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Wu T, Su B, Zhang H, Li D, Zhang H, Xiao G, Sun A, Zhao T, Xu X. SlJMJ14, identified via QTL‑seq and fine mapping, controls flowering time in tomatoes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:228. [PMID: 39304588 DOI: 10.1007/s00122-024-04737-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 09/04/2024] [Indexed: 09/22/2024]
Abstract
KEY MESSAGE A major QTL, qLF2.1, for flowering time in tomatoes, was fine mapped to chromosome 2 within a 51.37-kb interval, and the SlJMJ14 gene was verified as the causal gene by knockout. Tomato flowering time is an important agronomic trait that affects yield, fruit quality, and environmental adaptation. In this study, the high-generation inbred line 19108 with a late-flowering phenotype was selected for the mapping of the gene that causes late flowering. In the F2 population derived from 19108 (late flowering) × MM (early flowering), we identified a major late-flowering time quantitative trait locus (QTL) using QTL-seq, designated qLF2.1. This QTL was fine mapped to a 51.37-kb genomic interval using recombinant analysis. Through functional analysis of homologous genes, Solyc02g082400 (SlJMJ14), encoding a histone demethylase, was determined to be the most promising candidate gene. Knocking out SlJMJ14 in MM resulted in a flowering time approximately 5-6 days later than that in the wild-type plants. These results suggest that mutational SlJMJ14 is the major QTL for the late-flowering phenotype of the 19108 parental line.
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Affiliation(s)
- Tairu Wu
- Laboratory of Genetic Breeding in Tomato, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Baohang Su
- Laboratory of Genetic Breeding in Tomato, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - He Zhang
- Laboratory of Genetic Breeding in Tomato, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Dalong Li
- Laboratory of Genetic Breeding in Tomato, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Hanqiao Zhang
- Laboratory of Genetic Breeding in Tomato, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Guanglong Xiao
- Laboratory of Genetic Breeding in Tomato, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Ao Sun
- Laboratory of Genetic Breeding in Tomato, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Tingting Zhao
- Laboratory of Genetic Breeding in Tomato, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China.
| | - Xiangyang Xu
- Laboratory of Genetic Breeding in Tomato, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China.
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Cai K, Zhu S, Jiang Z, Xu K, Sun X, Li X. Biological macromolecules mediated by environmental signals affect flowering regulation in plants: A comprehensive review. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108931. [PMID: 39003975 DOI: 10.1016/j.plaphy.2024.108931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 07/07/2024] [Accepted: 07/10/2024] [Indexed: 07/16/2024]
Abstract
Flowering time is a crucial developmental stage in the life cycle of plants, as it determines the reproductive success and overall fitness of the organism. The precise regulation of flowering time is influenced by various internal and external factors, including genetic, environmental, and hormonal cues. This review provided a comprehensive overview of the molecular mechanisms and regulatory pathways of biological macromolecules (e.g. proteins and phytohormone) and environmental factors (e.g. light and temperature) involved in the control of flowering time in plants. We discussed the key proteins and signaling pathways that govern the transition from vegetative growth to reproductive development, highlighting the intricate interplay between genetic networks, environmental cues, and phytohormone signaling. Additionally, we explored the impact of flowering time regulation on plant adaptation, crop productivity, and agricultural practices. Moreover, we summarized the similarities and differences of flowering mechanisms between annual and perennial plants. Understanding the mechanisms underlying flowering time control is not only essential for fundamental plant biology research but also holds great potential for crop improvement and sustainable agriculture.
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Affiliation(s)
- Kefan Cai
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China; Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Siting Zhu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China; Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Zeyu Jiang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China; Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Kai Xu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China; Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China; Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
| | - Xiaolong Li
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China; Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
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3
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Dai S, Chen H, Shi Y, Xiao X, Xu L, Qin C, Zhu Y, Yi K, Lei M, Zeng H. PHOSPHATE1-mediated phosphate translocation from roots to shoots regulates floral transition in plants. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5054-5075. [PMID: 38753441 DOI: 10.1093/jxb/erae222] [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: 12/15/2023] [Accepted: 05/15/2024] [Indexed: 05/18/2024]
Abstract
Phosphorus nutrition has been known for a long time to influence floral transition in plants, but the underlying mechanism is unclear. Arabidopsis phosphate transporter PHOSPHATE1 (PHO1) plays a critical role in phosphate translocation from roots to shoots, but whether and how it regulates floral transition is unknown. Here, we show that knockout mutation of PHO1 delays flowering under both long- and short-day conditions. The late flowering of pho1 mutants can be partially rescued by Pi supplementation in rosettes or shoot apices. Grafting assay indicates that the late flowering of pho1 mutants is a result of impaired phosphate translocation from roots to shoots. Knockout mutation of SPX1 and SPX2, two negative regulators of the phosphate starvation response, partially rescues the late flowering of pho1 mutants. PHO1 is epistatic to PHO2, a negative regulator of PHO1, in flowering time regulation. Loss of PHO1 represses the expression of some floral activators, including FT encoding florigen, and induces the expression of some floral repressors in shoots. Genetic analyses indicate that at least jasmonic acid signaling is partially responsible for the late flowering of pho1 mutants. In addition, we find that rice PHO1;2, the homolog of PHO1, plays a similar role in floral transition. These results suggest that PHO1 integrates phosphorus nutrition and flowering time, and could be used as a potential target in modulating phosphorus nutrition-mediated flowering time in plants.
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Affiliation(s)
- Senhuan Dai
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Huiying Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yutao Shi
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Xinlong Xiao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Xu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cheng Qin
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yiyong Zhu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environment Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Keke Yi
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingguang Lei
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Houqing Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
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4
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Rafnsdottir S, Jang K, Halldorsdottir ST, Vinod M, Tomasdottir A, Möller K, Halldorsdottir K, Reynisdottir T, Atladottir LH, Allison KE, Ostacolo K, He J, Zhang L, Northington FJ, Magnusdottir E, Chavez-Valdez R, Anderson KJ, Bjornsson HT. SMYD5 is a regulator of the mild hypothermia response. Cell Rep 2024; 43:114554. [PMID: 39083378 PMCID: PMC11401508 DOI: 10.1016/j.celrep.2024.114554] [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: 04/18/2024] [Revised: 06/24/2024] [Accepted: 07/12/2024] [Indexed: 08/02/2024] Open
Abstract
The mild hypothermia response (MHR) maintains organismal homeostasis during cold exposure and is thought to be critical for the neuroprotection documented with therapeutic hypothermia. To date, little is known about the transcriptional regulation of the MHR. We utilize a forward CRISPR-Cas9 mutagenesis screen to identify the histone lysine methyltransferase SMYD5 as a regulator of the MHR. SMYD5 represses the key MHR gene SP1 at euthermia. This repression correlates with temperature-dependent levels of histone H3 lysine 26 trimethylation (H3K36me3) at the SP1 locus and globally, indicating that the mammalian MHR is regulated at the level of histone modifications. We have identified 37 additional SMYD5-regulated temperature-dependent genes, suggesting a broader MHR-related role for SMYD5. Our study provides an example of how histone modifications integrate environmental cues into the genetic circuitry of mammalian cells and provides insights that may yield therapeutic avenues for neuroprotection after catastrophic events.
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Affiliation(s)
- Salvor Rafnsdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Kijin Jang
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Sara Tholl Halldorsdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Meghna Vinod
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Arnhildur Tomasdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Katrin Möller
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Katrin Halldorsdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Tinna Reynisdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Laufey Halla Atladottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Kevin Ostacolo
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland; Department of Genetics and Molecular Medicine, Landspitali University Hospital, Reykjavik, Iceland
| | - Jin He
- Department of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University, East Lansing, MI, USA
| | - Li Zhang
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Frances J Northington
- Division of Neonatology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Neuroscience Intensive Care Nursery Program, Johns Hopkins University, Baltimore, MD, USA
| | - Erna Magnusdottir
- Department of Biomedical Science and Department of Anatomy, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Raul Chavez-Valdez
- Division of Neonatology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Neuroscience Intensive Care Nursery Program, Johns Hopkins University, Baltimore, MD, USA
| | - Kimberley Jade Anderson
- Department of Genetics and Molecular Medicine, Landspitali University Hospital, Reykjavik, Iceland
| | - Hans Tomas Bjornsson
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland, Reykjavik, Iceland; McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA; Department of Genetics and Molecular Medicine, Landspitali University Hospital, Reykjavik, Iceland.
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5
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Rafnsdottir S, Jang K, Halldorsdottir ST, Vinod M, Tomasdottir A, Möller K, Halldorsdottir K, Reynisdottir T, Atladottir LH, Allison KE, Ostacolo K, He J, Zhang L, Northington FJ, Magnusdottir E, Chavez-Valdez R, Anderson KJ, Bjornsson HT. SMYD5 is a regulator of the mild hypothermia response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.11.540170. [PMID: 37333301 PMCID: PMC10274674 DOI: 10.1101/2023.05.11.540170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The mild hypothermia response (MHR) maintains organismal homeostasis during cold exposure and is thought to be critical for the neuroprotection documented with therapeutic hypothermia. To date, little is known about the transcriptional regulation of the MHR. We utilize a forward CRISPR-Cas9 mutagenesis screen to identify the histone lysine methyltransferase SMYD5 as a regulator of the MHR. SMYD5 represses the key MHR gene SP1 at euthermia. This repression correlates with temperature-dependent levels of H3K36me3 at the SP1-locus and globally, indicating that the mammalian MHR is regulated at the level of histone modifications. We have identified 37 additional SMYD5 regulated temperature-dependent genes, suggesting a broader MHR-related role for SMYD5. Our study provides an example of how histone modifications integrate environmental cues into the genetic circuitry of mammalian cells and provides insights that may yield therapeutic avenues for neuroprotection after catastrophic events.
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Affiliation(s)
- Salvor Rafnsdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | - Kijin Jang
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | - Sara Tholl Halldorsdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | - Meghna Vinod
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | - Arnhildur Tomasdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | - Katrin Möller
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | - Katrin Halldorsdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | - Tinna Reynisdottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | - Laufey Halla Atladottir
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
| | | | - Kevin Ostacolo
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
- Department of Genetics and Molecular Medicine, Landspitali University Hospital; Reykjavik, Iceland
| | - Jin He
- Department of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University; MI, USA
| | - Li Zhang
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Frances J. Northington
- Division of Neonatology, Department of Pediatrics, Johns Hopkins University School of Medicine; Baltimore, MD, USA
- Neuroscience Intensive Care Nursery Program, Johns Hopkins University; Baltimore, MD, USA
| | - Erna Magnusdottir
- Department of Biomedical Science and Department of Anatomy, Faculty of Medicine, University of Iceland; Reykjavík, Iceland
| | - Raul Chavez-Valdez
- Division of Neonatology, Department of Pediatrics, Johns Hopkins University School of Medicine; Baltimore, MD, USA
- Neuroscience Intensive Care Nursery Program, Johns Hopkins University; Baltimore, MD, USA
| | - Kimberley Jade Anderson
- Department of Genetics and Molecular Medicine, Landspitali University Hospital; Reykjavik, Iceland
| | - Hans Tomas Bjornsson
- Louma G. Laboratory of Epigenetic Research, Faculty of Medicine, University of Iceland; Reykjavik, Iceland
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University; Baltimore, MD, USA
- Department of Genetics and Molecular Medicine, Landspitali University Hospital; Reykjavik, Iceland
- Lead contact
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6
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Des Marais DL. Timing is everything: How plants optimize reproduction in a variable environment. Cell 2024; 187:3504-3505. [PMID: 38996485 DOI: 10.1016/j.cell.2024.05.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 07/14/2024]
Abstract
Organisms experience a constantly changing environment and must adjust their development to maximize fitness. These "life histories" are fantastically diverse and have fascinated biologists for decades. Recent work published in Cell reveals the complex genetic mechanisms that drive life-history variation within and among species in the Brassicaceae plant family.
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Affiliation(s)
- David L Des Marais
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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7
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Liu B, Li C, Li X, Wang J, Xie W, Woods DP, Li W, Zhu X, Yang S, Dong A, Amasino RM. The H3K4 demethylase JMJ1 is required for proper timing of flowering in Brachypodium distachyon. THE PLANT CELL 2024; 36:2729-2745. [PMID: 38652680 PMCID: PMC11218787 DOI: 10.1093/plcell/koae124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/29/2024] [Accepted: 03/30/2024] [Indexed: 04/25/2024]
Abstract
Flowering is a key developmental transition in the plant life cycle. In temperate climates, flowering often occurs in response to the perception of seasonal cues such as changes in day-length and temperature. However, the mechanisms that have evolved to control the timing of flowering in temperate grasses are not fully understood. We identified a Brachypodium distachyon mutant whose flowering is delayed under inductive long-day conditions due to a mutation in the JMJ1 gene, which encodes a Jumonji domain-containing protein. JMJ1 is a histone demethylase that mainly demethylates H3K4me2 and H3K4me3 in vitro and in vivo. Analysis of the genome-wide distribution of H3K4me1, H3K4me2, and H3K4me3 in wild-type plants by chromatin immunoprecipitation and sequencing combined with RNA sequencing revealed that H3K4m1 and H3K4me3 are positively associated with gene transcript levels, whereas H3K4me2 is negatively correlated with transcript levels. Furthermore, JMJ1 directly binds to the chromatin of the flowering regulator genes VRN1 and ID1 and affects their transcription by modifying their H3K4me2 and H3K4me3 levels. Genetic analyses indicated that JMJ1 promotes flowering by activating VRN1 expression. Our study reveals a role for JMJ1-mediated chromatin modification in the proper timing of flowering in B. distachyon.
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Affiliation(s)
- Bing Liu
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Chengzhang Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Xiang Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Jiachen Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Wenhao Xie
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Daniel P Woods
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Weiya Li
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Xiaoyu Zhu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Shuoming Yang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Richard M Amasino
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
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8
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Zhai D, Zhang LY, Li LZ, Xu ZG, Liu XL, Shang GD, Zhao B, Gao J, Wang FX, Wang JW. Reciprocal conversion between annual and polycarpic perennial flowering behavior in the Brassicaceae. Cell 2024; 187:3319-3337.e18. [PMID: 38810645 DOI: 10.1016/j.cell.2024.04.047] [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: 11/16/2023] [Revised: 03/22/2024] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
The development of perennial crops holds great promise for sustainable agriculture and food security. However, the evolution of the transition between perenniality and annuality is poorly understood. Here, using two Brassicaceae species, Crucihimalaya himalaica and Erysimum nevadense, as polycarpic perennial models, we reveal that the transition from polycarpic perennial to biennial and annual flowering behavior is a continuum determined by the dosage of three closely related MADS-box genes. Diversification of the expression patterns, functional strengths, and combinations of these genes endows species with the potential to adopt various life-history strategies. Remarkably, we find that a single gene among these three is sufficient to convert winter-annual or annual Brassicaceae plants into polycarpic perennial flowering plants. Our work delineates a genetic basis for the evolution of diverse life-history strategies in plants and lays the groundwork for the generation of diverse perennial Brassicaceae crops in the future.
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Affiliation(s)
- Dong Zhai
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China; University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Lu-Yi Zhang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China; University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Ling-Zi Li
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Zhou-Geng Xu
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Xiao-Li Liu
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Guan-Dong Shang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China; University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Bo Zhao
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Jian Gao
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Fu-Xiang Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China; New Cornerstone Science Laboratory, Shanghai 200032, China.
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9
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Lin X, Yin J, Wang Y, Yao J, Li QQ, Latzel V, Bossdorf O, Zhang YY. Environment-induced heritable variations are common in Arabidopsis thaliana. Nat Commun 2024; 15:4615. [PMID: 38816460 PMCID: PMC11139905 DOI: 10.1038/s41467-024-49024-3] [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: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
Parental or ancestral environments can induce heritable phenotypic changes, but whether such environment-induced heritable changes are a common phenomenon remains unexplored. Here, we subject 14 genotypes of Arabidopsis thaliana to 10 different environmental treatments and observe phenotypic and genome-wide gene expression changes over four successive generations. We find that all treatments caused heritable phenotypic and gene expression changes, with a substantial proportion stably transmitted over all observed generations. Intriguingly, the susceptibility of a genotype to environmental inductions could be predicted based on the transposon abundance in the genome. Our study thus challenges the classic view that the environment only participates in the selection of heritable variation and suggests that the environment can play a significant role in generating of heritable variations.
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Affiliation(s)
- Xiaohe Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Junjie Yin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Yifan Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Jing Yao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA, USA
| | - Vit Latzel
- Institute of Botany of the CAS, Zamek 1, 252 43, Pruhonice, Czech Republic
| | - Oliver Bossdorf
- Institute of Evolution & Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China.
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10
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Qiu C, Wang T, Wang H, Tao Z, Wang C, Ma J, Li S, Zhao Y, Liu J, Li P. SISTER OF FCA physically associates with SKB1 to regulate flowering time in Arabidopsis thaliana. BMC PLANT BIOLOGY 2024; 24:188. [PMID: 38486139 PMCID: PMC10941358 DOI: 10.1186/s12870-024-04887-y] [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: 10/31/2023] [Accepted: 03/07/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND Proper flowering time is important for the growth and development of plants, and both too early and too late flowering impose strong negative influences on plant adaptation and seed yield. Thus, it is vitally important to study the mechanism underlying flowering time control in plants. In a previous study by the authors, genome-wide association analysis was used to screen the candidate gene SISTER OF FCA (SSF) that regulates FLOWERING LOCUS C (FLC), a central gene encoding a flowering suppressor in Arabidopsis thaliana. RESULTS SSF physically interacts with Protein arginine methyltransferase 5 (PRMT5, SKB1). Subcellular co-localization analysis showed that SSF and SKB1 interact in the nucleus. Genetically, SSF and SKB1 exist in the same regulatory pathway that controls FLC expression. Furthermore, RNA-sequencing analysis showed that both SSF and SKB1 regulate certain common pathways. CONCLUSIONS This study shows that PRMT5 interacts with SSF, thus controlling FLC expression and facilitating flowering time control.
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Affiliation(s)
- Chunhong Qiu
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Tengyue Wang
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hui Wang
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Zhen Tao
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Chuanhong Wang
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Jing Ma
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Shuai Li
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yibing Zhao
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Jifang Liu
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Peijin Li
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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11
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Zhang D, Ai G, Ji K, Huang R, Chen C, Yang Z, Wang J, Cui L, Li G, Tahira M, Wang X, Wang T, Ye J, Hong Z, Ye Z, Zhang J. EARLY FLOWERING is a dominant gain-of-function allele of FANTASTIC FOUR 1/2c that promotes early flowering in tomato. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:698-711. [PMID: 37929693 PMCID: PMC10893951 DOI: 10.1111/pbi.14217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
Flowering time, an important factor in plant adaptability and genetic improvement, is regulated by various genes in tomato (Solanum lycopersicum). In this study, we characterized a tomato mutant, EARLY FLOWERING (EF), that developed flowers much earlier than its parental control. EF is a dominant gain-of-function allele with a T-DNA inserted 139 bp downstream of the stop codon of FANTASTIC FOUR 1/2c (FAF1/2c). The transcript of SlFAF1/2c was at elevated levels in the EF mutant. Overexpressing SlFAF1/2c in tomato plants phenocopied the early flowering trait of the EF mutant. Knocking out SlFAF1/2c in the EF mutant reverted the early flowering phenotype of the mutant to the normal flowering time of the wild-type tomato plants. SlFAF1/2c promoted the floral transition by shortening the vegetative phase rather than by reducing the number of leaves produced before the emergence of the first inflorescence. The COP9 signalosome subunit 5B (CSN5B) was shown to interact with FAF1/2c, and knocking out CSN5B led to an early flowering phenotype in tomato. Interestingly, FAF1/2c was found to reduce the accumulation of the CSN5B protein by reducing its protein stability. These findings imply that FAF1/2c regulates flowering time in tomato by reducing the accumulation and stability of CSN5B, which influences the expression of SINGLE FLOWER TRUSS (SFT), JOINTLESS (J) and UNIFLORA (UF). Thus, a new allele of SlFAF1/2c was discovered and found to regulate flowering time in tomato.
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Affiliation(s)
- Dedi Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Guo Ai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Kangna Ji
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Rong Huang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Chunrui Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Zixuan Yang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Jiafa Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Long Cui
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Guobin Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Maryam Tahira
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Xin Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Taotao Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Jie Ye
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Zonglie Hong
- Department of Plant SciencesUniversity of IdahoMoscowIdahoUSA
| | - Zhibiao Ye
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Junhong Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
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12
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Liu Y, Luo C, Lan M, Guo Y, Li R, Liang R, Chen S, Zhong J, Li B, Xie F, Chen C, He X. MiCOL6, MiCOL7A and MiCOL7B isolated from mango regulate flowering and stress response in transgenic Arabidopsis. PHYSIOLOGIA PLANTARUM 2024; 176:e14242. [PMID: 38439528 DOI: 10.1111/ppl.14242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/02/2024] [Accepted: 02/20/2024] [Indexed: 03/06/2024]
Abstract
The CONSTANS/CONSTANS-Like (CO/COL) family has been shown to play important roles in flowering, stress tolerance, fruit development and ripening in higher plants. In this study, three COL genes, MiCOL6, MiCOL7A and MiCOL7B, which each contain only one CCT domain, were isolated from mango (Mangifera indica), and their functions were investigated. MiCOL7A and MiCOL7B were expressed mainly at 20 days after flowering (DAF), and all three genes were highly expressed during the flowering induction period. The expression levels of the three genes were affected by light conditions, but only MiCOL6 exhibited a clear circadian rhythm. Overexpression of MiCOL6 promoted earlier flowering, while overexpression of MiCOL7A or MiCOL7B delayed flowering compared to that in the control lines of Arabidopsis thaliana under long-day (LD) and short-day (SD) conditions. Overexpressing MiCOL6, MiCOL7A or MiCOL7B in transgenic plants increased superoxide dismutase (SOD) and proline levels, decreased malondialdehyde (MAD) levels, and improved survival under drought and salt stress. In addition, yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) analyses showed that the MiCOL6, MiCOL7A and MiCOL7B proteins interact with several stress- and flower-related proteins. This work demonstrates the functions of MiCOL6, MiCOL7A and MiCOL7B and provides a foundation for further research on the role of mango COL genes in flowering regulation and the abiotic stress response.
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Affiliation(s)
- Yuan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Cong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Moying Lan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Yihang Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
- College of Agronomy and Horticulture, Huaihua Polytechnic College, Huaihua, Hunan
| | - Ruoyan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Rongzhen Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Shuquan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Junjie Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Baijun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Fangfang Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Canbin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Xinhua He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
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13
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Luo X, Liu B, Xie L, Wang K, Xu D, Tian X, Xie L, Li L, Ye X, He Z, Xia X, Yan L, Cao S. The TaSOC1-TaVRN1 module integrates photoperiod and vernalization signals to regulate wheat flowering. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:635-649. [PMID: 37938892 PMCID: PMC10893938 DOI: 10.1111/pbi.14211] [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: 07/30/2022] [Revised: 09/12/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023]
Abstract
Wheat needs different durations of vernalization, which accelerates flowering by exposure to cold temperature, to ensure reproductive development at the optimum time, as that is critical for adaptability and high yield. TaVRN1 is the central flowering regulator in the vernalization pathway and encodes a MADS-box transcription factor (TF) that usually works by forming hetero- or homo-dimers. We previously identified that TaVRN1 bound to an MADS-box TF TaSOC1 whose orthologues are flowering activators in other plants. The specific function of TaSOC1 and the biological implication of its interaction with TaVRN1 remained unknown. Here, we demonstrated that TaSOC1 was a flowering repressor in the vernalization and photoperiod pathways by overexpression and knockout assays. We confirmed the physical interaction between TaSOC1 and TaVRN1 in wheat protoplasts and in planta, and further validated their genetic interplay. A Flowering Promoting Factor 1-like gene TaFPF1-2B was identified as a common downstream target of TaSOC1 and TaVRN1 through transcriptome and chromatin immunoprecipitation analyses. TaSOC1 competed with TaVRT2, another MADS-box flowering regulator, to bind to TaVRN1; their coding genes synergistically control TaFPF1-2B expression and flowering initiation in response to photoperiod and low temperature. We identified major haplotypes of TaSOC1 and found that TaSOC1-Hap1 conferred earlier flowering than TaSOC1-Hap2 and had been subjected to positive selection in wheat breeding. We also revealed that wheat SOC1 family members were important domestication loci and expanded by tandem and segmental duplication events. These findings offer new insights into the regulatory mechanism underlying flowering control along with useful genetic resources for wheat improvement.
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Affiliation(s)
- Xumei Luo
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Bingyan Liu
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Li Xie
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Ke Wang
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Dengan Xu
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xiuling Tian
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Lina Xie
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Lingli Li
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xingguo Ye
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Zhonghu He
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xianchun Xia
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Liuling Yan
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Shuanghe Cao
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
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14
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Poulet A, Zhao M, Peng Y, Tham F, Jaudal M, Zhang L, van Wolfswinkel JC, Putterill J. Gene-edited Mtsoc1 triple mutant Medicago plants do not flower. FRONTIERS IN PLANT SCIENCE 2024; 15:1357924. [PMID: 38469328 PMCID: PMC10926907 DOI: 10.3389/fpls.2024.1357924] [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: 12/19/2023] [Accepted: 02/02/2024] [Indexed: 03/13/2024]
Abstract
Optimized flowering time is an important trait that ensures successful plant adaptation and crop productivity. SOC1-like genes encode MADS transcription factors, which are known to play important roles in flowering control in many plants. This includes the best-characterized eudicot model Arabidopsis thaliana (Arabidopsis), where SOC1 promotes flowering and functions as a floral integrator gene integrating signals from different flowering-time regulatory pathways. Medicago truncatula (Medicago) is a temperate reference legume with strong genomic and genetic resources used to study flowering pathways in legumes. Interestingly, despite responding to similar floral-inductive cues of extended cold (vernalization) followed by warm long days (VLD), such as in winter annual Arabidopsis, Medicago lacks FLC and CO which are key regulators of flowering in Arabidopsis. Unlike Arabidopsis with one SOC1 gene, multiple gene duplication events have given rise to three MtSOC1 paralogs within the Medicago genus in legumes: one Fabaceae group A SOC1 gene, MtSOC1a, and two tandemly repeated Fabaceae group B SOC1 genes, MtSOC1b and MtSOC1c. Previously, we showed that MtSOC1a has unique functions in floral promotion in Medicago. The Mtsoc1a Tnt1 retroelement insertion single mutant showed moderately delayed flowering in long- and short-day photoperiods, with and without prior vernalization, compared to the wild-type. In contrast, Mtsoc1b Tnt1 single mutants did not have altered flowering time or flower development, indicating that it was redundant in an otherwise wild-type background. Here, we describe the generation of Mtsoc1a Mtsoc1b Mtsoc1c triple mutant lines using CRISPR-Cas9 gene editing. We studied two independent triple mutant lines that segregated plants that did not flower and were bushy under floral inductive VLD. Genotyping indicated that these non-flowering plants were homozygous for the predicted strong mutant alleles of the three MtSOC1 genes. Gene expression analyses using RNA-seq and RT-qPCR indicated that these plants remained vegetative. Overall, the non-flowering triple mutants were dramatically different from the single Mtsoc1a mutant and the Arabidopsis soc1 mutant; implicating multiple MtSOC1 genes in critical overlapping roles in the transition to flowering in Medicago.
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Affiliation(s)
- Axel Poulet
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, United States
| | - Min Zhao
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Yongyan Peng
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Mt Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - FangFei Tham
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Mauren Jaudal
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Mt Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Lulu Zhang
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Josien C. van Wolfswinkel
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, United States
| | - Joanna Putterill
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
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15
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Mahmood T, He S, Abdullah M, Sajjad M, Jia Y, Ahmar S, Fu G, Chen B, Du X. Epigenetic insight into floral transition and seed development in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111926. [PMID: 37984609 DOI: 10.1016/j.plantsci.2023.111926] [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: 08/12/2023] [Revised: 10/20/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Seasonal changes are crucial in shifting the developmental stages from the vegetative phase to the reproductive phase in plants, enabling them to flower under optimal conditions. Plants grown at different latitudes sense and interpret these seasonal variations, such as changes in day length (photoperiod) and exposure to cold winter temperatures (vernalization). These environmental factors influence the expression of various genes related to flowering. Plants have evolved to stimulate a rapid response to environmental conditions through genetic and epigenetic mechanisms. Multiple epigenetic regulation systems have emerged in plants to interpret environmental signals. During the transition to the flowering phase, changes in gene expression are facilitated by chromatin remodeling and small RNAs interference, particularly in annual and perennial plants. Key flowering regulators, such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT), interact with various factors and undergo chromatin remodeling in response to seasonal cues. The Polycomb silencing complex (PRC) controls the expression of flowering-related genes in photoperiodic flowering regulation. Under vernalization-dependent flowering, FLC acts as a potent flowering suppressor by downregulating the gene expression of various flower-promoting genes. Eventually, PRCs are critically involved in the regulation of FLC and FT locus interacting with several key genes in photoperiod and vernalization. Subsequently, PRCs also regulate Epigenetical events during gametogenesis and seed development as a driving force. Furthermore, DNA methylation in the context of CHG, CG, and CHH methylation plays a critical role in embryogenesis. DNA glycosylase DME (DEMETER) is responsible for demethylation during seed development. Thus, the review briefly discusses flowering regulation through light signaling, day length variation, temperature variation and seed development in plants.
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Affiliation(s)
- Tahir Mahmood
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Muhammad Abdullah
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Muhammad Sajjad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Guoyong Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Baojun Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China.
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16
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Ye X, Deng Q, Xu S, Huang Y, Wei D, Wang Z, Zhang H, Wang H, Tang Q. CsSPL13A directly binds and positively regulates CsFT and CsBAM to accelerate flowering in cucumber. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108395. [PMID: 38290342 DOI: 10.1016/j.plaphy.2024.108395] [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: 11/14/2023] [Revised: 01/15/2024] [Accepted: 01/21/2024] [Indexed: 02/01/2024]
Abstract
Flowering is an important developmental transition that greatly affects the yield of many vegetable crops. In cucumber (Cucumis sativus), flowering is regulated by various factors including squamosa promoter-binding-like (SPL) family proteins. However, the role of CsSPL genes in cucumber flowering remains largely unknown. In this study, we cloned the squamosa promoter-binding-like protein 13A (CsSPL13A) gene, which encodes a highly conserved SBP-domain protein that acts as a transcription factor and localizes to the nucleus. Quantitative real-time PCR (qRT-PCR) analysis showed that CsSPL13A was mainly expressed in flowers, and its expression level increased significantly nearing the flowering stage. Additionally, compared with the wild type(WT), CsSPL13A-overexpressing transgenic cucumber plants (CsSPL13A-OE) showed considerable differences in flowering phenotypes, such as early flowering, increased number of male flowers, and longer flower stalks. CsSPL13A upregulated the expression of the flowering integrator gene Flowering Locus T (CsFT) and the sugar-mediated flowering gene β-amylase (CsBAM) in cucumber. Yeast one-hybrid and firefly enzyme reporter assays confirmed that the CsSPL13A protein could directly bind to the promoters of CsFT and CsBAM, suggesting that CsSPL13A works together with CsFT and CsBAM to mediate flowering in cucumber. Overall, our results provide novel insights into the regulatory network of flowering in cucumber as well as new ideas for the genetic improvement of cucumber varieties.
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Affiliation(s)
- Xu Ye
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Qinlin Deng
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Shicheng Xu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Yifang Huang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Dayong Wei
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Zhimin Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Hongcheng Zhang
- Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Hebing Wang
- Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China.
| | - Qinglin Tang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China.
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17
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Kerr SC, Shehnaz S, Paudel L, Manivannan MS, Shaw LM, Johnson A, Velasquez JTJ, Tanurdžić M, Cazzonelli CI, Varkonyi-Gasic E, Prentis PJ. Advancing tree genomics to future proof next generation orchard production. FRONTIERS IN PLANT SCIENCE 2024; 14:1321555. [PMID: 38312357 PMCID: PMC10834703 DOI: 10.3389/fpls.2023.1321555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/26/2023] [Indexed: 02/06/2024]
Abstract
The challenges facing tree orchard production in the coming years will be largely driven by changes in the climate affecting the sustainability of farming practices in specific geographical regions. Identifying key traits that enable tree crops to modify their growth to varying environmental conditions and taking advantage of new crop improvement opportunities and technologies will ensure the tree crop industry remains viable and profitable into the future. In this review article we 1) outline climate and sustainability challenges relevant to horticultural tree crop industries, 2) describe key tree crop traits targeted for improvement in agroecosystem productivity and resilience to environmental change, and 3) discuss existing and emerging genomic technologies that provide opportunities for industries to future proof the next generation of orchards.
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Affiliation(s)
- Stephanie C Kerr
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Saiyara Shehnaz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lucky Paudel
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Mekaladevi S Manivannan
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Lindsay M Shaw
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
- School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
| | - Amanda Johnson
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Jose Teodoro J Velasquez
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Miloš Tanurdžić
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | | | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Peter J Prentis
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
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18
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Lee SW, Nugroho ABD, Park M, Moon H, Kim J, Kim DH. Identification of vernalization-related genes and cold memory element (CME) required for vernalization response in radish (Raphanus sativus L.). PLANT MOLECULAR BIOLOGY 2024; 114:5. [PMID: 38227117 DOI: 10.1007/s11103-023-01412-x] [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: 10/05/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024]
Abstract
Floral transition is accelerated by exposure to long-term cold like winter in plants, which is called as vernalization. Acceleration of floral transition by vernalization is observed in a diversity of biennial and perennial plants including Brassicaceae family plants. Scientific efforts to understand molecular mechanism underlying vernalization-mediated floral transition have been intensively focused in model plant Arabidopsis thaliana. To get a better understanding on floral transition by vernalization in radish (Raphanus sativus L.), we investigated transcriptomic changes taking place during vernalization in radish. Thousands of genes were differentially regulated along time course of vernalization compared to non-vernalization (NV) sample. Twelve major clusters of DEGs were identified based on distinctive expression profiles during vernalization. Radish FLC homologs were shown to exert an inhibition of floral transition when transformed into Arabidopsis plants. In addition, DNA region containing RY motifs located within a Raphanus sativus FLC homolog, RsFLC1 was found to be required for repression of RsFLC1 by vernalization. Transgenic plants harboring disrupted RY motifs were impaired in the enrichment of H3K27me3 on RsFLC1 chromatin, thus resulting in the delayed flowering in Arabidopsis. Taken together, we report transcriptomic profiles of radish during vernalization and demonstrate the requirement of RY motif for vernalization-mediated repression of RsFLC homologs in radish (Raphanus sativus L.).
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Affiliation(s)
- Sang Woo Lee
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | | | | | - Heewon Moon
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Jun Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Dong-Hwan Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea.
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19
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Magar ND, Shah P, Barbadikar KM, Bosamia TC, Madhav MS, Mangrauthia SK, Pandey MK, Sharma S, Shanker AK, Neeraja CN, Sundaram RM. Long non-coding RNA-mediated epigenetic response for abiotic stress tolerance in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108165. [PMID: 38064899 DOI: 10.1016/j.plaphy.2023.108165] [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: 12/25/2022] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 02/15/2024]
Abstract
Plants perceive environmental fluctuations as stress and confront several stresses throughout their life cycle individually or in combination. Plants have evolved their sensing and signaling mechanisms to perceive and respond to a variety of stresses. Epigenetic regulation plays a critical role in the regulation of genes, spatiotemporal expression of genes under stress conditions and imparts a stress memory to encounter future stress responses. It is quintessential to integrate our understanding of genetics and epigenetics to maintain plant fitness, achieve desired genetic gains with no trade-offs, and durable long-term stress tolerance. The long non-coding RNA >200 nts having no coding potential (or very low) play several roles in epigenetic memory, contributing to the regulation of gene expression and the maintenance of cellular identity which include chromatin remodeling, imprinting (dosage compensation), stable silencing, facilitating nuclear organization, regulation of enhancer-promoter interactions, response to environmental signals and epigenetic switching. The lncRNAs are involved in a myriad of stress responses by activation or repression of target genes and hence are potential candidates for deploying in climate-resilient breeding programs. This review puts forward the significant roles of long non-coding RNA as an epigenetic response during abiotic stresses in plants and the prospects of deploying lncRNAs for designing climate-resilient plants.
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Affiliation(s)
- Nakul D Magar
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India; Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - Priya Shah
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, 502324, India
| | - Kalyani M Barbadikar
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India.
| | - Tejas C Bosamia
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute, Gujarat, 364002, India
| | - M Sheshu Madhav
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | | | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, 502324, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - Arun K Shanker
- Plant Physiology, ICAR-Central Research Institute for Dryland Agriculture, Hyderabad, 500059, India
| | - C N Neeraja
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - R M Sundaram
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
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20
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Zhao B, Wang JW. Perenniality: From model plants to applications in agriculture. MOLECULAR PLANT 2024; 17:141-157. [PMID: 38115580 DOI: 10.1016/j.molp.2023.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/04/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023]
Abstract
To compensate for their sessile nature, plants have evolved sophisticated mechanisms enabling them to adapt to ever-changing environments. One such prominent feature is the evolution of diverse life history strategies, particularly such that annuals reproduce once followed by seasonal death, while perennials live longer by cycling growth seasonally. This intrinsic phenology is primarily genetic and can be altered by environmental factors. Although evolutionary transitions between annual and perennial life history strategies are common, perennials account for most species in nature because they survive well under year-round stresses. This proportion, however, is reversed in agriculture. Hence, perennial crops promise to likewise protect and enhance the resilience of agricultural ecosystems in response to climate change. Despite significant endeavors that have been made to generate perennial crops, progress is slow because of barriers in studying perennials, and many developed species await further improvement. Recent findings in model species have illustrated that simply rewiring existing genetic networks can lead to lifestyle variation. This implies that engineering plant life history strategy can be achieved by manipulating only a few key genes. In this review, we summarize our current understanding of genetic basis of perenniality and discuss major questions and challenges that remain to be addressed.
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Affiliation(s)
- Bo Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China; New Cornerstone Science Laboratory, Shanghai 200032, China.
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21
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Duk MA, Gursky VV, Samsonova MG, Surkova SY. Modeling the Flowering Activation Motif during Vernalization in Legumes: A Case Study of M. trancatula. Life (Basel) 2023; 14:26. [PMID: 38255642 PMCID: PMC10817331 DOI: 10.3390/life14010026] [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: 10/23/2023] [Revised: 12/04/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
In many plant species, flowering is promoted by the cold treatment or vernalization. The mechanism of vernalization-induced flowering has been extensively studied in Arabidopsis but remains largely unknown in legumes. The orthologs of the FLC gene, a major regulator of vernalization response in Arabidopsis, are absent or non-functional in the vernalization-sensitive legume species. Nevertheless, the legume integrator genes FT and SOC1 are involved in the transition of the vernalization signal to meristem identity genes, including PIM (AP1 ortholog). However, the regulatory contribution of these genes to PIM activation in legumes remains elusive. Here, we presented the theoretical and data-driven analyses of a feed-forward regulatory motif that includes a vernalization-responsive FT gene and several SOC1 genes, which independently activate PIM and thereby mediate floral transition. Our theoretical model showed that the multiple regulatory branches in this regulatory motif facilitated the elimination of no-sense signals and amplified useful signals from the upstream regulator. We further developed and analyzed four data-driven models of PIM activation in Medicago trancatula in vernalized and non-vernalized conditions in wild-type and fta1-1 mutants. The model with FTa1 providing both direct activation and indirect activation via three intermediate activators, SOC1a, SOC1b, and SOC1c, resulted in the most relevant PIM dynamics. In this model, the difference between regulatory inputs of SOC1 genes was nonessential. As a result, in the M. trancatula model, the cumulative action of SOC1a, SOC1b, and SOC1c was favored. Overall, in this study, we first presented the in silico analysis of vernalization-induced flowering in legumes. The considered vernalization network motif can be supplemented with additional regulatory branches as new experimental data become available.
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Affiliation(s)
- Maria A. Duk
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia
- Theoretical Department, Ioffe Institute, 194021 St. Petersburg, Russia
| | - Vitaly V. Gursky
- Theoretical Department, Ioffe Institute, 194021 St. Petersburg, Russia
| | - Maria G. Samsonova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Svetlana Yu. Surkova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia
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22
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Ding T, Cai L, He Y, Li Y, Tian E, Zhou Q, Zhou X, Wang X, Yu K, Shen X. BnPLP1 Positively Regulates Flowering Time, Plant Height, and Main Inflorescence Length in Brassica napus. Genes (Basel) 2023; 14:2206. [PMID: 38137028 PMCID: PMC10743044 DOI: 10.3390/genes14122206] [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: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Protein prenylation mediated by the Arabidopsis thaliana PLURIPETALA (AtPLP) gene plays a crucial role in plant growth, development, and environmental response by adding a 15-carbon farnesyl group or one to two 20-carbon geranylgeranyl groups onto one to two cysteine residues at the C-terminus of the target protein. However, the homologous genes and their functions of AtPLP in rapeseed are unclear. In this study, bioinformatics analysis and gene cloning demonstrated the existence of two homologous genes of AtPLP in the Brassica napus L. genome, namely, BnPLP1 and BnPLP2. Evolutionary analysis revealed that BnPLP1 originated from the B. rapa L. genome, while BnPLP2 originated from the B. oleracea L. genome. Genetic transformation analysis revealed that the overexpression of BnPLP1 in Arabidopsis plants exhibited earlier flowering initiation, a prolonged flowering period, increased plant height, and longer main inflorescence length compared to the wild type. Contrarily, the downregulation of BnPLP1 expression in B. napus plants led to delayed flowering initiation, shortened flowering period, decreased plant height, and reduced main inflorescence length compared to the wild type. These findings indicate that the BnPLP1 gene positively regulates flowering time, plant height, and main inflorescence length. This provides a new gene for the genetic improvement of flowering time and plant architecture in rapeseed.
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Affiliation(s)
- Ting Ding
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Lei Cai
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
- Center for Research and Development of Fine Chemical of Guizhou University, Guiyang 550025, China
| | - Yuqi He
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Yuanhong Li
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Entang Tian
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Qianhui Zhou
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Xufan Zhou
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Xiaodong Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China;
| | - Kunjiang Yu
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
- Center for Research and Development of Fine Chemical of Guizhou University, Guiyang 550025, China
| | - Xinjie Shen
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
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23
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Chaudhary R, Higgins EE, Eynck C, Sharpe AG, Parkin IAP. Mapping QTL for vernalization requirement identified adaptive divergence of the candidate gene Flowering Locus C in polyploid Camelina sativa. THE PLANT GENOME 2023; 16:e20397. [PMID: 37885362 DOI: 10.1002/tpg2.20397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
Vernalization requirement is an integral component of flowering in winter-type plants. The availability of winter ecotypes among Camelina species facilitated the mapping of quantitative trait loci (QTL) for vernalization requirement in Camelina sativa. An inter and intraspecific crossing scheme between related Camelina species, where one spring and two different sources of winter-type habit were used, resulted in the development of two segregating populations. Linkage maps generated with sequence-based markers identified three QTLs associated with vernalization requirement in C. sativa; two from the interspecific (chromosomes 13 and 20) and one from the intraspecific cross (chromosome 8). Notably, the three loci were mapped to different homologous regions of the hexaploid C. sativa genome. All three QTLs were found in proximity to Flowering Locus C (FLC), variants of which have been reported to affect the vernalization requirement in plants. Temporal transcriptome analysis for winter-type Camelina alyssum demonstrated reduction in expression of FLC on chromosomes 13 and 20 during cold treatment, which would trigger flowering, since FLC would be expected to suppress floral initiation. FLC on chromosome 8 also showed reduced expression in the C. sativa ssp. pilosa winter parent upon cold treatment, but was expressed at very high levels across all time points in the spring-type C. sativa. The chromosome 8 copy carried a deletion in the spring-type line, which could impact its functionality. Contrary to previous reports, all three FLC loci can contribute to controlling the vernalization response in C. sativa and provide opportunities for manipulating this requirement in the crop.
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Affiliation(s)
- Raju Chaudhary
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
- Global Institute for Food Security, Saskatoon, Saskatchewan, Canada
| | - Erin E Higgins
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Christina Eynck
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Andrew G Sharpe
- Global Institute for Food Security, Saskatoon, Saskatchewan, Canada
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Iqbal A, Rehman ZU, Khan MR, Khan AM, Khan SU, Arif M, Iqbal J, Rehman MU, Ali M, Qasim M, Ali I, Facho ZH, Hussain M, Hussain I, Ahmad J, Ali S. Field response and molecular screening of European wheat germplasm against powdery mildew at the Himalayan region of Pakistan. J Appl Genet 2023; 64:667-678. [PMID: 37749479 DOI: 10.1007/s13353-023-00789-1] [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: 02/28/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/27/2023]
Abstract
Wheat powdery mildew possesses a significant threat to wheat crops not only on a global scale but also in the northern region of Pakistan. Recognizing the need for effective measures, the exploration and utilization of exotic germplasm take on critical importance. To address this, a series of trials were made to investigate the response of 30 European (EU) lines, in addition to the local checks (Siran, Atta-Habib (AH) and Ghanimat-e-IBGE) against wheat powdery mildew at the Himalayan region of Pakistan. The study involved field testing from 2018 to 2022 across multiple locations, resulting in 38 different environments (location × year). In addition to field evaluations, molecular genotyping was also performed. The disease was absent on the tested lines during 2018, 2019, and 2020 whereas it ranged from 0 to 100% at Chitral location during 2021, where 100% was observed only for one EU wheat line "Matrix." The disease prevailed only at Gilgit location (0-60% for EU wheat line "F236") and at Nagar location (0-10% for EU wheat lines Substance and Nelson) during the disease season of 2022. Most of the EU wheat lines showed very low ACI values, due to an overall low disease pressure. Matrix showed the maximum ACI (1.54) followed by Ritter (1.25) and Bli_autrichion (0.87), whereas the minimum (0.1) was for Substance, JB_Asano, and KWS_Loft followed by Canon (0.19), all exhibiting partial resistance. The molecular marker-based screening revealed that Pm38 was the most prevalent and detected in 100% of wheat lines followed by Pm39 (60%) and Pm8 (30%). Six wheat lines (20%) possessed all three Pm genes (Pm8, Pm38, and Pm39) concurrently. The variability observed in this study can be utilized in future breeding efforts aimed at developing resistant wheat varieties.
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Affiliation(s)
- Aamir Iqbal
- The University of Agriculture, Peshawar, Pakistan.
| | | | | | | | | | | | - Javaid Iqbal
- Department of Environmental Sciences, University of Lakki-Marwat, 28420, Khyber Pakhtunkhwa, Pakistan
| | - Mujeeb Ur Rehman
- The University of Agriculture, Peshawar, Pakistan
- Department of Soil Conservation, Chitral, Pakistan
| | - Minhaj Ali
- The University of Agriculture, Peshawar, Pakistan
- Department of Agriculture Extension, Parachinar, Pakistan
| | - Muhammad Qasim
- The University of Agriculture, Peshawar, Pakistan
- Department of Agriculture Research, Quetta, Pakistan
| | - Imran Ali
- The University of Agriculture, Peshawar, Pakistan
| | - Zakir Hussain Facho
- The University of Agriculture, Peshawar, Pakistan
- Department of Agriculture Extension, Skardu, Pakistan
| | - Muhammad Hussain
- The University of Agriculture, Peshawar, Pakistan
- Department of Agriculture Extension, Nagar, Pakistan
| | - Ijlal Hussain
- The University of Agriculture, Peshawar, Pakistan
- Department of Agriculture Extension, Hunza, Pakistan
| | - Jamshaid Ahmad
- University of Veterinary and & Animal Sciences, Lahore, Pakistan
| | - Sajid Ali
- The University of Agriculture, Peshawar, Pakistan.
- Department of Agriculture (Plant Breeding and Genetics), Hazara University, Mansehra, Pakistan.
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25
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Rehman S, Bahadur S, Xia W. An overview of floral regulatory genes in annual and perennial plants. Gene 2023; 885:147699. [PMID: 37567454 DOI: 10.1016/j.gene.2023.147699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/31/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
The floral initiation in angiosperms is a complex process influenced by endogenous and exogenous signals. With this approach, we aim to provide a comprehensive review to integrate this complex floral regulatory process and summarize the regulatory genes and their functions in annuals and perennials. Seven primary paths leading to flowering have been discovered in Arabidopsis under several growth condition that include; photoperiod, ambient temperature, vernalization, gibberellins, autonomous, aging and carbohydrates. These pathways involve a series of interlinked signaling pathways that respond to both internal and external signals, such as light, temperature, hormones, and developmental cues, to coordinate the expression of genes that are involved in flower development. Among them, the photoperiodic pathway was the most important and conserved as some of the fundamental loci and mechanisms are shared even by closely related plant species. The activation of floral regulatory genes such as FLC, FT, LFY, and SOC1 that determine floral meristem identity and the transition to the flowering stage result from the merging of these pathways. Recent studies confirmed that alternative splicing, antisense RNA and epigenetic modification play crucial roles by regulating the expression of genes related to blooming. In this review, we documented recent progress in the floral transition time in annuals and perennials, with emphasis on the specific regulatory mechanisms along with the application of various molecular approaches including overexpression studies, RNA interference and Virus-induced flowering. Furthermore, the similarities and differences between annual and perennial flowering will aid significant contributions to the field by elucidating the mechanisms of perennial plant development and floral initiation regulation.
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Affiliation(s)
- Shazia Rehman
- Sanya Nanfan Research Institution, Hainan University, Haikou 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Saraj Bahadur
- College of Forestry, Hainan University, Haikou 570228 China
| | - Wei Xia
- Sanya Nanfan Research Institution, Hainan University, Haikou 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China.
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26
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Shi M, Wang C, Wang P, Yun F, Liu Z, Ye F, Wei L, Liao W. Role of methylation in vernalization and photoperiod pathway: a potential flowering regulator? HORTICULTURE RESEARCH 2023; 10:uhad174. [PMID: 37841501 PMCID: PMC10569243 DOI: 10.1093/hr/uhad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/23/2023] [Indexed: 10/17/2023]
Abstract
Recognized as a pivotal developmental transition, flowering marks the continuation of a plant's life cycle. Vernalization and photoperiod are two major flowering pathways orchestrating numerous florigenic signals. Methylation, including histone, DNA and RNA methylation, is one of the recent foci in plant development. Considerable studies reveal that methylation seems to show an increasing potential regulatory role in plant flowering via altering relevant gene expression without altering the genetic basis. However, little has been reviewed about whether and how methylation acts on vernalization- and photoperiod-induced flowering before and after FLOWERING LOCUS C (FLC) reactivation, what role RNA methylation plays in vernalization- and photoperiod-induced flowering, how methylation participates simultaneously in both vernalization- and photoperiod-induced flowering, the heritability of methylation memory under the vernalization/photoperiod pathway, and whether and how methylation replaces vernalization/photoinduction to regulate flowering. Our review provides insight about the crosstalk among the genetic control of the flowering gene network, methylation (methyltransferases/demethylases) and external signals (cold, light, sRNA and phytohormones) in vernalization and photoperiod pathways. The existing evidence that RNA methylation may play a potential regulatory role in vernalization- and photoperiod-induced flowering has been gathered and represented for the first time. This review speculates about and discusses the possibility of substituting methylation for vernalization and photoinduction to promote flowering. Current evidence is utilized to discuss the possibility of future methylation reagents becoming flowering regulators at the molecular level.
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Affiliation(s)
- Meimei Shi
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Chunlei Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Peng Wang
- Vegetable and Flower Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fahong Yun
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhiya Liu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Fujin Ye
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Lijuan Wei
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Weibiao Liao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
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Kumar M, Rani K. Epigenomics in stress tolerance of plants under the climate change. Mol Biol Rep 2023:10.1007/s11033-023-08539-6. [PMID: 37294468 DOI: 10.1007/s11033-023-08539-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND Climate change has had a tremendous impact on the environment in general as well as agricultural crops grown in these situations as time passed. Agricultural production of crops is less suited and of lower quality due to disturbances in plant metabolism brought on by sensitivity to environmental stresses, which are brought on by climate change. Abiotic stressors that are specific to climate change, including as drought, extremes in temperature, increasing CO2, waterlogging from heavy rain, metal toxicity, and pH changes, are known to negatively affect an array of species. Plants adapt to these challenges by undergoing genome-wide epigenetic changes, which are frequently accompanied by differences in transcriptional gene expression. The sum of a cell's biochemical modifications to its nuclear DNA, post-translational modifications to histones, and variations in the synthesis of non-coding RNAs is called an epigenome. These modifications frequently lead to variations in gene expression that occur without any alteration in the underlying base sequence. EPIGENETIC MECHANISMS AND MARKS The methylation of homologous loci by three different modifications-genomic (DNA methylation), chromatin (histone modifications), and RNA-directed DNA methylation (RdDM)-could be regarded as epigenetic mechanisms that control the regulation of differential gene expression. Stresses from the environment cause chromatin remodelling, which enables plant cells to adjust their expression patterns temporarily or permanently. EPIGENOMICS' CONSEQUENCES FOR GENOME STABILITY AND GENE EXPRESSION: DNA methylation affects gene expression in response to abiotic stressors by blocking or suppressing transcription. Environmental stimuli cause changes in DNA methylation levels, either upward in the case of hypermethylation or downward in the case of hypomethylation. The type of stress response that occurs as a result also affects the degree of DNA methylation alterations. Stress is also influenced by DRM2 and CMT3 methylating CNN, CNG, and CG. Both plant development and stress reactions depend on histone changes. Gene up-regulation is associated with histone tail phosphorylation, ubiquitination, and acetylation, while gene down-regulation is associated with de-acetylation and biotinylation. Plants undergo a variety of dynamic changes to histone tails in response to abiotic stressors. The relevance of these transcripts against stress is highlighted by the accumulation of numerous additional antisense transcripts, a source of siRNAs, caused by abiotic stresses. The study highlights the finding that plants can be protected from a range of abiotic stresses by epigenetic mechanisms such DNA methylation, histone modification, and RNA-directed DNA methylation. TRANSGENERATIONAL INHERITANCE AND SOURCES OF EPIGENETIC VARIATION: Stress results in the formation of epialleles, which are either transient or enduring epigenetic stress memory in plants. After the stress is gone, the stable memory is kept for the duration of the plant's remaining developmental cycles or passed on to the next generations, leading to plant evolution and adaptability. The bulk of epigenetic changes brought on by stress are temporary and return to normal after the stress has passed. Some of the modifications, however, might be long-lasting and transmitted across mitotic or even meiotic cell divisions. Epialleles often have genetic or non-genetic causes. Epialleles can arise spontaneously due to improper methylation state maintenance, short RNA off-target effects, or other non-genetic causes. Developmental or environmental variables that influence the stability of epigenetic states or direct chromatin modifications may also be non-genetic drivers of epigenetic variation. Transposon insertions that change local chromatin and structural rearrangements, such copy number changes that are genetically related or unrelated, are two genetic sources of epialleles. EPIGENOMICS IN CROP IMPROVEMENT To include epigenetics into crop breeding, it is necessary to create epigenetic variation as well as to identify and evaluate epialleles. Epigenome editing or epi-genomic selection may be required for epiallele creation and identification. In order to combat the challenges given by changing environments, these epigenetic mechanisms have generated novel epialleles that can be exploited to develop new crop types that are more climate-resilient. Numerous techniques can be used to alter the epigenome generally or at specific target loci in order to induce the epigenetic alterations necessary for crop development. Technologies like CRISPR/Cas9 and dCas, which have recently advanced, have opened up new avenues for the study of epigenetics. Epialleles could be employed in epigenomics-assisted breeding in addition to sequence-based markers for crop breeding. CONCLUSIONS AND FUTURE PROSPECTUS A few of the exciting questions that still need to be resolved in the area of heritable epigenetic variation include a better understanding of the epigenetic foundation of characteristics, the stability and heritability of epialleles, and the sources of epigenetic variation in crops. Investigating long intergenic non-coding RNAs (lincRNAs) as an epigenetic process might open up a new path to understanding crop plant's ability to withstand abiotic stress. For many of these technologies and approaches to be more applicable and deployable at a lower cost, technological breakthroughs will also be necessary. Breeders will probably need to pay closer attention to crop epialleles and how they can affect future responses to climate changes. The development of epialleles suitable for particular environmental circumstances may be made possible by creating targeted epigenetic changes in pertinent genes and by comprehending the molecular underpinnings of trans generational epigenetic inheritance. More research on a wider variety of plant species is required in order to fully comprehend the mechanisms that produce and stabilise epigenetic variation in crops. In addition to a collaborative and multidisciplinary effort by researchers in many fields of plant science, this will require a greater integration of the epigenomic data gathered in many crops. Before it may be applied generally, more study is required.
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Affiliation(s)
- Mithlesh Kumar
- AICRN On Potential Crops, ARS Mandor, Agriculture University, Jodhpur, 342 304, Rajasthan, India.
| | - Kirti Rani
- ICAR-National Bureau of Plant Genetic Resources (NBPGR), Regional Station, Jodhpur, 342 003, Rajasthan, India
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Marand AP, Eveland AL, Kaufmann K, Springer NM. cis-Regulatory Elements in Plant Development, Adaptation, and Evolution. ANNUAL REVIEW OF PLANT BIOLOGY 2023; 74:111-137. [PMID: 36608347 PMCID: PMC9881396 DOI: 10.1146/annurev-arplant-070122-030236] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
cis-Regulatory elements encode the genomic blueprints that ensure the proper spatiotemporal patterning of gene expression necessary for appropriate development and responses to the environment. Accumulating evidence implicates changes to gene expression as a major source of phenotypic novelty in eukaryotes, including acute phenotypes such as disease and cancer in mammals. Moreover, genetic and epigenetic variation affecting cis-regulatory sequences over longer evolutionary timescales has become a recurring theme in studies of morphological divergence and local adaptation. Here, we discuss the functions of and methods used to identify various classes of cis-regulatory elements, as well as their role in plant development and response to the environment. We highlight opportunities to exploit cis-regulatory variants underlying plant development and environmental responses for crop improvement efforts. Although a comprehensive understanding of cis-regulatory mechanisms in plants has lagged behind that in animals, we showcase several breakthrough findings that have profoundly influenced plant biology and shaped the overall understanding of transcriptional regulation in eukaryotes.
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Affiliation(s)
| | | | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany;
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA;
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Liu FF, Wan YX, Cao WX, Zhang QQ, Li Y, Li Y, Zhang PZ, Si HQ. Novel function of a putative TaCOBL ortholog associated with cold response. Mol Biol Rep 2023; 50:4375-4384. [PMID: 36944863 DOI: 10.1007/s11033-023-08297-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 01/19/2023] [Indexed: 03/23/2023]
Abstract
The plant COBRA protein family plays an important role in secondary cell wall biosynthesis and the orientation of cell expansion. The COBRA gene family has been well studied in Arabidopsis thaliana, maize, rice, etc., but no systematic studies were conducted in wheat. In this study, the full-length sequence of TaCOBLs was obtained by homology cloning from wheat, and a conserved motif analysis confirmed that TaCOBLs belonged to the COBRA protein family. qRT-PCR results showed that the TaCOBL transcripts were induced by abiotic stresses, including cold, drought, salinity, and abscisic acid (ABA). Two haplotypes of TaCOBL-5B (Hap5B-a and Hap5B-b), harboring one indel (----/TATA) in the 5' flanking region (- 550 bp), were found on chromosome 5BS. A co-dominant marker, Ta5BF/Ta5BR, was developed based on the polymorphism of the two TaCOBL-5B haplotypes. Significant correlations between the two TaCOBL-5B haplotypes and cold resistance were observed under four environmental conditions. Hap5B-a, a favored haplotype acquired during wheat polyploidization, may positively contribute to enhanced cold resistance in wheat. Based on the promoter activity analysis, the Hap5B-a promoter containing a TATA-box was more active than that of Hap5B-b without the TATA-box under low temperature. Our study provides valuable information indicating that the TaCOBL genes are associated with cold response in wheat.
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Affiliation(s)
- Fang-Fang Liu
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Anhui Key Laboratory of Crop Quality Improvement, Hefei, 230031, China
| | - Ying-Xiu Wan
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Anhui Key Laboratory of Crop Quality Improvement, Hefei, 230031, China
| | - Wen-Xin Cao
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Anhui Key Laboratory of Crop Quality Improvement, Hefei, 230031, China
| | - Qi-Qi Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Anhui Key Laboratory of Crop Quality Improvement, Hefei, 230031, China
| | - Yao Li
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Anhui Key Laboratory of Crop Quality Improvement, Hefei, 230031, China
| | - Yan Li
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Anhui Key Laboratory of Crop Quality Improvement, Hefei, 230031, China
| | - Ping-Zhi Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Anhui Key Laboratory of Crop Quality Improvement, Hefei, 230031, China.
| | - Hong-Qi Si
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
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Kinoshita Y, Motoki K, Hosokawa M. Upregulation of tandem duplicated BoFLC1 genes is associated with the non-flowering trait in Brassica oleracea var. capitata. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:41. [PMID: 36897379 DOI: 10.1007/s00122-023-04311-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Tandem duplicated BoFLC1 genes (BoFLC1a and BoFLC1b), which were identified as the candidate causal genes for the non-flowering trait in the cabbage mutant 'nfc', were upregulated during winter in 'nfc'. The non-flowering natural cabbage mutant 'nfc' was discovered from the breeding line 'T15' with normal flowering characteristics. In this study, we investigated the molecular basis underlying the non-flowering trait of 'nfc'. First, 'nfc' was induced to flower using the grafting floral induction method, and three F2 populations were generated. The flowering phenotype of each F2 population was widely distributed with non-flowering individuals appearing in two populations. QTL-seq analysis detected a genomic region associated with flowering date at approximately 51 Mb on chromosome 9 in two of the three F2 populations. Subsequent validation and fine mapping of the candidate genomic region using QTL analysis identified the quantitative trait loci (QTL) at 50,177,696-51,474,818 bp on chromosome 9 covering 241 genes. Additionally, RNA-seq analysis in leaves and shoot apices of 'nfc' and 'T15' plants identified 19 and 15 differentially expressed genes related to flowering time, respectively. Based on these results, we identified tandem duplicated BoFLC1 genes, which are homologs of the floral repressor FLOWERING LOCUS C, as the candidate genes responsible for the non-flowering trait of 'nfc'. We designated the tandem duplicated BoFLC1 genes as BoFLC1a and BoFLC1b. Expression analysis revealed that the expression levels of BoFLC1a and BoFLC1b were downregulated during winter in 'T15' but were upregulated and maintained during winter in 'nfc'. Additionally, the expression level of the floral integrator BoFT was upregulated in the spring in 'T15' but hardly upregulated in 'nfc'. These results suggest that the upregulated levels of BoFLC1a and BoFLC1b contributed to the non-flowering trait of 'nfc'.
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Affiliation(s)
- Yu Kinoshita
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Ko Motoki
- Graduate School of Agriculture, Kyoto University, Kizugawa, Kyoto 619-0218, Japan
| | - Munetaka Hosokawa
- Faculty of Agriculture, Kindai University, Nara, Nara 631-8505, Japan.
- Agricultural Technology and Innovation Research Institute (ATIRI), Kindai University, Nara, Nara 631-8505, Japan.
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Ahn G, Park HJ, Jeong SY, Shin GI, Ji MG, Cha JY, Kim J, Kim MG, Yun DJ, Kim WY. HOS15 represses flowering by promoting GIGANTEA degradation in response to low temperature in Arabidopsis. PLANT COMMUNICATIONS 2023:100570. [PMID: 36864727 PMCID: PMC10363504 DOI: 10.1016/j.xplc.2023.100570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/13/2023] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Flowering is the primary stage of the plant developmental transition and is tightly regulated by environmental factors such as light and temperature. However, the mechanisms by which temperature signals are integrated into the photoperiodic flowering pathway are still poorly understood. Here, we demonstrate that HOS15, which is known as a GI transcriptional repressor in the photoperiodic flowering pathway, controls flowering time in response to low ambient temperature. At 16°C, the hos15 mutant exhibits an early flowering phenotype, and HOS15 acts upstream of photoperiodic flowering genes (GI, CO, and FT). GI protein abundance is increased in the hos15 mutant and is insensitive to the proteasome inhibitor MG132. Furthermore, the hos15 mutant has a defect in low ambient temperature-mediated GI degradation, and HOS15 interacts with COP1, an E3 ubiquitin ligase for GI degradation. Phenotypic analyses of the hos15 cop1 double mutant revealed that repression of flowering by HOS15 is dependent on COP1 at 16°C. However, the HOS15-COP1 interaction was attenuated at 16°C, and GI protein abundance was additively increased in the hos15 cop1 double mutant, indicating that HOS15 acts independently of COP1 in GI turnover at low ambient temperature. This study proposes that HOS15 controls GI abundance through multiple modes as an E3 ubiquitin ligase and transcriptional repressor to coordinate appropriate flowering time in response to ambient environmental conditions such as temperature and day length.
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Affiliation(s)
- Gyeongik Ahn
- Research Institute of Life Science, Institute of Agricultural and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; Division of Applied Life Science (BK21 Four), Plant Biological Rhythm Research Center, Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Hee Jin Park
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Song Yi Jeong
- Research Institute of Life Science, Institute of Agricultural and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; Division of Applied Life Science (BK21 Four), Plant Biological Rhythm Research Center, Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Gyeong-Im Shin
- Research Institute of Life Science, Institute of Agricultural and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; Division of Applied Life Science (BK21 Four), Plant Biological Rhythm Research Center, Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Myung Geun Ji
- Research Institute of Life Science, Institute of Agricultural and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; Division of Applied Life Science (BK21 Four), Plant Biological Rhythm Research Center, Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Joon-Yung Cha
- Research Institute of Life Science, Institute of Agricultural and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; Division of Applied Life Science (BK21 Four), Plant Biological Rhythm Research Center, Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jeongsik Kim
- Faculty of Science Education and Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju 63243, Republic of Korea
| | - Min Gab Kim
- College of Pharmacy and Research Institute of Pharmaceutical Science, PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Dae-Jin Yun
- Institute of Glocal Disease Control, Konkuk University, Seoul 05029, Republic of Korea; Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Woe-Yeon Kim
- Research Institute of Life Science, Institute of Agricultural and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; Division of Applied Life Science (BK21 Four), Plant Biological Rhythm Research Center, Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea.
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Pan J, Zhang H, Zhan Z, Zhao T, Jiang D. A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis. J Genet Genomics 2023; 50:178-191. [PMID: 36113770 DOI: 10.1016/j.jgg.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022]
Abstract
Seed germination is a critical developmental switch from a quiescent state to active growth, which involves extensive changes in metabolism, gene expression, and cellular identity. However, our understanding of epigenetic and transcriptional reprogramming during this process is limited. The histone H3 lysine 27 trimethylation (H3K27me3) plays a key role in regulating gene repression and cell fate specification. Here, we profile H3K27me3 dynamics and dissect the function of H3K27 demethylation during germination in Arabidopsis. Our temporal genome-wide profiling of H3K27me3 and transcription reveals delayed H3K27me3 reprogramming compared with transcriptomic changes during germination, with H3K27me3 changes mainly occurring when the embryo is entering into vegetative development. RELATIVE OF EARLY FLOWERING 6 (REF6)-mediated H3K27 demethylation is necessary for robust germination but does not significantly contribute to H3K27me3 dynamics during germination, but rather stably establishes an H3K27me3-depleted state that facilitates the activation of hormone-related and expansin-coding genes important for germination. We also show that the REF6 chromatin occupancy is gradually established during germination to counteract increased Polycomb repressive complex 2 (PRC2). Our study provides key insights into the H3K27me3 dynamics during germination and suggests the function of H3K27me3 in facilitating cell fate switch. Furthermore, we reveal the importance of H3K27 demethylation-established transcriptional competence in gene activation during germination and likely other developmental processes.
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Affiliation(s)
- Jie Pan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huairen Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenping Zhan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Danhua Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Lemus T, Mason GA, Bubb KL, Alexandre CM, Queitsch C, Cuperus JT. AGO1 and HSP90 buffer different genetic variants in Arabidopsis thaliana. Genetics 2023; 223:iyac163. [PMID: 36303325 PMCID: PMC9910400 DOI: 10.1093/genetics/iyac163] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/18/2022] [Indexed: 11/14/2022] Open
Abstract
Argonaute 1 (AGO1), the principal protein component of microRNA-mediated regulation, plays a key role in plant growth and development. AGO1 physically interacts with the chaperone HSP90, which buffers cryptic genetic variation in plants and animals. We sought to determine whether genetic perturbation of AGO1 in Arabidopsis thaliana would also reveal cryptic genetic variation, and if so, whether AGO1-dependent loci overlap with those dependent on HSP90. To address these questions, we introgressed a hypomorphic mutant allele of AGO1 into a set of mapping lines derived from the commonly used Arabidopsis strains Col-0 and Ler. Although we identified several cases in which AGO1 buffered genetic variation, none of the AGO1-dependent loci overlapped with those buffered by HSP90 for the traits assayed. We focused on 1 buffered locus where AGO1 perturbation uncoupled the traits days to flowering and rosette leaf number, which are otherwise closely correlated. Using a bulk segregant approach, we identified a nonfunctional Ler hua2 mutant allele as the causal AGO1-buffered polymorphism. Introduction of a nonfunctional hua2 allele into a Col-0 ago1 mutant background recapitulated the Ler-dependent ago1 phenotype, implying that coupling of these traits involves different molecular players in these closely related strains. Taken together, our findings demonstrate that even though AGO1 and HSP90 buffer genetic variation in the same traits, these robustness regulators interact epistatically with different genetic loci, suggesting that higher-order epistasis is uncommon. Plain Language Summary Argonaute 1 (AGO1), a key player in plant development, interacts with the chaperone HSP90, which buffers environmental and genetic variation. We found that AGO1 buffers environmental and genetic variation in the same traits; however, AGO1-dependent and HSP90-dependent loci do not overlap. Detailed analysis of a buffered locus found that a nonfunctional HUA2 allele decouples days to flowering and rosette leaf number in an AGO1-dependent manner, suggesting that the AGO1-dependent buffering acts at the network level.
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Affiliation(s)
- Tzitziki Lemus
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Grace Alex Mason
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | | | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
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Transcriptome Analysis Reveals Putative Induction of Floral Initiation by Old Leaves in Tea-Oil Tree (Camellia oleifera ‘changlin53’). Int J Mol Sci 2022; 23:ijms232113021. [PMID: 36361817 PMCID: PMC9655362 DOI: 10.3390/ijms232113021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022] Open
Abstract
Floral initiation is a major phase change in the spermatophyte, where developmental programs switch from vegetative growth to reproductive growth. It is a key phase of flowering in tea-oil trees that can affect flowering time and yield, but very little is known about the molecular mechanism of floral initiation in tea-oil trees. A 12-year-old Camellia oleifera (cultivar ‘changlin53’) was the source of experimental materials in the current study. Scanning electron microscopy was used to identify the key stage of floral initiation, and transcriptome analysis was used to reveal the transcriptional regulatory network in old leaves involved in floral initiation. We mined 5 DEGs related to energy and 55 DEGs related to plant hormone signal transduction, and we found floral initiation induction required a high level of energy metabolism, and the phytohormones signals in the old leaves regulate floral initiation, which occurred at stage I and II. Twenty-seven rhythm-related DEGs and 107 genes associated with flowering were also identified, and the circadian rhythm interacted with photoperiod pathways to induce floral initiation. Unigene0017292 (PSEUDO-RESPONSE REGULATOR), Unigene0046809 (LATE ELONGATED HYPOCOTYL), Unigene0009932 (GIGANTEA), Unigene0001842 (CONSTANS), and Unigene0084708 (FLOWER LOCUS T) were the key genes in the circadian rhythm-photoperiod regulatory network. In conjunction with morphological observations and transcriptomic analysis, we concluded that the induction of floral initiation by old leaves in C. oleifera ‘changlin53’ mainly occurred during stages I and II, floral initiation was completed during stage III, and rhythm–photoperiod interactions may be the source of the main signals in floral initiation induced by old leaves.
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Pan Y, Li Y, Liu Z, Zou J, Li Q. Computational genomics insights into cold acclimation in wheat. Front Genet 2022; 13:1015673. [PMID: 36338961 PMCID: PMC9632429 DOI: 10.3389/fgene.2022.1015673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Development of cold acclimation in crops involves transcriptomic reprograming, metabolic shift, and physiological changes. Cold responses in transcriptome and lipid metabolism has been examined in separate studies for various crops. In this study, integrated computational approaches was employed to investigate the transcriptomics and lipidomics data associated with cold acclimation and vernalization in four wheat genotypes of distinct cold tolerance. Differential expression was investigated between cold treated and control samples and between the winter-habit and spring-habit wheat genotypes. Collectively, 12,676 differentially expressed genes (DEGs) were identified. Principal component analysis of these DEGs indicated that the first, second, and third principal components (PC1, PC2, and PC3) explained the variance in cold treatment, vernalization and cold hardiness, respectively. Differential expression feature extraction (DEFE) analysis revealed that the winter-habit wheat genotype Norstar had high number of unique DEGs (1884 up and 672 down) and 63 winter-habit genes, which were clearly distinctive from the 64 spring-habit genes based on PC1, PC2 and PC3. Correlation analysis revealed 64 cold hardy genes and 39 anti-hardy genes. Cold acclimation encompasses a wide spectrum of biological processes and the involved genes work cohesively as revealed through network propagation and collective association strength of local subnetworks. Integration of transcriptomics and lipidomics data revealed that the winter-habit genes, such as COR413-TM1, CIPKs and MYB20, together with the phosphatidylglycerol lipids, PG(34:3) and PG(36:6), played a pivotal role in cold acclimation and coordinated cohesively associated subnetworks to confer cold tolerance.
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Affiliation(s)
- Youlian Pan
- Digital Technologies, National Research Council Canada, Ottawa, ON, Canada
| | - Yifeng Li
- Digital Technologies, National Research Council Canada, Ottawa, ON, Canada
- Department of Computer Science, Department of Biological Science, Brock University, St. Catharines, ON, Canada
| | - Ziying Liu
- Digital Technologies, National Research Council Canada, Ottawa, ON, Canada
| | - Jitao Zou
- Aquatic and Crop Research and Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Qiang Li
- Aquatic and Crop Research and Development, National Research Council Canada, Saskatoon, SK, Canada
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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Mou Y, Yuan C, Sun Q, Yan C, Zhao X, Wang J, Wang Q, Shan S, Li C. MIKC-type MADS-box transcription factor gene family in peanut: Genome-wide characterization and expression analysis under abiotic stress. FRONTIERS IN PLANT SCIENCE 2022; 13:980933. [PMID: 36340369 PMCID: PMC9631947 DOI: 10.3389/fpls.2022.980933] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Peanut (Arachis hypogaea) is one of the most important economic crops around the world, especially since it provides vegetable oil and high-quality protein for humans. Proteins encoded by MADS-box transcription factors are widely involved in regulating plant growth and development as well as responses to abiotic stresses. However, the MIKC-type MADS-box TFs in peanut remains currently unclear. Hence, in this study, 166 MIKC-type MADS-box genes were identified in both cultivated and wild-type peanut genomes, which were divided into 12 subfamilies. We found a variety of development-, hormone-, and stress-related cis-acting elements in the promoter region of peanut MIKC-type MADS-box genes. The chromosomal distribution of peanut MADS-box genes was not random, and gene duplication contributed to the expansion of the MADS-box gene family. The interaction network of the peanut AhMADS proteins was established. Expression pattern analysis showed that AhMADS genes were specifically expressed in tissues and under abiotic stresses. It was further confirmed via the qRT-PCR technique that five selected AhMADS genes could be induced by abiotic and hormone treatments and presented different expressive profiles under various stresses. Taken together, these findings provide valuable information for the exploration of candidate genes in molecular breeding and further study of AhMADS gene functions.
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Weng X, Haque T, Zhang L, Razzaque S, Lovell JT, Palacio-Mejía JD, Duberney P, Lloyd-Reilley J, Bonnette J, Juenger TE. A Pleiotropic Flowering Time QTL Exhibits Gene-by-Environment Interaction for Fitness in a Perennial Grass. Mol Biol Evol 2022; 39:msac203. [PMID: 36149808 PMCID: PMC9550986 DOI: 10.1093/molbev/msac203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Appropriate flowering time is a crucial adaptation impacting fitness in natural plant populations. Although the genetic basis of flowering variation has been extensively studied, its mechanisms in nonmodel organisms and its adaptive value in the field are still poorly understood. Here, we report new insights into the genetic basis of flowering time and its effect on fitness in Panicum hallii, a native perennial grass. Genetic mapping in populations derived from inland and coastal ecotypes identified flowering time quantitative trait loci (QTL) and many exhibited extensive QTL-by-environment interactions. Patterns of segregation within recombinant hybrids provide strong support for directional selection driving ecotypic divergence in flowering time. A major QTL on chromosome 5 (q-FT5) was detected in all experiments. Fine-mapping and expression studies identified a gene with orthology to a rice FLOWERING LOCUS T-like 9 (PhFTL9) as the candidate underlying q-FT5. We used a reciprocal transplant experiment to test for local adaptation and the specific impact of q-FT5 on performance. We did not observe local adaptation in terms of fitness tradeoffs when contrasting ecotypes in home versus away habitats. However, we observed that the coastal allele of q-FT5 conferred a fitness advantage only in its local habitat but not at the inland site. Sequence analyses identified an excess of low-frequency polymorphisms at the PhFTL9 promoter in the inland lineage, suggesting a role for either selection or population expansion on promoter evolution. Together, our findings demonstrate the genetic basis of flowering variation in a perennial grass and provide evidence for conditional neutrality underlying flowering time divergence.
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Affiliation(s)
- Xiaoyu Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Taslima Haque
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Li Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Samsad Razzaque
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Juan Diego Palacio-Mejía
- Corporación Colombiana de Investigación Agropecuaria – AGROSAVIA, Centro de Investigación Tibaitatá. Kilómetro 14 vía Mosquera-Bogotá, Mosquera. Código postal 250047, Colombia
| | - Perla Duberney
- Kika de la Garza Plant Materials Center, USDA-NRCS, Kingsville, TX, USA
| | | | - Jason Bonnette
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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Yang Z, Yan H, Wang J, Nie G, Feng G, Xu X, Li D, Huang L, Zhang X. DNA hypermethylation promotes the flowering of orchardgrass during vernalization. PLANT PHYSIOLOGY 2022; 190:1490-1505. [PMID: 35861426 PMCID: PMC9516772 DOI: 10.1093/plphys/kiac335] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Vernalization, influenced by environmental factors, is an essential process associated with the productivity of temperate crops, during which epigenetic regulation of gene expression plays an important role. Although DNA methylation is one of the major epigenetic mechanisms associated with the control of gene expression, global changes in DNA methylation in the regulation of gene expression during vernalization-induced flowering of temperate plants remain largely undetermined. To characterize vernalization-associated DNA methylation dynamics, we performed whole-genome bisulfite-treated sequencing and transcriptome sequencing in orchardgrass (Dactylis glomerata) during vernalization. The results revealed that increased levels of genome DNA methylation during the early vernalization of orchardgrass were associated with transcriptional changes in DNA methyltransferase and demethylase genes. Upregulated expression of vernalization-related genes during early vernalization was attributable to an increase in mCHH in the promoter regions of these genes. Application of an exogenous DNA methylation accelerator or overexpression of orchardgrass NUCLEAR POLY(A) POLYMERASE (DgPAPS4) promoted earlier flowering, indicating that DNA hypermethylation plays an important role in vernalization-induced flowering. Collectively, our findings revealed that vernalization-induced hypermethylation is responsible for floral primordium initiation and development. These observations provide a theoretical foundation for further studies on the molecular mechanisms underlying the control of vernalization in temperate grasses.
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Affiliation(s)
| | | | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, Florida 32611, USA
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Dandan Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
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Wang H, Han X, Fu X, Sun X, Chen H, Wei X, Cui S, Liu Y, Guo W, Li X, Xing J, Zhang Y. Overexpression of TaLBD16-4D alters plant architecture and heading date in transgenic wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:911993. [PMID: 36212357 PMCID: PMC9533090 DOI: 10.3389/fpls.2022.911993] [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: 04/03/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Lateral organ boundaries domain (LBD) proteins, a class of plant-specific transcription factors with a special domain of lateral organ boundaries (LOB), play essential roles in plant growth and development. However, there is little known about the functions of these genes in wheat to date. Our previous study demonstrated that TaLBD16-4D is conducive to increasing lateral root number in wheat. In the present work, we further examined important agronomical traits of the aerial part of transgenic wheat overexpressing TaLBD16-4D. Interestingly, it was revealed that overexpressing TaLBD16-4D could lead to early heading and multiple alterations of plant architecture, including decreased plant height, increased flag leaf size and stem diameter, reduced spike length and tillering number, improved spike density and grain width, and decreased grain length. Moreover, auxin-responsive experiments demonstrated that the expression of TaLBD16-4D in wild-type (WT) wheat plants showed a significant upregulation through 2,4-D treatment. TaLBD16-4D-overexpression lines displayed a hyposensitivity to 2,4-D treatment and reduced shoot gravitropic response. The expressions of a set of auxin-responsive genes were markedly different between WT and transgenic plants. In addition, overexpressing TaLBD16-4D affected the transcript levels of flowering-related genes (TaGI, TaCO1, TaHd1, TaVRN1, TaVRN2, and TaFT1). Notably, the expression of TaGI, TaCO1, TaHd1, TaVRN1, and TaFT1 displayed significant upregulation under IAA treatment. Collectively, our observations indicated that overexpressing TaLBD16-4D could affect aerial architecture and heading time possibly though participating in the auxin pathway.
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Affiliation(s)
- Huifang Wang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xiaofan Han
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xiaofeng Fu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xinling Sun
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Hailong Chen
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xirui Wei
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Shubin Cui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yiguo Liu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Weiwei Guo
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Ximei Li
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yumei Zhang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
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Surkova SY, Samsonova MG. Mechanisms of Vernalization-Induced Flowering in Legumes. Int J Mol Sci 2022; 23:ijms23179889. [PMID: 36077286 PMCID: PMC9456104 DOI: 10.3390/ijms23179889] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Vernalization is the requirement for exposure to low temperatures to trigger flowering. The best knowledge about the mechanisms of vernalization response has been accumulated for Arabidopsis and cereals. In Arabidopsis thaliana, vernalization involves an epigenetic silencing of the MADS-box gene FLOWERING LOCUS C (FLC), which is a flowering repressor. FLC silencing releases the expression of the main flowering inductor FLOWERING LOCUS T (FT), resulting in a floral transition. Remarkably, no FLC homologues have been identified in the vernalization-responsive legumes, and the mechanisms of cold-mediated transition to flowering in these species remain elusive. Nevertheless, legume FT genes have been shown to retain the function of the main vernalization signal integrators. Unlike Arabidopsis, legumes have three subclades of FT genes, which demonstrate distinct patterns of regulation with respect to environmental cues and tissue specificity. This implies complex mechanisms of vernalization signal propagation in the flowering network, that remain largely elusive. Here, for the first time, we summarize the available information on the genetic basis of cold-induced flowering in legumes with a special focus on the role of FT genes.
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Liu Y, Cai Y, Li Y, Zhang X, Shi N, Zhao J, Yang H. Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stress. FRONTIERS IN PLANT SCIENCE 2022; 13:983460. [PMID: 36110360 PMCID: PMC9468617 DOI: 10.3389/fpls.2022.983460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Plants must reprogram gene expression to adapt constantly changing environmental temperatures. With the increased occurrence of extremely low temperatures, the negative effects on plants, especially on growth and development, from cold stress are becoming more and more serious. In this research, strand-specific RNA sequencing (ssRNA-seq) was used to explore the dynamic changes in the transcriptome landscape of Arabidopsis thaliana exposed to cold temperatures (4°C) at different times. In total, 7,623 differentially expressed genes (DEGs) exhibited dynamic temporal changes during the cold treatments. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the DEGs were enriched in cold response, secondary metabolic processes, photosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction pathways. Meanwhile, long non-coding RNAs (lncRNAs) were identified after the assembly of the transcripts, from which 247 differentially expressed lncRNAs (DElncRNAs) and their potential target genes were predicted. 3,621 differentially alternatively spliced (DAS) genes related to RNA splicing and spliceosome were identified, indicating enhanced transcriptome complexity due to the alternative splicing (AS) in the cold. In addition, 739 cold-regulated transcription factors (TFs) belonging to 52 gene families were identified as well. This research analyzed the dynamic changes of the transcriptome landscape in response to cold stress, which reveals more complete transcriptional patterns during short- and long-term cold treatment and provides new insights into functional studies of that how plants are affected by cold stress.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yajun Cai
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yanzhuo Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaoling Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Nan Shi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jingze Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Hongchun Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- RNA Institute, Wuhan University, Wuhan, China
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42
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A Long Noncoding RNA Derived from lncRNA-mRNA Networks Modulates Seed Vigor. Int J Mol Sci 2022; 23:ijms23169472. [PMID: 36012737 PMCID: PMC9409430 DOI: 10.3390/ijms23169472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/03/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
The discovery of long noncoding RNAs (lncRNAs) has filled a great gap in our understanding of posttranscriptional gene regulation in a variety of biological processes related to plant stress responses. However, systematic analyses of the lncRNAs expressed in rice seeds that germinate under cold stress have been elusive. In this study, we performed strand-specific whole transcriptome sequencing in germinated rice seeds under cold stress and normal temperature. A total of 6258 putative lncRNAs were identified and expressed in a stage-specific manner compared to mRNA. By investigating the targets of differentially expressed (DE) lncRNAs of LT-I (phase I of low temperature)/NT-I (phase I of normal temperature), it was shown that the auxin-activated signaling pathway was significantly enriched, and twenty-three protein-coding genes with most of the members of the SAUR family located in chromosome 9 were identified as the candidate target genes that may interact with five lncRNAs. A seed vigor-related lncRNA, SVR, which interplays with the members of the SAUR gene family in cis was eventually identified. The CRISPR/Cas 9 engineered mutations in SVR cause delay of germination. The findings provided new insights into the connection between lncRNAs and the auxin-activated signaling pathway in the regulation of rice seed vigor.
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Cha JK, O'Connor K, Alahmad S, Lee JH, Dinglasan E, Park H, Lee SM, Hirsz D, Kwon SW, Kwon Y, Kim KM, Ko JM, Hickey LT, Shin D, Dixon LE. Speed vernalization to accelerate generation advance in winter cereal crops. MOLECULAR PLANT 2022; 15:1300-1309. [PMID: 35754174 DOI: 10.1016/j.molp.2022.06.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/02/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
There are many challenges facing the development of high-yielding, nutritious crops for future environments. One limiting factor is generation time, which prolongs research and plant breeding timelines. Recent advances in speed breeding protocols have dramatically reduced generation time for many short-day and long-day species by optimizing light and temperature conditions during plant growth. However, winter crops with a vernalization requirement still require up to 6-10 weeks in low-temperature conditions before the transition to reproductive development. Here, we tested a suite of environmental conditions and protocols to investigate whether the vernalization process can be accelerated. We identified a vernalization method consisting of exposing seeds at the soil surface to an extended photoperiod of 22 h day:2 h night at 10°C with transfer to speed breeding conditions that dramatically reduces generation time in both winter wheat (Triticum aestivum) and winter barley (Hordeum vulgare). Implementation of the speed vernalization protocol followed by speed breeding allowed the completion of up to five generations per year for winter wheat or barley, whereas only two generations can be typically completed under standard vernalization and plant growth conditions. The speed vernalization protocol developed in this study has great potential to accelerate biological research and breeding outcomes for winter crops.
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Affiliation(s)
- Jin-Kyung Cha
- National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Kathryn O'Connor
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Samir Alahmad
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Jong-Hee Lee
- National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Eric Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Hyeonjin Park
- National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - So-Myeong Lee
- National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Dominique Hirsz
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Soon-Wook Kwon
- Department of Plant Bioscience, Pusan National University, Miryang 60463, Korea
| | - Youngho Kwon
- National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Kyeong-Min Kim
- National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Jong-Min Ko
- National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia.
| | - Dongjin Shin
- National Institute of Crop Science, RDA, Miryang 50424, Korea.
| | - Laura E Dixon
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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Li Q, Peng A, Yang J, Zheng S, Li Z, Mu Y, Chen L, Si J, Ren X, Song H. A 215-bp indel at intron I of BoFLC2 affects flowering time in Brassica oleracea var. capitata during vernalization. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2785-2797. [PMID: 35760921 DOI: 10.1007/s00122-022-04149-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
In response to cold, a 215-bp deletion at intron I of BoFLC2 slows its silencing activity by feedback to the core genes of the PHD-PRC2 complex, resulting in late flowering in cabbage. Cabbage is a plant-vernalization-responsive flowering type. In response to cold, BoFLC2 is an important transcription factor, which allows cabbage plants to remain in the vegetative phase. However, there have been few reports on the detailed and functional effects of genetic variation in BoFLC2 on flowering time in cabbage. Herein, BoFLC2E and BoFLC2L, cloned from extremely early and extremely late flowering cabbages, respectively, exhibited a 215-bp indel at intron I, three non-synonymous SNPs and a 3-bp indel at exon II. BoFLC2L was found to be related to late flowering, as verified in 40 extremely early/late flowering accessions, a diverse set of cabbage inbred lines and two F2 generations by using indel-FLC2 marker. Among the genetic variation of BoFLC2, the 215-bp deletion at intron I was the main reason for the delayed flowering time, as verified in the transgenic progenies of seed-vernalization-responsive Arabidopsis thaliana (Col) and rapid cycler B. oleracea (TO1000, boflc2). This is the first report to show that the intron I indel of BoFLC2 affects the flowering time of cabbage. Although the intron I 215-bp indel between BoFLC2E and BoFLC2L did not cause alternative splicing, it slowed BoFLC2L silencing during vernalization and feedback to the core genes of the PHD-PRC2 complex, resulting in their lower transcription levels. Our study not only provides an effective molecular marker-assisted selective strategy for identifying bolting-resistant resources and breeding improved varieties in cabbage, but also provides an entry point for exploring the mechanisms of flowering time in plant-vernalization-responsive plants.
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Affiliation(s)
- Qinfei Li
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Ao Peng
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Jiaqin Yang
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Sidi Zheng
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Zhangping Li
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Yinhui Mu
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Lei Chen
- Chongqing Academy of Agricultural Sciences, Chongqing Sanqian Seed Industry Co., Ltd, Chongqing, 400060, China
| | - Jun Si
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Xuesong Ren
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China.
| | - Hongyuan Song
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China.
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Genomewide Identification and Characterization of the Genes Involved in the Flowering of Cotton. Int J Mol Sci 2022; 23:ijms23147940. [PMID: 35887288 PMCID: PMC9323069 DOI: 10.3390/ijms23147940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 01/27/2023] Open
Abstract
Flowering is a prerequisite for flowering plants to complete reproduction, and flowering time has an important effect on the high and stable yields of crops. However, there are limited reports on flowering-related genes at the genomic level in cotton. In this study, genomewide analysis of the evolutionary relationship of flowering-related genes in different cotton species shows that the numbers of flowering-related genes in the genomes of tetraploid cotton species Gossypium hirsutum and Gossypium barbadense were similar, and that these numbers were approximately twice as much as the number in diploid cotton species Gossypium arboretum. The classification of flowering-related genes shows that most of them belong to the photoperiod and circadian clock flowering pathway. The distribution of flowering-related genes on the chromosomes of the At and Dt subgenomes was similar, with no subgenomic preference detected. In addition, most of the flowering-related core genes in Arabidopsis thaliana had homologs in the cotton genome, but the copy numbers and expression patterns were disparate; moreover, flowering-related genes underwent purifying selection throughout the evolutionary and selection processes. Although the differentiation and reorganization of many key genes of the cotton flowering regulatory network occurred throughout the evolutionary and selection processes, most of them, especially those involved in the important flowering regulatory networks, have been relatively conserved and preferentially selected.
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Wang Q, Wang GL, Song SY, Zhao YN, Lu S, Zhou F. ORANGE negatively regulates flowering time in Arabidopsisthaliana. JOURNAL OF PLANT PHYSIOLOGY 2022; 274:153719. [PMID: 35598433 DOI: 10.1016/j.jplph.2022.153719] [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: 03/02/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Floral transition is an important process in plant development, which is regulated by at least four flowering pathways: the photoperiod, vernalization, autonomous, and gibberellin (GA)-dependent pathways. The DnaJ-like zinc finger domain-containing protein ORANGE (OR) was originally cloned from the cauliflower or mutant, which has distinct phenotypes of the carotenoid-accumulating curd, the elongated petioles, and the delayed-flowering time. OR has been demonstrated to interact with phytoene synthase for carotenoid biosynthesis in plastids and with eukaryotic release factor 1-2 (eRF1-2) in the nucleus for the first two phenotypes, respectively. In this study, we showed that overexpression of OR in Arabidopsis thaliana resulted in a delayed-flowering phenotype resembling the cauliflower or mutant. Our results indicated that OR negatively regulates the expression of the flowering integrator genes FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). Both GA3 and vernalization treatments could not rescue the delayed-flowering phenotype of the OR-overexpressing seedlings, suggesting the repression of floral transition by OR does not depend on SOC1-mediated vernalization or GA-dependent pathways. Moreover, our analysis revealed that transcripts of OR and FT fluctuated in opposite directions diurnally, and the overexpression of OR repressed the accumulation of CONSTANS (CO), FT, and SOC1 transcripts in a 16 h/8 h light/dark long-day cycle. Our results indicated the possibility that OR represses flowering through the CO-FT-SOC1-mediated photoperiodic flowering pathway.
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Affiliation(s)
- Qi Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Guang-Ling Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Shu-Yuan Song
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ya-Nan Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Shan Lu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
| | - Fei Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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Integrative Analyses of Transcriptomes and Metabolomes Reveal Associated Genes and Metabolites with Flowering Regulation in Common Vetch ( Vicia sativa L.). Int J Mol Sci 2022; 23:ijms23126818. [PMID: 35743262 PMCID: PMC9224626 DOI: 10.3390/ijms23126818] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/17/2022] [Accepted: 06/17/2022] [Indexed: 11/26/2022] Open
Abstract
As an important source of protein for livestock and human consumption, Vicia sativa is cultivated worldwide, but its seed production is hampered at high altitudes because of the short frost-free period. Flowering represents the transition from a vegetative to a reproductive period, and early flowering benefits plant seed production at high altitudes. However, the molecular mechanisms of flowering regulation in V. sativa remain elusive. In the present study, two V. sativa accessions with different flowering characteristics were used: Lan3 (early-flowering) was cultivated by our laboratory, and 503 (late-flowering) was selected from 222 V. sativa accessions after three years of field experiments. The shoot samples (shoot tip length = 10 cm) of these two accessions were collected 63, 70, and 77 days after sowing, and the molecular regulatory mechanism of the flowering process was identified by integrative analyses of the transcriptomes and metabolomes. Kyoto Encyclopedia of Genes and Genomes enrichment showed that the synthesis and signal transduction of plant hormone pathways were the most enriched pathways in 4274 differentially expressed genes (DEGs) and in 259 differential metabolites between Lan3 and 503. Moreover, the contents of three metabolites related to salicylic acid biosynthesis and the transcription levels of two DEGs related to salicylic acid signal transduction in Lan3 were higher than those in 503. Further verification in various accessions indicated that salicylic acid metabolism may be involved in the flowering regulation process of V. sativa. These findings provide valuable information for understanding the flowering mechanism and for promoting breeding research in V. sativa.
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Sharma M, Charron JB, Rani M, Jabaji S. Bacillus velezensis strain B26 modulates the inflorescence and root architecture of Brachypodium distachyon via hormone homeostasis. Sci Rep 2022; 12:7951. [PMID: 35562386 PMCID: PMC9106653 DOI: 10.1038/s41598-022-12026-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 04/29/2022] [Indexed: 11/09/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) influence plant health. However, the genotypic variations in host organisms affect their response to PGPR. To understand the genotypic effect, we screened four diverse B. distachyon genotypes at varying growth stages for their ability to be colonized by B. velezensis strain B26. We reasoned that B26 may have an impact on the phenological growth stages of B. distachyon genotypes. Phenotypic data suggested the role of B26 in increasing the number of awns and root weight in wild type genotypes and overexpressing transgenic lines. Thus, we characterized the expression patterns of flowering pathway genes in inoculated plants and found that strain B26 modulates the transcript abundance of flowering genes. An increased root volume of inoculated plants was estimated by CT-scanning which suggests the role of B26 in altering the root architecture. B26 also modulated plant hormone homeostasis. A differential response was observed in the transcript abundance of auxin and gibberellins biosynthesis genes in inoculated roots. Our results reveal that B. distachyon plant genotype is an essential determinant of whether a PGPR provides benefit or harm to the host and shed new insight into the involvement of B. velezensis in the expression of flowering genes.
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Affiliation(s)
- Meha Sharma
- Department of Plant Science, Macdonald Campus of McGill University, 21,111 Lakeshore Rd., Ste-Anne de Bellevue, QC, H9X 3V9, Canada
| | - Jean-Benoit Charron
- Department of Plant Science, Macdonald Campus of McGill University, 21,111 Lakeshore Rd., Ste-Anne de Bellevue, QC, H9X 3V9, Canada
| | - Mamta Rani
- Department of Plant Science, Macdonald Campus of McGill University, 21,111 Lakeshore Rd., Ste-Anne de Bellevue, QC, H9X 3V9, Canada
| | - Suha Jabaji
- Department of Plant Science, Macdonald Campus of McGill University, 21,111 Lakeshore Rd., Ste-Anne de Bellevue, QC, H9X 3V9, Canada.
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Márquez Gutiérrez R, Cherubino Ribeiro TH, de Oliveira RR, Benedito VA, Chalfun-Junior A. Genome-Wide Analyses of MADS-Box Genes in Humulus lupulus L. Reveal Potential Participation in Plant Development, Floral Architecture, and Lupulin Gland Metabolism. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11091237. [PMID: 35567239 PMCID: PMC9100628 DOI: 10.3390/plants11091237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 05/14/2023]
Abstract
MADS-box transcription factors (TFs) are involved in multiple plant development processes and are most known during the reproductive transition and floral organ development. Very few genes have been characterized in the genome of Humulus lupulus L. (Cannabaceae), an important crop for the pharmaceutical and beverage industries. The MADS-box family has not been studied in this species yet. We identified 65 MADS-box genes in the hop genome, of which 29 encode type-II TFs (27 of subgroup MIKCC and 2 MIKC*) and 36 type-I proteins (26 α, 9 β, and 1 γ). Type-II MADS-box genes evolved more complex architectures than type-I genes. Interestingly, we did not find FLOWERING LOCUS C (FLC) homologs, a transcription factor that acts as a floral repressor and is negatively regulated by cold. This result provides a molecular explanation for a previous work showing that vernalization is not a requirement for hop flowering, which has implications for its cultivation in the tropics. Analysis of gene ontology and expression profiling revealed genes potentially involved in the development of male and female floral structures based on the differential expression of ABC homeotic genes in each whorl of the flower. We identified a gene exclusively expressed in lupulin glands, suggesting a role in specialized metabolism in these structures. In toto, this work contributes to understanding the evolutionary history of MADS-box genes in hop, and provides perspectives on functional genetic studies, biotechnology, and crop breeding.
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Affiliation(s)
- Robert Márquez Gutiérrez
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-900, MG, Brazil; (R.M.G.); (T.H.C.R.); (R.R.d.O.)
| | - Thales Henrique Cherubino Ribeiro
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-900, MG, Brazil; (R.M.G.); (T.H.C.R.); (R.R.d.O.)
| | - Raphael Ricon de Oliveira
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-900, MG, Brazil; (R.M.G.); (T.H.C.R.); (R.R.d.O.)
| | - Vagner Augusto Benedito
- Laboratory of Plant Functional Genetics, Plant and Soil Sciences Division, 3425 Agricultural Sciences Building, West Virginia University, Morgantown, WV 26506-6108, USA
- Correspondence: (V.A.B.); (A.C.-J.)
| | - Antonio Chalfun-Junior
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-900, MG, Brazil; (R.M.G.); (T.H.C.R.); (R.R.d.O.)
- Correspondence: (V.A.B.); (A.C.-J.)
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50
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Liu T, Liu Y, Fu G, Chen J, Lv T, Su D, Wang Y, Hu X, Su X, Harris AJ. Identification of genes involved in drought tolerance in seedlings of the desert grass, Psammochloa villosa (Poaceae), based on full-length isoform sequencing and de novo assembly from short reads. JOURNAL OF PLANT PHYSIOLOGY 2022; 271:153630. [PMID: 35193087 DOI: 10.1016/j.jplph.2022.153630] [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: 10/22/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Psammochloa villosa is a perennial herbaceous plant that is dominant within arid regions of the Inner Mongolian Plateau and the Qinghai-Tibet Plateau in China, where it is an endemic species and exhibits strong drought tolerance and wind resistance. To study drought tolerance in P. villosa and determine its molecular basis, we simulated high and moderate drought stress in a controlled environment and then analyzed transcriptome sequences by combining long-read sequences from a representative, wild-grown individual with short reads from the treatment groups. We obtained 184,076 high-quality isoforms as a reference and 168,650 genes (91.6%), which we were able to annotate according to public databases. Ultimately, we obtained 119,005 unigenes representing the transcriptome of P. villosa under drought stress and, among these, we identified 3089 differentially expressed genes and 1484 transcription factors. Physiologically, P. villosa that was exposed to high and moderate drought stress had reduced germination rates and shorter buds but generated more chlorophyll, which is atypical under drought stress and possibly reflects an adaptation of these plants to their arid environment. We inferred that significantly upregulated genes were annotated as 'Chlorophyll a-b binding protein' and 'Light-harvesting chlorophyll-protein' among drought and control groups. Broadly, our analyses revealed that drought stress triggered many genome-level responses, especially related to mitigation of radical oxygen species (ROS), which increase in concentration under drought stress. In particular, in the high drought stress group compared with the control, GO enrichment analysis revealed a significant enrichment of upregulated genes (n = 10) involved in mitigation of oxidative stress. Similarly, using KEGG we found significant enrichment of genes in the phenylpropanoid biosynthesis pathway (11 genes), which yields phenols that scavenge ROS. We also inferred that many genes involved in metabolism of arginine and proline, which may serve as both scavengers of ROS and osmoprotectants that interact with stress response genes based on our protein-protein interaction network analysis. We verified the relative expression levels of eight genes associated with mitigation of ROS, DNA repair, and transmembrane transporter activity using qRT-PCR, and the results were consistent with our inferences from transcriptomes. This study provides insights into the genomic and physiological basis of drought tolerance in P. villosa and represents a resource for development of the species as a forage crop via molecular breeding within arid lands.
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Affiliation(s)
- Tao Liu
- School of Geography, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Yuping Liu
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Gui Fu
- School of Geography, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Jinyuan Chen
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Ting Lv
- School of Geography, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Dandan Su
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Yanan Wang
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Xiayu Hu
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Xu Su
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China; Academy of Plateau Science and Sustainability, Xueyuan Road, Xining, 810016, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China; Key Laboratory of Education Ministry of Earth Surface Processes and Ecological Conservation of the Qinghai-Tibet Plateau, Qinghai Normal University, No. 38 Wusixi Road, Xining, Xining, 810008, China.
| | - A J Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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