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Li C, Zhang X, Gao W, Liang S, Wang S, Zhang X, Wang J, Yao J, Li Y, Liu Y. The chromosome-level Elaeagnus mollis genome and transcriptomes provide insights into genome evolution, glycerolipid and vitamin E biosynthesis in seeds. Int J Biol Macromol 2024; 281:136273. [PMID: 39370078 DOI: 10.1016/j.ijbiomac.2024.136273] [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: 06/12/2024] [Revised: 09/29/2024] [Accepted: 10/02/2024] [Indexed: 10/08/2024]
Abstract
Elaeagnus mollis, which has seeds with high lipid and vitamin E contents, is a valuable woody oil plant with potential for utilization. Currently, the biosynthesis and regulation mechanism of glycerolipids and vitamin E are still unknown in E. mollis. Here, we present the chromosome-level reference genome of E. mollis (scaffold N50: ~40.66Mbp, genome size: ~591.48Mbp) by integrating short-read, long-read, and Hi-C sequencing platforms. A total of 36,796 protein-coding sequences, mainly located on 14 proto-chromosomes, were predicted. Additionally, two whole genome duplication (WGD) events were suggested to have occurred ~54.07 and ~35.06 million years ago (MYA), with Elaeagnaceae plants probably experiencing both WGD events. Furthermore, the long terminal retrotransposons in E. mollis were active ~0.23MYA, and one of them was inferred to insert into coding sequence of the negative regulatory lipid synthesis gene, EMF2. Through transcriptomic and metabonomic analysis, key genes contributing to the high lipid and vitamin E levels of E. mollis seeds were identified, while miRNA regulation was also considered. This comprehensive work on the E. mollis genome not only provides a solid theoretical foundation and experimental basis for the efficient utilization of seed lipids and vitamin E, but also contributes to the exploration of new genetic resources.
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Affiliation(s)
- Changle Li
- College of Forestry, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China
| | - Xianzhi Zhang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, China
| | - Weilong Gao
- College of Forestry, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China
| | - Shuoqing Liang
- College of Forestry, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China
| | - Shengshu Wang
- College of Forestry, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China
| | - Xueli Zhang
- College of Forestry, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China
| | - Jianxin Wang
- College of Forestry, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China
| | - Jia Yao
- College of Forestry, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China
| | - Yongquan Li
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, China.
| | - Yulin Liu
- College of Forestry, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China.
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2
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Liew LC, You Y, Auroux L, Oliva M, Peirats-Llobet M, Ng S, Tamiru-Oli M, Berkowitz O, Hong UVT, Haslem A, Stuart T, Ritchie ME, Bassel GW, Lister R, Whelan J, Gouil Q, Lewsey MG. Establishment of single-cell transcriptional states during seed germination. NATURE PLANTS 2024; 10:1418-1434. [PMID: 39256563 PMCID: PMC11410669 DOI: 10.1038/s41477-024-01771-3] [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: 01/19/2023] [Accepted: 07/25/2024] [Indexed: 09/12/2024]
Abstract
Germination involves highly dynamic transcriptional programs as the cells of seeds reactivate and express the functions necessary for establishment in the environment. Individual cell types have distinct roles within the embryo, so must therefore have cell type-specific gene expression and gene regulatory networks. We can better understand how the functions of different cell types are established and contribute to the embryo by determining how cell type-specific transcription begins and changes through germination. Here we describe a temporal analysis of the germinating Arabidopsis thaliana embryo at single-cell resolution. We define the highly dynamic cell type-specific patterns of gene expression and how these relate to changing cellular function as germination progresses. Underlying these are unique gene regulatory networks and transcription factor activity. We unexpectedly discover that most embryo cells transition through the same initial transcriptional state early in germination, even though cell identity has already been established during embryogenesis. Cells later transition to cell type-specific gene expression patterns. Furthermore, our analyses support previous findings that the earliest events leading to the induction of seed germination take place in the vasculature. Overall, our study constitutes a general framework with which to characterize Arabidopsis cell transcriptional states through seed germination, allowing investigation of different genotypes and other plant species whose seed strategies may differ.
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Affiliation(s)
- Lim Chee Liew
- La Trobe Institute for Sustainable Agriculture and Food, AgriBio, La Trobe University, Melbourne, Victoria, Australia
| | - Yue You
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lucas Auroux
- La Trobe Institute for Sustainable Agriculture and Food, AgriBio, La Trobe University, Melbourne, Victoria, Australia
| | - Marina Oliva
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Marta Peirats-Llobet
- La Trobe Institute for Sustainable Agriculture and Food, AgriBio, La Trobe University, Melbourne, Victoria, Australia
| | - Sophia Ng
- La Trobe Institute for Sustainable Agriculture and Food, AgriBio, La Trobe University, Melbourne, Victoria, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Melbourne, Victoria, Australia
| | - Muluneh Tamiru-Oli
- La Trobe Institute for Sustainable Agriculture and Food, AgriBio, La Trobe University, Melbourne, Victoria, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Melbourne, Victoria, Australia
| | - Oliver Berkowitz
- La Trobe Institute for Sustainable Agriculture and Food, AgriBio, La Trobe University, Melbourne, Victoria, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Melbourne, Victoria, Australia
| | - Uyen Vu Thuy Hong
- La Trobe Institute for Sustainable Agriculture and Food, AgriBio, La Trobe University, Melbourne, Victoria, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Melbourne, Victoria, Australia
| | - Asha Haslem
- La Trobe Institute for Sustainable Agriculture and Food, AgriBio, La Trobe University, Melbourne, Victoria, Australia
| | - Tim Stuart
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Matthew E Ritchie
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - George W Bassel
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - James Whelan
- La Trobe Institute for Sustainable Agriculture and Food, AgriBio, La Trobe University, Melbourne, Victoria, Australia.
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Melbourne, Victoria, Australia.
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building, La Trobe University, Melbourne, Victoria, Australia.
- College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China.
| | - Quentin Gouil
- La Trobe Institute for Sustainable Agriculture and Food, AgriBio, La Trobe University, Melbourne, Victoria, Australia.
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Mathew G Lewsey
- La Trobe Institute for Sustainable Agriculture and Food, AgriBio, La Trobe University, Melbourne, Victoria, Australia.
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Melbourne, Victoria, Australia.
- Australian Research Council Centre of Excellence in Plants for Space, AgriBio, La Trobe University, Melbourne, Victoria, Australia.
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3
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Oubohssaine M, Hnini M, Rabeh K. Exploring lipid signaling in plant physiology: From cellular membranes to environmental adaptation. JOURNAL OF PLANT PHYSIOLOGY 2024; 300:154295. [PMID: 38885581 DOI: 10.1016/j.jplph.2024.154295] [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: 02/15/2024] [Revised: 05/23/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024]
Abstract
Lipids have evolved as versatile signaling molecules that regulate a variety of physiological processes in plants. Convincing evidence highlights their critical role as mediators in a wide range of plant processes required for survival, growth, development, and responses to environmental conditions such as water availability, temperature changes, salt, pests, and diseases. Understanding lipid signaling as a critical process has helped us expand our understanding of plant biology by explaining how plants sense and respond to environmental cues. Lipid signaling pathways constitute a complex network of lipids, enzymes, and receptors that coordinate important cellular responses and stressing plant biology's changing and adaptable traits. Plant lipid signaling involves a wide range of lipid classes, including phospholipids, sphingolipids, oxylipins, and sterols, each of which contributes differently to cellular communication and control. These lipids function not only as structural components, but also as bioactive molecules that transfer signals. The mechanisms entail the production of lipid mediators and their detection by particular receptors, which frequently trigger downstream cascades that affect gene expression, cellular functions, and overall plant growth. This review looks into lipid signaling in plant physiology, giving an in-depth look and emphasizing its critical function as a master regulator of vital activities.
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Affiliation(s)
- Malika Oubohssaine
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, Rabat, 10000, Morocco.
| | - Mohamed Hnini
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, Rabat, 10000, Morocco
| | - Karim Rabeh
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, Rabat, 10000, Morocco
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4
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Go D, Lu B, Alizadeh M, Gazzarrini S, Song L. Voice from both sides: a molecular dialogue between transcriptional activators and repressors in seed-to-seedling transition and crop adaptation. FRONTIERS IN PLANT SCIENCE 2024; 15:1416216. [PMID: 39166233 PMCID: PMC11333834 DOI: 10.3389/fpls.2024.1416216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/20/2024] [Indexed: 08/22/2024]
Abstract
High-quality seeds provide valuable nutrients to human society and ensure successful seedling establishment. During maturation, seeds accumulate storage compounds that are required to sustain seedling growth during germination. This review focuses on the epigenetic repression of the embryonic and seed maturation programs in seedlings. We begin with an extensive overview of mutants affecting these processes, illustrating the roles of core proteins and accessory components in the epigenetic machinery by comparing mutants at both phenotypic and molecular levels. We highlight how omics assays help uncover target-specific functional specialization and coordination among various epigenetic mechanisms. Furthermore, we provide an in-depth discussion on the Seed dormancy 4 (Sdr4) transcriptional corepressor family, comparing and contrasting their regulation of seed germination in the dicotyledonous species Arabidopsis and two monocotyledonous crops, rice and wheat. Finally, we compare the similarities in the activation and repression of the embryonic and seed maturation programs through a shared set of cis-regulatory elements and discuss the challenges in applying knowledge largely gained in model species to crops.
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Affiliation(s)
- Dongeun Go
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Bailan Lu
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Milad Alizadeh
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Sonia Gazzarrini
- Department of Biological Science, University of Toronto Scarborough, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Liang Song
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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5
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Rolletschek H, Muszynska A, Schwender J, Radchuk V, Heinemann B, Hilo A, Plutenko I, Keil P, Ortleb S, Wagner S, Kalms L, Gündel A, Shi H, Fuchs J, Szymanski JJ, Braun HP, Borisjuk L. Mechanical forces orchestrate the metabolism of the developing oilseed rape embryo. THE NEW PHYTOLOGIST 2024. [PMID: 39044722 DOI: 10.1111/nph.19990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 06/18/2024] [Indexed: 07/25/2024]
Abstract
The initial free expansion of the embryo within a seed is at some point inhibited by its contact with the testa, resulting in its formation of folds and borders. Although less obvious, mechanical forces appear to trigger and accelerate seed maturation. However, the mechanistic basis for this effect remains unclear. Manipulation of the mechanical constraints affecting either the in vivo or in vitro growth of oilseed rape embryos was combined with analytical approaches, including magnetic resonance imaging and computer graphic reconstruction, immunolabelling, flow cytometry, transcriptomic, proteomic, lipidomic and metabolomic profiling. Our data implied that, in vivo, the imposition of mechanical restraints impeded the expansion of testa and endosperm, resulting in the embryo's deformation. An acceleration in embryonic development was implied by the cessation of cell proliferation and the stimulation of lipid and protein storage, characteristic of embryo maturation. The underlying molecular signature included elements of cell cycle control, reactive oxygen species metabolism and transcriptional reprogramming, along with allosteric control of glycolytic flux. Constricting the space allowed for the expansion of in vitro grown embryos induced a similar response. The conclusion is that the imposition of mechanical constraints over the growth of the developing oilseed rape embryo provides an important trigger for its maturation.
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Affiliation(s)
- Hardy Rolletschek
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - Aleksandra Muszynska
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
- Amatera Biosciences, 4 rue Pierre Fontaine, Evry, 91000, France
| | - Jörg Schwender
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Volodymyr Radchuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - Björn Heinemann
- Institut für Pflanzengenetik, Universität Hannover, Herrenhäuser Strasse, Hannover, 30419, Germany
| | - Alexander Hilo
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - Iaroslav Plutenko
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - Peter Keil
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - Stefan Ortleb
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - Steffen Wagner
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - Laura Kalms
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - André Gündel
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
- Department of Ecology, Environment and Plant Sciences, University of Stockholm, Stockholm, 10691, Sweden
| | - Hai Shi
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Jörg Fuchs
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
| | - Jedrzej Jakub Szymanski
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
- Institute of Bio- and Geosciences, IBG-4: Bioinformatics, Forschungszentrum Jülich, Jülich, D-52428, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-Universität Düsseldorf, Düsseldorf, 40225, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Universität Hannover, Herrenhäuser Strasse, Hannover, 30419, Germany
| | - Ljudmilla Borisjuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Seeland, OT Gatersleben, 06466, Germany
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6
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Gazzarrini S, Song L. LAFL Factors in Seed Development and Phase Transitions. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:459-488. [PMID: 38657282 DOI: 10.1146/annurev-arplant-070623-111458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Development is a chain reaction in which one event leads to another until the completion of a life cycle. Phase transitions are milestone events in the cycle of life. LEAFY COTYLEDON1 (LEC1), ABA INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2 proteins, collectively known as LAFL, are master transcription factors (TFs) regulating seed and other developmental processes. Since the initial characterization of the LAFL genes, more than three decades of active research has generated tremendous amounts of knowledge about these TFs, whose roles in seed development and germination have been comprehensively reviewed. Recent advances in cell biology with genetic and genomic tools have allowed the characterization of the LAFL regulatory networks in previously challenging tissues at a higher throughput and resolution in reference species and crops. In this review, we provide a holistic perspective by integrating advances at the epigenetic, transcriptional, posttranscriptional, and protein levels to exemplify the spatiotemporal regulation of the LAFL networks in Arabidopsis seed development and phase transitions, and we briefly discuss the evolution of these TF networks.
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Affiliation(s)
- Sonia Gazzarrini
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada;
| | - Liang Song
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada;
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7
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Chen J, Hu Y, Zhao T, Huang C, Chen J, He L, Dai F, Chen S, Wang L, Jin S, Zhang T. Comparative transcriptomic analysis provides insights into the genetic networks regulating oil differential production in oil crops. BMC Biol 2024; 22:110. [PMID: 38735918 PMCID: PMC11089805 DOI: 10.1186/s12915-024-01909-x] [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] [Accepted: 05/02/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Plants differ more than threefold in seed oil contents (SOCs). Soybean (Glycine max), cotton (Gossypium hirsutum), rapeseed (Brassica napus), and sesame (Sesamum indicum) are four important oil crops with markedly different SOCs and fatty acid compositions. RESULTS Compared to grain crops like maize and rice, expanded acyl-lipid metabolism genes and relatively higher expression levels of genes involved in seed oil synthesis (SOS) in the oil crops contributed to the oil accumulation in seeds. Here, we conducted comparative transcriptomics on oil crops with two different SOC materials. In common, DIHYDROLIPOAMIDE DEHYDROGENASE, STEAROYL-ACYL CARRIER PROTEIN DESATURASE, PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE, and oil-body protein genes were both differentially expressed between the high- and low-oil materials of each crop. By comparing functional components of SOS networks, we found that the strong correlations between genes in "glycolysis/gluconeogenesis" and "fatty acid synthesis" were conserved in both grain and oil crops, with PYRUVATE KINASE being the common factor affecting starch and lipid accumulation. Network alignment also found a conserved clique among oil crops affecting seed oil accumulation, which has been validated in Arabidopsis. Differently, secondary and protein metabolism affected oil synthesis to different degrees in different crops, and high SOC was due to less competition of the same precursors. The comparison of Arabidopsis mutants and wild type showed that CINNAMYL ALCOHOL DEHYDROGENASE 9, the conserved regulator we identified, was a factor resulting in different relative contents of lignins to oil in seeds. The interconnection of lipids and proteins was common but in different ways among crops, which partly led to differential oil production. CONCLUSIONS This study goes beyond the observations made in studies of individual species to provide new insights into which genes and networks may be fundamental to seed oil accumulation from a multispecies perspective.
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Affiliation(s)
- Jinwen Chen
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Yan Hu
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
- Hainan Institute of Zhejiang University, Sanya, 572025, Hainan, China
| | - Ting Zhao
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Chujun Huang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Jiani Chen
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Lu He
- Hainan Institute of Zhejiang University, Sanya, 572025, Hainan, China
| | - Fan Dai
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Shuqi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Luyao Wang
- Hainan Institute of Zhejiang University, Sanya, 572025, Hainan, China
| | - Shangkun Jin
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Tianzhen Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China.
- Hainan Institute of Zhejiang University, Sanya, 572025, Hainan, China.
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8
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Ranjan R, Srijan S, Balekuttira S, Agarwal T, Ramey M, Dobbins M, Kuhn R, Wang X, Hudson K, Li Y, Varala K. Organ-delimited gene regulatory networks provide high accuracy in candidate transcription factor selection across diverse processes. Proc Natl Acad Sci U S A 2024; 121:e2322751121. [PMID: 38652750 PMCID: PMC11066984 DOI: 10.1073/pnas.2322751121] [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: 01/04/2024] [Accepted: 03/14/2024] [Indexed: 04/25/2024] Open
Abstract
Organ-specific gene expression datasets that include hundreds to thousands of experiments allow the reconstruction of organ-level gene regulatory networks (GRNs). However, creating such datasets is greatly hampered by the requirements of extensive and tedious manual curation. Here, we trained a supervised classification model that can accurately classify the organ-of-origin for a plant transcriptome. This K-Nearest Neighbor-based multiclass classifier was used to create organ-specific gene expression datasets for the leaf, root, shoot, flower, and seed in Arabidopsis thaliana. A GRN inference approach was used to determine the: i. influential transcription factors (TFs) in each organ and, ii. most influential TFs for specific biological processes in that organ. These genome-wide, organ-delimited GRNs (OD-GRNs), recalled many known regulators of organ development and processes operating in those organs. Importantly, many previously unknown TF regulators were uncovered as potential regulators of these processes. As a proof-of-concept, we focused on experimentally validating the predicted TF regulators of lipid biosynthesis in seeds, an important food and biofuel trait. Of the top 20 predicted TFs, eight are known regulators of seed oil content, e.g., WRI1, LEC1, FUS3. Importantly, we validated our prediction of MybS2, TGA4, SPL12, AGL18, and DiV2 as regulators of seed lipid biosynthesis. We elucidated the molecular mechanism of MybS2 and show that it induces purple acid phosphatase family genes and lipid synthesis genes to enhance seed lipid content. This general approach has the potential to be extended to any species with sufficiently large gene expression datasets to find unique regulators of any trait-of-interest.
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Affiliation(s)
- Rajeev Ranjan
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN47907
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
| | - Sonali Srijan
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN47907
| | - Somaiah Balekuttira
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN47907
| | - Tina Agarwal
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN47907
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
| | - Melissa Ramey
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN47907
| | - Madison Dobbins
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN47907
| | - Rachel Kuhn
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN47907
| | - Xiaojin Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN47907
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
| | - Karen Hudson
- United States Department of Agriculture-Agricultural Research Service Crop Production and Pest Control Research Unit, West Lafayette, IN47907
| | - Ying Li
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN47907
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
| | - Kranthi Varala
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN47907
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
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9
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Hembach L, Niemeyer PW, Schmitt K, Zegers JMS, Scholz P, Brandt D, Dabisch JJ, Valerius O, Braus GH, Schwarzländer M, de Vries J, Rensing SA, Ischebeck T. Proteome plasticity during Physcomitrium patens spore germination - from the desiccated phase to heterotrophic growth and reconstitution of photoautotrophy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1466-1486. [PMID: 38059656 DOI: 10.1111/tpj.16574] [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: 08/07/2023] [Revised: 11/13/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023]
Abstract
The establishment of moss spores is considered a milestone in plant evolution. They harbor protein networks underpinning desiccation tolerance and accumulation of storage compounds that can be found already in algae and that are also utilized in seeds and pollen. Furthermore, germinating spores must produce proteins that drive the transition through heterotrophic growth to the autotrophic plant. To get insight into the plasticity of this proteome, we investigated it at five timepoints of moss (Physcomitrium patens) spore germination and in protonemata and gametophores. The comparison to previously published Arabidopsis proteome data of seedling establishment showed that not only the proteomes of spores and seeds are functionally related, but also the proteomes of germinating spores and young seedlings. We observed similarities with regard to desiccation tolerance, lipid droplet proteome composition, control of dormancy, and β-oxidation and the glyoxylate cycle. However, there were also striking differences. For example, spores lacked any obvious storage proteins. Furthermore, we did not detect homologs to the main triacylglycerol lipase in Arabidopsis seeds, SUGAR DEPENDENT1. Instead, we discovered a triacylglycerol lipase of the oil body lipase family and a lipoxygenase as being the overall most abundant proteins in spores. This finding indicates an alternative pathway for triacylglycerol degradation via oxylipin intermediates in the moss. The comparison of spores to Nicotiana tabacum pollen indicated similarities for example in regards to resistance to desiccation and hypoxia, but the overall developmental pattern did not align as in the case of seedling establishment and spore germination.
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Affiliation(s)
- Lea Hembach
- Green Biotechnology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
| | - Philipp W Niemeyer
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
| | - Kerstin Schmitt
- Department for Molecular Microbiology and Genetics, Genetics and Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Institute for Microbiology, University of Göttingen, 37077, Göttingen, Germany
| | - Jaccoline M S Zegers
- Department of Applied Bioinformatics, Göttingen Center for Molecular Biosciences (GZMB) and Campus Institute Data Science (CIDAS), Institute for Microbiology and Genetics, University of Göttingen, 37077, Göttingen, Germany
| | - Patricia Scholz
- Laboratoire Reproduction et Développement des Plantes (RDP), UCB Lyon 1, CNRS, INRAE, Université de Lyon, ENS de Lyon, Lyon, France
| | - Dennis Brandt
- Plant Energy Biology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
| | - Janis J Dabisch
- Green Biotechnology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
| | - Oliver Valerius
- Department for Molecular Microbiology and Genetics, Genetics and Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Institute for Microbiology, University of Göttingen, 37077, Göttingen, Germany
| | - Gerhard H Braus
- Department for Molecular Microbiology and Genetics, Genetics and Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Institute for Microbiology, University of Göttingen, 37077, Göttingen, Germany
| | - Markus Schwarzländer
- Plant Energy Biology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Göttingen Center for Molecular Biosciences (GZMB) and Campus Institute Data Science (CIDAS), Institute for Microbiology and Genetics, University of Göttingen, 37077, Göttingen, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Till Ischebeck
- Green Biotechnology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
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10
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Li H, Yu K, Zhang Z, Yu Y, Wan J, He H, Fan C. Targeted mutagenesis of flavonoid biosynthesis pathway genes reveals functional divergence in seed coat colour, oil content and fatty acid composition in Brassica napus L. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:445-459. [PMID: 37856327 PMCID: PMC10826991 DOI: 10.1111/pbi.14197] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/08/2023] [Accepted: 09/23/2023] [Indexed: 10/21/2023]
Abstract
Yellow-seed is widely accepted as a good-quality trait in Brassica crops. Previous studies have shown that the flavonoid biosynthesis pathway is essential for the development of seed colour, but its function in Brassica napus, an important oil crop, is poorly understood. To systematically explore the gene functions of the flavonoid biosynthesis pathway in rapeseed, several representative TRANSPARENT TESTA (TT) genes, including three structural genes (BnaTT7, BnaTT18, BnaTT10), two regulatory genes (BnaTT1, BnaTT2) and a transporter (BnaTT12), were selected for targeted mutation by CRISPR/Cas9 in the present study. Seed coat colour, lignin content, seed quality and yield-related traits were investigated in these Bnatt mutants together with Bnatt8 generated previously. These Bnatt mutants produced seeds with an elevated seed oil content and decreased pigment and lignin accumulation in the seed coat without any serious defects in the yield-related traits. In addition, the fatty acid (FA) composition was also altered to different degrees, i.e., decreased oleic acid and increased linoleic acid and α-linolenic acid, in all Bnatt mutants except Bnatt18. Furthermore, gene expression analysis revealed that most of BnaTT mutations resulted in the down-regulation of key genes related to flavonoid and lignin synthesis, and the up-regulation of key genes related to lipid synthesis and oil body formation, which may contribute to the phenotype. Collectively, our study generated valuable resources for breeding programs, and more importantly demonstrated the functional divergence and overlap of flavonoid biosynthesis pathway genes in seed coat colour, oil content and FA composition of rapeseed.
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Affiliation(s)
- Huailin Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Hubei Hongshan LaboratoryWuhanHubeiChina
| | - Kaidi Yu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Hubei Hongshan LaboratoryWuhanHubeiChina
| | - Zilu Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Hubei Hongshan LaboratoryWuhanHubeiChina
| | - Yalun Yu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Hubei Hongshan LaboratoryWuhanHubeiChina
| | - Jiakai Wan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Hubei Hongshan LaboratoryWuhanHubeiChina
| | - Hanzi He
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Hubei Hongshan LaboratoryWuhanHubeiChina
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Hubei Hongshan LaboratoryWuhanHubeiChina
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11
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Yue D, Hao X, Han B, Xu J, Sun W, Guo X, Zhang X, Yang X. GhL1L1 regulates the contents of unsaturated fatty acids by activating the expression of GhFAD2 genes in cotton. Gene 2024; 893:147899. [PMID: 37839764 DOI: 10.1016/j.gene.2023.147899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/02/2023] [Accepted: 10/12/2023] [Indexed: 10/17/2023]
Abstract
Edible oils with high unsaturated fatty acids, particularly oleic acid, are beneficial to human health. Cotton is one of the top five oil crops in the world, but the mechanism of high-quality oil synthesis and regulatory networks in cotton are largely unclear. Here, we identified Leafy cotyledon1-like 1 (GhL1L1), a NF-YB subfamily gene that is specifically expressed during somatic embryogenesis and seed maturation in cotton. Overexpression of GhL1L1 regulates the contents of unsaturated fatty acids in cotton, especially in the seeds, which is associated with altered expression of the cotton fatty acid biosynthesis-related genes. GhL1L1 synergistically enhanced the expression of GhFAD2-1A by binding to the G-box in its promoter, leading to an increase in the content of linoleic acid. Furthermore, this activation could be enhanced by GhNF-YC2 and GhNF-YA1 by form a transcriptional complex. Collectively, these results contribute to provide new insights into the molecular mechanism of oil biosynthesis in cotton and can facilitate genetic manipulation of cotton varieties with enhanced oil content.
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Affiliation(s)
- Dandan Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Xuyang Hao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Bei Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Jiao Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Resource Institute for Chinese Medicine and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang 550000, Guizhou, China.
| | - Weinan Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Xiaoping Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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12
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Smolikova G, Krylova E, Petřík I, Vilis P, Vikhorev A, Strygina K, Strnad M, Frolov A, Khlestkina E, Medvedev S. Involvement of Abscisic Acid in Transition of Pea ( Pisum sativum L.) Seeds from Germination to Post-Germination Stages. PLANTS (BASEL, SWITZERLAND) 2024; 13:206. [PMID: 38256760 PMCID: PMC10819913 DOI: 10.3390/plants13020206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/30/2023] [Accepted: 01/07/2024] [Indexed: 01/24/2024]
Abstract
The transition from seed to seedling represents a critical developmental step in the life cycle of higher plants, dramatically affecting plant ontogenesis and stress tolerance. The release from dormancy to acquiring germination ability is defined by a balance of phytohormones, with the substantial contribution of abscisic acid (ABA), which inhibits germination. We studied the embryonic axis of Pisum sativum L. before and after radicle protrusion. Our previous work compared RNA sequencing-based transcriptomics in the embryonic axis isolated before and after radicle protrusion. The current study aims to analyze ABA-dependent gene regulation during the transition of the embryonic axis from the germination to post-germination stages. First, we determined the levels of abscisates (ABA, phaseic acid, dihydrophaseic acid, and neo-phaseic acid) using ultra-high-performance liquid chromatography-tandem mass spectrometry. Second, we made a detailed annotation of ABA-associated genes using RNA sequencing-based transcriptome profiling. Finally, we analyzed the DNA methylation patterns in the promoters of the PsABI3, PsABI4, and PsABI5 genes. We showed that changes in the abscisate profile are characterized by the accumulation of ABA catabolites, and the ABA-related gene profile is accompanied by the upregulation of genes controlling seedling development and the downregulation of genes controlling water deprivation. The expression of ABI3, ABI4, and ABI5, which encode crucial transcription factors during late maturation, was downregulated by more than 20-fold, and their promoters exhibited high levels of methylation already at the late germination stage. Thus, although ABA remains important, other regulators seems to be involved in the transition from seed to seedling.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.K.); (S.M.)
| | - Ekaterina Krylova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.K.); (S.M.)
- Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190000 St. Petersburg, Russia;
| | - Ivan Petřík
- Laboratory of Growth Regulators, The Czech Academy of Sciences, Institute of Experimental Botany & Palacky University, Faculty of Science, Slechtitelu 27, CZ-78371 Olomouc, Czech Republic; (I.P.); (M.S.)
| | - Polina Vilis
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.K.); (S.M.)
| | - Aleksander Vikhorev
- School of Advanced Engineering Studies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | | | - Miroslav Strnad
- Laboratory of Growth Regulators, The Czech Academy of Sciences, Institute of Experimental Botany & Palacky University, Faculty of Science, Slechtitelu 27, CZ-78371 Olomouc, Czech Republic; (I.P.); (M.S.)
| | - Andrej Frolov
- Laboratory of Analytical Biochemistry and Biotechnology, K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia;
| | - Elena Khlestkina
- Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190000 St. Petersburg, Russia;
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.K.); (S.M.)
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13
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Zhang L, Liu L, Li H, He J, Chao H, Yan S, Yin Y, Zhao W, Li M. 3D genome structural variations play important roles in regulating seed oil content of Brassica napus. PLANT COMMUNICATIONS 2024; 5:100666. [PMID: 37496273 PMCID: PMC10811347 DOI: 10.1016/j.xplc.2023.100666] [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: 03/06/2023] [Revised: 07/01/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023]
Abstract
Dissecting the complex regulatory mechanism of seed oil content (SOC) is one of the main research goals in Brassica napus. Increasing evidence suggests that genome architecture is linked to multiple biological functions. However, the effect of genome architecture on SOC regulation remains unclear. Here, we used high-throughput chromatin conformation capture to characterize differences in the three-dimensional (3D) landscape of genome architecture of seeds from two B. napus lines, N53-2 (with high SOC) and Ken-C8 (with low SOC). Bioinformatics analysis demonstrated that differentially accessible regions and differentially expressed genes between N53-2 and Ken-C8 were preferentially enriched in regions with quantitative trait loci (QTLs)/associated genomic regions (AGRs) for SOC. A multi-omics analysis demonstrated that expression of SOC-related genes was tightly correlated with genome structural variations in QTLs/AGRs of B. napus. The candidate gene BnaA09g48250D, which showed structural variation in a QTL/AGR on chrA09, was identified by fine-mapping of a KN double-haploid population derived from hybridization of N53-2 and Ken-C8. Overexpression and knockout of BnaA09g48250D led to significant increases and decreases in SOC, respectively, in the transgenic lines. Taken together, our results reveal the 3D genome architecture of B. napus seeds and the roles of genome structural variations in SOC regulation, enriching our understanding of the molecular mechanisms of SOC regulation from the perspective of spatial chromatin structure.
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Affiliation(s)
- Libin Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Lin Liu
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan 430075, China
| | - Huaixin Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Jianjie He
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Hongbo Chao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shuxiang Yan
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Yontai Yin
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Weiguo Zhao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China.
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14
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Wu D, Zhang K, Li CY, Xie GW, Lu MT, Qian Y, Shu YP, Shen Q. Genome-wide comprehensive characterization and transcriptomic analysis of AP2/ERF gene family revealed its role in seed oil and ALA formation in perilla (Perilla frutescens). Gene 2023; 889:147808. [PMID: 37722611 DOI: 10.1016/j.gene.2023.147808] [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: 07/05/2023] [Revised: 09/06/2023] [Accepted: 09/15/2023] [Indexed: 09/20/2023]
Abstract
Perilla (Perilla frutescens) is a potential specific oilseed crop with an extremely high α-linolenic acid (ALA) content in its seeds. AP2/ERF transcription factors (TFs) play important roles in multiple biological processes. However, limited information is known about the regulatory mechanism of the AP2/ERF family in perilla's oil accumulation. In this research, we identified 212 AP2/ERF family members in the genome of perilla, and their domain characteristics, collinearity, and sub-genome differentiation were comprehensively analyzed. Transcriptome sequencing revealed that genes encoding key enzymes involved in oil biosynthesis (e.g., ACCs, KASII, GPAT, PDAT and LPAAT) were up-regulated in the high-oil variety. Moreover, the endoplasmic reticulum-localized FAD2 and FAD3 were significantly up-regulated in the high-ALA variety. To investigate the roles of AP2/ERFs in lipid biosynthesis, we conducted a correlation analysis between non-redundant AP2/ERFs and key lipid metabolism genes using WGCNA. A significant correlation was found between 36 AP2/ERFs and 90 lipid metabolism genes. Among them, 12 AP2/ERFs were identified as hub genes and showed significant correlation with lipid synthase genes (e.g., FADs, GPAT and ACSL) and key regulatory TFs (e.g., LEC2, IAA, MYB, UPL3). Furthermore, gene expression analysis identified three AP2/ERFs (WRI, ABI4, and RAVI) potentially playing an important role in the regulation of oil accumulation in perilla. Our study suggests that PfAP2/ERFs are important regulatory TFs in the lipid biosynthesis pathway, providing a foundation for the molecular understanding of oil accumulation in perilla and other oilseed crops.
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Affiliation(s)
- Duan Wu
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Ke Zhang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Chun-Yu Li
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Guan-Wen Xie
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Ming-Ting Lu
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Yong Qian
- Shanghai Standard Technology Co., Ltd, Building 25, 15 Gudan Road, Pudong, Shanghai 201314, China.
| | - Ya-Ping Shu
- Shanghai Standard Technology Co., Ltd, Building 25, 15 Gudan Road, Pudong, Shanghai 201314, China.
| | - Qi Shen
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
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15
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Tang M, Zhao G, Awais M, Gao X, Meng W, Lin J, Zhao B, Lai Z, Lin Y, Chen Y. Genome-Wide Identification and Expression Analysis Reveals the B3 Superfamily Involved in Embryogenesis and Hormone Responses in Dimocarpus longan Lour. Int J Mol Sci 2023; 25:127. [PMID: 38203301 PMCID: PMC10779397 DOI: 10.3390/ijms25010127] [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: 10/25/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
B3 family transcription factors play an essential regulatory role in plant growth and development processes. This study performed a comprehensive analysis of the B3 family transcription factor in longan (Dimocarpus longan Lour.), and a total of 75 DlB3 genes were identified. DlB3 genes were unevenly distributed on the 15 chromosomes of longan. Based on the protein domain similarities and functional diversities, the DlB3 family was further clustered into four subgroups (ARF, RAV, LAV, and REM). Bioinformatics and comparative analyses of B3 superfamily expression were conducted in different light and with different temperatures and tissues, and early somatic embryogenesis (SE) revealed its specific expression profile and potential biological functions during longan early SE. The qRT-PCR results indicated that DlB3 family members played a crucial role in longan SE and zygotic embryo development. Exogenous treatments of 2,4-D (2,4-dichlorophenoxyacetic acid), NPA (N-1-naphthylphthalamic acid), and PP333 (paclobutrazol) could significantly inhibit the expression of the DlB3 family. Supplementary ABA (abscisic acid), IAA (indole-3-acetic acid), and GA3 (gibberellin) suppressed the expressions of DlLEC2, DlARF16, DlTEM1, DlVAL2, and DlREM40, but DlFUS3, DlARF5, and DlREM9 showed an opposite trend. Furthermore, subcellular localization indicated that DlLEC2 and DlFUS3 were located in the nucleus, suggesting that they played a role in the nucleus. Therefore, DlB3s might be involved in complex plant hormone signal transduction pathways during longan SE and zygotic embryo development.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.T.); (G.Z.); (M.A.); (X.G.); (W.M.); (J.L.); (B.Z.); (Z.L.)
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.T.); (G.Z.); (M.A.); (X.G.); (W.M.); (J.L.); (B.Z.); (Z.L.)
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16
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Bu M, Fan W, Li R, He B, Cui P. Lipid Metabolism and Improvement in Oilseed Crops: Recent Advances in Multi-Omics Studies. Metabolites 2023; 13:1170. [PMID: 38132852 PMCID: PMC10744971 DOI: 10.3390/metabo13121170] [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: 10/27/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023] Open
Abstract
Oilseed crops are rich in plant lipids that not only provide essential fatty acids for the human diet but also play important roles as major sources of biofuels and indispensable raw materials for the chemical industry. The regulation of lipid metabolism genes is a major factor affecting oil production. In this review, we systematically summarize the metabolic pathways related to lipid production and storage in plants and highlight key research advances in characterizing the genes and regulatory factors influencing lipid anabolic metabolism. In addition, we integrate the latest results from multi-omics studies on lipid metabolism to provide a reference to better understand the molecular mechanisms underlying oil anabolism in oilseed crops.
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Affiliation(s)
- Mengjia Bu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Fan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ruonan Li
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Bing He
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Peng Cui
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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17
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Klajn N, Kapczyńska K, Pasikowski P, Glazińska P, Kugiel H, Kęsy J, Wojciechowski W. Regulatory Effects of ABA and GA on the Expression of Conglutin Genes and LAFL Network Genes in Yellow Lupine ( Lupinus luteus L.) Seeds. Int J Mol Sci 2023; 24:12380. [PMID: 37569754 PMCID: PMC10418516 DOI: 10.3390/ijms241512380] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
The maturation of seeds is a process of particular importance both for the plant itself by assuring the survival of the species and for the human population for nutritional and economic reasons. Controlling this process requires a strict coordination of many factors at different levels of the functioning of genetic and hormonal changes as well as cellular organization. One of the most important examples is the transcriptional activity of the LAFL gene regulatory network, which includes LEAFY COTYLEDON1 (LEC1) and LEC1-LIKE (L1L) and ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2 (LEAFY COTYLEDON2), as well as hormonal homeostasis-of abscisic acid (ABA) and gibberellins (GA) in particular. From the nutritional point of view, the key to seed development is the ability of seeds to accumulate large amounts of proteins with different structures and properties. The world's food deficit is mainly related to shortages of protein, and taking into consideration the environmental changes occurring on Earth, it is becoming necessary to search for a way to obtain large amounts of plant-derived protein while maintaining the diversity of its origin. Yellow lupin, whose storage proteins are conglutins, is one of the plant species native to Europe that accumulates large amounts of this nutrient in its seeds. In this article we have shown the key changes occurring in the developing seeds of the yellow-lupin cultivar Taper by means of modern molecular biology techniques, including RNA-seq, chromatographic techniques and quantitative PCR analysis. We identified regulatory genes fundamental to the seed-filling process, as well as genes encoding conglutins. We also investigated how exogenous application of ABA and GA3 affects the expression of LlLEC2, LlABI3, LlFUS3, and genes encoding β- and δ-conglutins and whether it results in the amount of accumulated seed storage proteins. The research shows that for each species, even related plants, very specific changes can be identified. Thus the analysis and possibility of using such an approach to improve and stabilize yields requires even more detailed and extended research.
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Affiliation(s)
- Natalia Klajn
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland; (P.G.); (J.K.)
| | - Katarzyna Kapczyńska
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland;
| | - Paweł Pasikowski
- Life Sciences and Biotechnology Center, Łukasiewicz Research Network–PORT Polish Center for Technology Development, Stabłowicka 147, 54-066 Wroclaw, Poland;
- Captor Therapeutics S.A., Duńska 11, 54-427 Wroclaw, Poland
| | - Paulina Glazińska
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland; (P.G.); (J.K.)
| | - Hubert Kugiel
- LABcenter Life Agro Biotechnology Ltd., Gliniana 14, 97-300 Piotrków Trybunalski, Poland; (H.K.); (W.W.)
| | - Jacek Kęsy
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland; (P.G.); (J.K.)
| | - Waldemar Wojciechowski
- LABcenter Life Agro Biotechnology Ltd., Gliniana 14, 97-300 Piotrków Trybunalski, Poland; (H.K.); (W.W.)
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Zhai Z, Blanford JK, Cai Y, Sun J, Liu H, Shi H, Schwender J, Shanklin J. CYCLIN-DEPENDENT KINASE 8 positively regulates oil synthesis by activating WRINKLED1 transcription. THE NEW PHYTOLOGIST 2023; 238:724-736. [PMID: 36683527 DOI: 10.1111/nph.18764] [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: 10/31/2022] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
CYCLIN-DEPENDENT KINASE 8 (CDK8), a component of the kinase module of the Mediator complex in Arabidopsis, is involved in many processes, including flowering, plant defense, drought, and energy stress responses. Here, we investigated cdk8 mutants and CDK8-overexpressing lines to evaluate whether CDK8 also plays a role in regulating lipid synthesis, an energy-demanding anabolism. Quantitative lipid analysis demonstrated significant reductions in lipid synthesis rates and lipid accumulation in developing siliques and seedlings of cdk8, and conversely, elevated lipid contents in wild-type seed overexpressing CDK8. Transactivation assays show that CDK8 is necessary for maximal transactivation of the master seed oil activator WRINKLED1 (WRI1) by the seed maturation transcription factor ABSCISIC ACID INSENSITIVE3, supporting a direct regulatory role of CDK8 in oil synthesis. Thermophoretic studies show GEMINIVIRUS REP INTERACTING KINASE1, an activating kinase of KIN10 (a catalytic subunit of SUCROSE NON-FERMENTING1-RELATED KINASE1), physically interacts with CDK8, resulting in its phosphorylation and degradation in the presence of KIN10. This work defines a mechanism whereby, once activated, KIN10 downregulates WRI1 expression and suppresses lipid synthesis via promoting the degradation of CDK8. The KIN10-CDK8-dependent regulation of lipid synthesis described herein is additional to our previously reported KIN10-dependent phosphorylation and degradation of WRI1.
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Affiliation(s)
- Zhiyang Zhai
- Department of Biology, Brookhaven National Laboratory, Building 463, 50 Bell Ave, Upton, NY, 11973, USA
| | - Jantana K Blanford
- Department of Biology, Brookhaven National Laboratory, Building 463, 50 Bell Ave, Upton, NY, 11973, USA
| | - Yingqi Cai
- Department of Biology, Brookhaven National Laboratory, Building 463, 50 Bell Ave, Upton, NY, 11973, USA
| | - Jing Sun
- Department of Biology, Brookhaven National Laboratory, Building 463, 50 Bell Ave, Upton, NY, 11973, USA
| | - Hui Liu
- Department of Biology, Brookhaven National Laboratory, Building 463, 50 Bell Ave, Upton, NY, 11973, USA
| | - Hai Shi
- Department of Biology, Brookhaven National Laboratory, Building 463, 50 Bell Ave, Upton, NY, 11973, USA
| | - Jorg Schwender
- Department of Biology, Brookhaven National Laboratory, Building 463, 50 Bell Ave, Upton, NY, 11973, USA
| | - John Shanklin
- Department of Biology, Brookhaven National Laboratory, Building 463, 50 Bell Ave, Upton, NY, 11973, USA
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19
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Sagun JV, Yadav UP, Alonso AP. Progress in understanding and improving oil content and quality in seeds. FRONTIERS IN PLANT SCIENCE 2023; 14:1116894. [PMID: 36778708 PMCID: PMC9909563 DOI: 10.3389/fpls.2023.1116894] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
The world's population is projected to increase by two billion by 2050, resulting in food and energy insecurity. Oilseed crops have been identified as key to address these challenges: they produce and store lipids in the seeds as triacylglycerols that can serve as a source of food/feed, renewable fuels, and other industrially-relevant chemicals. Therefore, improving seed oil content and composition has generated immense interest. Research efforts aiming to unravel the regulatory pathways involved in fatty acid synthesis and to identify targets for metabolic engineering have made tremendous progress. This review provides a summary of the current knowledge of oil metabolism and discusses how photochemical activity and unconventional pathways can contribute to high carbon conversion efficiency in seeds. It also highlights the importance of 13C-metabolic flux analysis as a tool to gain insights on the pathways that regulate oil biosynthesis in seeds. Finally, a list of key genes and regulators that have been recently targeted to enhance seed oil production are reviewed and additional possible targets in the metabolic pathways are proposed to achieve desirable oil content and quality.
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Affiliation(s)
| | | | - Ana Paula Alonso
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
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Zhang C, Ren H, Yao X, Wang K, Chang J, Shao W. Metabolomics and Transcriptomics Analyses Reveal Regulatory Networks Associated with Fatty Acid Accumulation in Pecan Kernels. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:16010-16020. [PMID: 36472227 DOI: 10.1021/acs.jafc.2c06947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Pecans are a globally important tree nut crop. Pecan nuts are rich in fatty acids (FAs), proteins, and flavonoids in addition to thiamine and numerous micronutrients. Although several of these nutriments have been studied in this plant, the comprehensive metabolite variations and molecular mechanisms associated with them have not been fully elucidated. In this study, untargeted metabolomics and transcriptomics were integrated to reveal the metabolite accumulation patterns and their associated molecular mechanisms during pecan kernel development. In total, 4260 (under positive mode) and 2726 (under negative mode) high quality features were retained. Overall, 163 differentially accumulated metabolites were identified. Most components were classified into the categories "organic acids and derivatives" and "lipids and lipid-like molecules." The accumulation patterns of amino acids, FAs, carbohydrates, organic acids, vitamins, flavonoids, and phenylpropanoids alongside embryo development were determined. Furthermore, transcriptomes from four pecan kernel developmental stages were used to assess transcript expression levels. Coexpression analyses were performed between FAs and their related genes. This study provides a comprehensive overview of the metabolic changes and regulations during pecan kernel development. We believe that the identification of nutriment accumulation trends and hub genes associated with the biosynthesis of the components will be valuable for genetically improving this plant.
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Affiliation(s)
- Chengcai Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang District, Hangzhou, Zhejiang Province 311400, China
| | - Huadong Ren
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang District, Hangzhou, Zhejiang Province 311400, China
| | - Xiaohua Yao
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang District, Hangzhou, Zhejiang Province 311400, China
| | - Kailiang Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang District, Hangzhou, Zhejiang Province 311400, China
| | - Jun Chang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang District, Hangzhou, Zhejiang Province 311400, China
| | - Weizhong Shao
- Forestry Bureau of Jiande, Jiande, Zhejiang Province 311600, China
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21
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Yang Y, Kong Q, Lim ARQ, Lu S, Zhao H, Guo L, Yuan L, Ma W. Transcriptional regulation of oil biosynthesis in seed plants: Current understanding, applications, and perspectives. PLANT COMMUNICATIONS 2022; 3:100328. [PMID: 35605194 PMCID: PMC9482985 DOI: 10.1016/j.xplc.2022.100328] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/28/2022] [Accepted: 04/14/2022] [Indexed: 05/11/2023]
Abstract
Plants produce and accumulate triacylglycerol (TAG) in their seeds as an energy reservoir to support the processes of seed germination and seedling development. Plant seed oils are vital not only for the human diet but also as renewable feedstocks for industrial use. TAG biosynthesis consists of two major steps: de novo fatty acid biosynthesis in the plastids and TAG assembly in the endoplasmic reticulum. The latest advances in unraveling transcriptional regulation have shed light on the molecular mechanisms of plant oil biosynthesis. We summarize recent progress in understanding the regulatory mechanisms of well-characterized and newly discovered transcription factors and other types of regulators that control plant fatty acid biosynthesis. The emerging picture shows that plant oil biosynthesis responds to developmental and environmental cues that stimulate a network of interacting transcriptional activators and repressors, which in turn fine-tune the spatiotemporal regulation of the pathway genes.
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Affiliation(s)
- Yuzhou Yang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Que Kong
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Audrey R Q Lim
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Ling Yuan
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
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