content of anti-nutritional compounds in the fruit. From the literature, we collected information on mapping quantitative trait loci (QTLs) affecting eggplant's traits following a biparental or multi-parent approach as well as genome-wide association (GWA) studies. The positions of QTLs were lifted according to the eggplant reference line (v4.1) and more than 700 QTLs were identified, here organized into 180 quantitative genomic regions (QGRs). Our findings thus provide a tool to: (i) determine the best donor genotypes for specific traits; (ii) narrow down QTL regions affecting a trait by combining information from different populations; (iii) pinpoint potential candidate genes.
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Saeed F, Chaudhry UK, Raza A, Charagh S, Bakhsh A, Bohra A, Ali S, Chitikineni A, Saeed Y, Visser RGF, Siddique KHM, Varshney RK. Developing future heat-resilient vegetable crops. Funct Integr Genomics 2023; 23:47. [PMID: 36692535 PMCID: PMC9873721 DOI: 10.1007/s10142-023-00967-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/06/2023] [Accepted: 01/06/2023] [Indexed: 01/25/2023]
Abstract
Climate change seriously impacts global agriculture, with rising temperatures directly affecting the yield. Vegetables are an essential part of daily human consumption and thus have importance among all agricultural crops. The human population is increasing daily, so there is a need for alternative ways which can be helpful in maximizing the harvestable yield of vegetables. The increase in temperature directly affects the plants' biochemical and molecular processes; having a significant impact on quality and yield. Breeding for climate-resilient crops with good yields takes a long time and lots of breeding efforts. However, with the advent of new omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics, the efficiency and efficacy of unearthing information on pathways associated with high-temperature stress resilience has improved in many of the vegetable crops. Besides omics, the use of genomics-assisted breeding and new breeding approaches such as gene editing and speed breeding allow creation of modern vegetable cultivars that are more resilient to high temperatures. Collectively, these approaches will shorten the time to create and release novel vegetable varieties to meet growing demands for productivity and quality. This review discusses the effects of heat stress on vegetables and highlights recent research with a focus on how omics and genome editing can produce temperature-resilient vegetables more efficiently and faster.
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Affiliation(s)
- Faisal Saeed
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, 51240, Nigde, Turkey
| | - Usman Khalid Chaudhry
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, 51240, Nigde, Turkey
| | - Ali Raza
- College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Allah Bakhsh
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, 6150, Australia
| | - Sumbul Ali
- Akhuwat Faisalabad Institute of Research Science and Technology, Faisalabad, Pakistan
| | - Annapurna Chitikineni
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, 6150, Australia
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Yasir Saeed
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, 15, Wageningen, The Netherlands
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, 6001, Australia
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, 6150, Australia.
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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Li D, Tang X, Dong Y, Wang Y, Shi S, Li S, Liu Y, Ge H, Chen H. Comparative genomic investigation of TCP gene family in eggplant (Solanum melongena L.) and expression analysis under divergent treatments. PLANT CELL REPORTS 2022; 41:2213-2228. [PMID: 36001130 DOI: 10.1007/s00299-022-02918-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
The putative TCP genes and their responses to abiotic stress in eggplant were comprehensively characterized, and SmTCP genes (Smechr0202855.1 and Smechr0602431.1) may be involved in anthocyanin synthesis. The Teosinte branched1/Cycloidea/Proliferating cell factors (TCPs), a family of plant-specific transcription factors, plays paramount roles in a plethora of developmental and physiological processes. We here systematically characterized putative TCP genes and their response to abiotic stress in eggplant. In total, 30 SmTCP genes were categorized into two subfamilies based on the classical TCP conserved domains. Chromosomal location analysis illustrated the random distribution of putative SmTCP genes along 12 eggplant chromosomes. Cis-acting elements and miRNA target prediction suggested that versatile and complicated regulatory mechanisms that control SmTCPs gene expression, and 3 miRNAs (miR319a, miR319b, and miR319c-3p) might act as major regulators targeting SmTCPs. Tissue expression profiles indicated divergent spatiotemporal expression patterns of SmTCPs. qRT-PCR assays demonstrated different expression profiles of SmTCP under 4 °C, drought and ABA treatment conditions, suggesting the possible participation of SmTCP genes in multiple signaling pathways. Furthermore, RNA-seq data of eggplant anthocyanin synthesis coupled with yeast one-hybrid and dual-luciferase assays suggested the involvement of SmTCP genes (Smechr0202855.1 and Smechr0602431.1) in the mediation of anthocyanin synthesis. Our study will facilitate further investigation on the putative functional characterization of eggplant TCP genes and lay a solid foundation for the in-depth study of the involvement of SmTCP genes in the regulation of anthocyanin synthesis.
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Affiliation(s)
- Dalu Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Xin Tang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Yanxiao Dong
- Shanghai Agricultural Science and Technology Service Center, Shanghai, 200335, China
| | - Yingying Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Suli Shi
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Shaohang Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Yang Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Haiyan Ge
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China.
| | - Huoying Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China.
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Li D, He Y, Li S, Shi S, Li L, Liu Y, Chen H. Genome-wide characterization and expression analysis of AP2/ERF genes in eggplant (Solanum melongena L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:492-503. [PMID: 34425394 DOI: 10.1016/j.plaphy.2021.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 05/20/2023]
Abstract
The AP2/ERF (APETALA2/Ethylene Response Factor) transcription factor superfamily plays crucial roles in a slew of physiological processes, such as plant growth and development, stress response, and secondary metabolites biosynthesis. Eggplant, especially the one rich with anthocyanins, is an economically important horticultural vegetable cultivated worldwide. In this study, we comprehensively analyzed the putative AP2/ERF gene family members and their response to abiotic stress in eggplant. As per the phylogenetic, conserved domains, and motif analysis, 178 AP2/ERF genes in this study belonged to five subfamilies. Chromosomal distributions analysis elucidated stochastic distribution of 178 putative SmAP2/ERF genes across the twelve chromosomes of eggplant. Expression profiles of sixteen selected AP2/ERF genes response to low temperature, drought, salt, abscisic acid, and ethylene treatments were analyzed, which revealed the involvement of SmAP2/ERF genes in diverse signaling pathways. In addition, we integrated RNA-Seq data on anthocyanin biosynthesis in eggplant with yeast one-hybrid and dual-luciferase assays and identified involvement of the SmAP2/ERF genes (Smechr0902114.1 and Smechr1102075.1) in the regulation of anthocyanin biosynthesis. This study will enable further functional characterization of AP2/ERF genes in eggplant and extend the current understanding of the role played by AP2/ERF genes in anthocyanin biosynthesis regulation.
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Affiliation(s)
- Dalu Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - YongJun He
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Shaohang Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Suli Shi
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Linzhi Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Yang Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Huoying Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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