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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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2
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Zhang WJ, Tang LP, Peng J, Zhai LM, Ma QL, Zhang XS, Su YH. A WRI1-dependent module is essential for the accumulation of auxin and lipid in somatic embryogenesis of Arabidopsis thaliana. THE NEW PHYTOLOGIST 2024; 242:1098-1112. [PMID: 38515249 DOI: 10.1111/nph.19689] [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: 11/21/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024]
Abstract
The potential for totipotency exists in all plant cells; however, the underlying mechanisms remain largely unknown. Earlier findings have revealed that the overexpression of LEAFY COTYLEDON 2 (LEC2) can directly trigger the formation of somatic embryos on the cotyledons of Arabidopsis. Furthermore, cotyledon cells that overexpress LEC2 accumulate significant lipid reserves typically found in seeds. The precise mechanisms and functions governing lipid accumulation in this process remain unexplored. In this study, we demonstrate that WRINKLED1 (WRI1), the key regulator of lipid biosynthesis, is essential for somatic embryo formation, suggesting that WRI1-mediated lipid biosynthesis plays a crucial role in the transition from vegetative to embryonic development. Our findings indicate a direct interaction between WRI1 and LEC2, which enhances the enrichment of LEC2 at downstream target genes and stimulates their induction. Besides, our data suggest that WRI1 forms a complex with LEC1, LEC2, and FUSCA3 (FUS3) to facilitate the accumulation of auxin and lipid for the somatic embryo induction, through strengthening the activation of YUCCA4 (YUC4) and OLEOSIN3 (OLE3) genes. Our results uncover a regulatory module controlled by WRI1, crucial for somatic embryogenesis. These findings provide valuable insights into our understanding of plant cell totipotency.
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Affiliation(s)
- Wen Jie Zhang
- National Key Laboratory of Wheat Improvement, College of Life Science, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Li Ping Tang
- National Key Laboratory of Wheat Improvement, College of Life Science, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Jing Peng
- National Key Laboratory of Wheat Improvement, College of Life Science, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Li Ming Zhai
- National Key Laboratory of Wheat Improvement, College of Life Science, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Qiu Li Ma
- National Key Laboratory of Wheat Improvement, College of Life Science, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xian Sheng Zhang
- National Key Laboratory of Wheat Improvement, College of Life Science, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Ying Hua Su
- National Key Laboratory of Wheat Improvement, College of Life Science, Shandong Agricultural University, Tai'an, Shandong, 271018, China
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3
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Thakro V, Varshney N, Malik N, Daware A, Srivastava R, Mohanty JK, Basu U, Narnoliya L, Jha UC, Tripathi S, Tyagi AK, Parida SK. Functional allele of a MATE gene selected during domestication modulates seed color in chickpea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:53-71. [PMID: 37738381 DOI: 10.1111/tpj.16469] [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: 05/17/2023] [Revised: 08/14/2023] [Accepted: 08/29/2023] [Indexed: 09/24/2023]
Abstract
Seed color is one of the key target traits of domestication and artificial selection in chickpeas due to its implications on consumer preference and market value. The complex seed color trait has been well dissected in several crop species; however, the genetic mechanism underlying seed color variation in chickpea remains poorly understood. Here, we employed an integrated genomics strategy involving QTL mapping, high-density mapping, map-based cloning, association analysis, and molecular haplotyping in an inter-specific RIL mapping population, association panel, wild accessions, and introgression lines (ILs) of Cicer gene pool. This delineated a MATE gene, CaMATE23, encoding a Transparent Testa (TT) and its natural allele (8-bp insertion) and haplotype underlying a major QTL governing seed color on chickpea chromosome 4. Signatures of selective sweep and a strong purifying selection reflected that CaMATE23, especially its 8-bp insertion natural allelic variant, underwent selection during chickpea domestication. Functional investigations revealed that the 8-bp insertion containing the third cis-regulatory RY-motif element in the CaMATE23 promoter is critical for enhanced binding of CaFUSCA3 transcription factor, a key regulator of seed development and flavonoid biosynthesis, thereby affecting CaMATE23 expression and proanthocyanidin (PA) accumulation in the seed coat to impart varied seed color in chickpea. Consequently, overexpression of CaMATE23 in Arabidopsis tt12 mutant partially restored the seed color phenotype to brown pigmentation, ascertaining its functional role in PA accumulation in the seed coat. These findings shed new light on the seed color regulation and evolutionary history, and highlight the transcriptional regulation of CaMATE23 by CaFUSCA3 in modulating seed color in chickpea. The functionally relevant InDel variation, natural allele, and haplotype from CaMATE23 are vital for translational genomic research, including marker-assisted breeding, for developing chickpea cultivars with desirable seed color that appeal to consumers and meet global market demand.
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Affiliation(s)
- Virevol Thakro
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Nidhi Varshney
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Malik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, 303002, India
| | - Anurag Daware
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rishi Srivastava
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Mohanty
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Udita Basu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Laxmi Narnoliya
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | - Shailesh Tripathi
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
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4
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Otani M, Zheng L, Kawakami N. Genetic, Epigenetic, and Environmental Control of Seed Dormancy and Germination. Methods Mol Biol 2024; 2830:3-12. [PMID: 38977563 DOI: 10.1007/978-1-0716-3965-8_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] [Indexed: 07/10/2024]
Abstract
Seed germination is controlled by a combination of the seed dormancy level and environmental conditions such as light, temperature, moisture, and nitrate levels. Seed dormancy is programed genetically, but it is also sensitive to maternal environmental conditions before and after anthesis. Recent developments in molecular genetics and bioinformatics have greatly enhanced our understanding of the molecular mechanisms of seed dormancy and germination in model plants and economically important crop species. This chapter focuses on temperature as an environmental factor and discusses the genetic and epigenetic mechanisms of dormancy and germination.
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Affiliation(s)
- Masahiko Otani
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
- Organization for the Strategic Coordination of Research and Intellectual Properties, Meiji University, Kawasaki, Japan
| | - Lipeng Zheng
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, China
| | - Naoto Kawakami
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan.
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Yao S, Kim SC, Li J, Tang S, Wang X. Phosphatidic acid signaling and function in nuclei. Prog Lipid Res 2024; 93:101267. [PMID: 38154743 PMCID: PMC10843600 DOI: 10.1016/j.plipres.2023.101267] [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: 10/18/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 12/30/2023]
Abstract
Membrane lipidomes are dynamic and their changes generate lipid mediators affecting various biological processes. Phosphatidic acid (PA) has emerged as an important class of lipid mediators involved in a wide range of cellular and physiological responses in plants, animals, and microbes. The regulatory functions of PA have been studied primarily outside the nuclei, but an increasing number of recent studies indicates that some of the PA effects result from its action in nuclei. PA levels in nuclei are dynamic in response to stimuli. Changes in nuclear PA levels can result from activities of enzymes associated with nuclei and/or from movements of PA generated extranuclearly. PA has also been found to interact with proteins involved in nuclear functions, such as transcription factors and proteins undergoing nuclear translocation in response to stimuli. The nuclear action of PA affects various aspects of plant growth, development, and response to stress and environmental changes.
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Affiliation(s)
- Shuaibing Yao
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Sang-Chul Kim
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Jianwu Li
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Shan Tang
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Xuemin Wang
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
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Guo F, Wang H, Lian G, Cai G, Liu W, Zhang H, Li D, Zhou C, Han N, Zhu M, Su Y, Seo PJ, Xu L, Bian H. Initiation of scutellum-derived callus is regulated by an embryo-like developmental pathway in rice. Commun Biol 2023; 6:457. [PMID: 37100819 PMCID: PMC10130139 DOI: 10.1038/s42003-023-04835-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
In rice (Oryza sativa) tissue culture, callus can be induced from the scutellum in embryo or from the vasculature of non-embryonic organs such as leaves, nodes, or roots. Here we show that the auxin signaling pathway triggers cell division in the epidermis of the scutellum to form an embryo-like structure, which leads to callus formation. Our transcriptome data show that embryo-, stem cell-, and auxin-related genes are upregulated during scutellum-derived callus initiation. Among those genes, the embryo-specific gene OsLEC1 is activated by auxin and involved in scutellum-derived callus initiation. However, OsLEC1 is not required for vasculature-derived callus initiation from roots. In addition, OsIAA11 and OsCRL1, which are involved in root development, are required for vasculature-derived callus formation but not for scutellum-derived callus formation. Overall, our data indicate that scutellum-derived callus initiation is regulated by an embryo-like development program, and this is different from vasculature-derived callus initiation which borrows a root development program.
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Affiliation(s)
- Fu Guo
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
- Yazhou Bay Seed Laboratory, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, China
| | - Hua Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Guiwei Lian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Gui Cai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Haidao Zhang
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Dandan Li
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
| | - Chun Zhou
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ning Han
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Muyuan Zhu
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yinghua Su
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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Liu S, Liu Z, Hou X, Li X. Genetic mapping and functional genomics of soybean seed protein. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:29. [PMID: 37313523 PMCID: PMC10248706 DOI: 10.1007/s11032-023-01373-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/25/2023] [Indexed: 06/15/2023]
Abstract
Soybean is an utterly important crop for high-quality meal protein and vegetative oil. Soybean seed protein content has become a key factor in nutrients for livestock feed as well as human dietary consumption. Genetic improvement of soybean seed protein is highly desired to meet the demands of rapidly growing world population. Molecular mapping and genomic analysis in soybean have identified many quantitative trait loci (QTL) underlying seed protein content control. Exploring the mechanisms of seed storage protein regulation will be helpful to achieve the improvement of protein content. However, the practice of breeding higher protein soybean is challenging because soybean seed protein is negatively correlated with seed oil content and yield. To overcome the limitation of such inverse relationship, deeper insights into the property and genetic control of seed protein are required. Recent advances of soybean genomics have strongly enhanced the understandings for molecular mechanisms of soybean with better seed quality. Here, we review the research progress in the genetic characteristics of soybean storage protein, and up-to-date advances of molecular mappings and genomics of soybean protein. The key factors underlying the mechanisms of the negative correlation between protein and oil in soybean seeds are elaborated. We also briefly discuss the future prospects of breaking the bottleneck of the negative correlation to develop high protein soybean without penalty of oil and yield. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01373-5.
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Affiliation(s)
- Shu Liu
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhaojun Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 China
| | - Xingliang Hou
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025 China
| | - Xiaoming Li
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025 China
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Khanday I, Santos-Medellín C, Sundaresan V. Somatic embryo initiation by rice BABY BOOM1 involves activation of zygote-expressed auxin biosynthesis genes. THE NEW PHYTOLOGIST 2023; 238:673-687. [PMID: 36707918 DOI: 10.1111/nph.18774] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 01/12/2023] [Indexed: 05/02/2023]
Abstract
Plant embryogenesis results from the fusion of male and female gametes but can also be induced in somatic cells. The molecular pathways for embryo initiation are poorly understood, especially in monocots. In rice, the male gamete expressed BABY BOOM1 (OsBBM1) transcription factor functions as an embryogenic trigger in the zygote and can also promote somatic embryogenesis when ectopically expressed in somatic tissues. We used gene editing, transcriptome profiling, and chromatin immunoprecipitation to determine the molecular players involved in embryo initiation downstream of OsBBM1. We identify OsYUCCA (OsYUC) auxin biosynthesis genes as direct targets of OsBBM1. Unexpectedly, these OsYUC targets in zygotes are expressed only from the maternal genome, whereas the paternal genome exclusively provides functional OsBBM1 to initiate embryogenesis. Induction of somatic embryogenesis by exogenous auxin requires OsBBM genes and downstream OsYUC targets. Ectopic OsBBM1 initiates somatic embryogenesis without exogenous auxins but requires functional OsYUC genes. Thus, an OsBBM-OsYUC module is a key player for both somatic and zygotic embryogenesis in rice. Zygotic embryo initiation involves a partnership of male and female genomes, through which paternal OsBBM1 activates maternal OsYUC genes. In somatic embryogenesis, exogenous auxin triggers OsBBM1 expression, which then activates endogenous auxin biosynthesis OsYUC genes.
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Affiliation(s)
- Imtiyaz Khanday
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
| | | | - Venkatesan Sundaresan
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
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Awada R, Lepelley M, Breton D, Charpagne A, Campa C, Berry V, Georget F, Breitler JC, Léran S, Djerrab D, Martinez-Seidel F, Descombes P, Crouzillat D, Bertrand B, Etienne H. Global transcriptome profiling reveals differential regulatory, metabolic and hormonal networks during somatic embryogenesis in Coffea arabica. BMC Genomics 2023; 24:41. [PMID: 36694132 PMCID: PMC9875526 DOI: 10.1186/s12864-022-09098-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/22/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) is one of the most promising processes for large-scale dissemination of elite varieties. However, for many plant species, optimizing SE protocols still relies on a trial and error approach. We report the first global scale transcriptome profiling performed at all developmental stages of SE in coffee to unravel the mechanisms that regulate cell fate and totipotency. RESULTS RNA-seq of 48 samples (12 developmental stages × 4 biological replicates) generated 90 million high quality reads per sample, approximately 74% of which were uniquely mapped to the Arabica genome. First, the statistical analysis of transcript data clearly grouped SE developmental stages into seven important phases (Leaf, Dedifferentiation, Primary callus, Embryogenic callus, Embryogenic cell clusters, Redifferentiation and Embryo) enabling the identification of six key developmental phase switches, which are strategic for the overall biological efficiency of embryo regeneration. Differential gene expression and functional analysis showed that genes encoding transcription factors, stress-related genes, metabolism-related genes and hormone signaling-related genes were significantly enriched. Second, the standard environmental drivers used to control SE, i.e. light, growth regulators and cell density, were clearly perceived at the molecular level at different developmental stages. Third, expression profiles of auxin-related genes, transcription factor-related genes and secondary metabolism-related genes were analyzed during SE. Gene co-expression networks were also inferred. Auxin-related genes were upregulated during dedifferentiation and redifferentiation while transcription factor-related genes were switched on from the embryogenic callus and onward. Secondary metabolism-related genes were switched off during dedifferentiation and switched back on at the onset of redifferentiation. Secondary metabolites and endogenous IAA content were tightly linked with their respective gene expression. Lastly, comparing Arabica embryogenic and non-embryogenic cell transcriptomes enabled the identification of biological processes involved in the acquisition of embryogenic capacity. CONCLUSIONS The present analysis showed that transcript fingerprints are discriminating signatures of cell fate and are under the direct influence of environmental drivers. A total of 23 molecular candidates were successfully identified overall the 12 developmental stages and can be tested in many plant species to optimize SE protocols in a rational way.
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Affiliation(s)
- Rayan Awada
- Nestlé Research - Plant Science Research Unit, Tours, France ,grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Maud Lepelley
- Nestlé Research - Plant Science Research Unit, Tours, France
| | - David Breton
- Nestlé Research - Plant Science Research Unit, Tours, France
| | - Aline Charpagne
- grid.419905.00000 0001 0066 4948Nestlé Research, Société Des Produits Nestlé SA, Lausanne, Switzerland ,grid.511382.c0000 0004 7595 5223Sophia Genetics, Genève, Switzerland
| | - Claudine Campa
- grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France ,grid.4399.70000000122879528UMR DIADE, IRD, Montpellier, France
| | - Victoria Berry
- Nestlé Research - Plant Science Research Unit, Tours, France
| | - Frédéric Georget
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Jean-Christophe Breitler
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Sophie Léran
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Doâa Djerrab
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Federico Martinez-Seidel
- grid.418390.70000 0004 0491 976XMax Planck Institute for Molecular Plant Physiology, Golm, Germany ,grid.1008.90000 0001 2179 088XSchool of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Patrick Descombes
- grid.419905.00000 0001 0066 4948Nestlé Research, Société Des Produits Nestlé SA, Lausanne, Switzerland
| | | | - Benoît Bertrand
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Hervé Etienne
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
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10
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Guo J, Liu H, Dai K, Yuan X, Guo P, Shi W, Zhou M. Identification of Brachypodium distachyon B3 genes reveals that BdB3-54 regulates primary root growth. FRONTIERS IN PLANT SCIENCE 2022; 13:1050171. [PMID: 36438129 PMCID: PMC9686306 DOI: 10.3389/fpls.2022.1050171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
B3 is a class of plant-specific transcription factors with important roles in plant development and growth. Here, we identified 69 B3 transcription factors in Brachypodium distachyon that were unevenly distributed across all five chromosomes. The ARF, REM, LAV, and RAV subfamilies were grouped based on sequence characteristics and phylogenetic relationships. The phylogenetically related members in the B3 family shared conserved domains and gene structures. Expression profiles showed that B3 genes were widely expressed in different tissues and varied in response to different abiotic stresses. BdB3-54 protein from the REM subfamily was located in the nucleus by subcellular localization and processed transcriptional activation activity. Overexpression of BdB3-54 in Arabidopsis increased primary root length. Our study provides a basis for further research on the functions of BdB3 genes.
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Affiliation(s)
- Jie Guo
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Hanxiao Liu
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Keli Dai
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Xiangyang Yuan
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Pingyi Guo
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Weiping Shi
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Meixue Zhou
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS, Australia
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11
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Král D, Šenkyřík JB, Ondřej V. Expression of Genes Involved in ABA and Auxin Metabolism and LEA Gene during Embryogenesis in Hemp. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212995. [PMID: 36365448 PMCID: PMC9657790 DOI: 10.3390/plants11212995] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 05/14/2023]
Abstract
The level of phytohormones such as abscisic acid (ABA) and auxins (Aux) changes dynamically during embryogenesis. Knowledge of the transcriptional activity of the genes of their metabolic pathways is essential for a deeper understanding of embryogenesis itself; however, it could also help breeding programs of important plants, such as Cannabis sativa, attractive for the pharmaceutical, textile, cosmetic, and food industries. This work aimed to find out how genes of metabolic pathways of Aux (IAA-1, IAA-2, X15-1, X15-2) and ABA (PP2C-1) alongside one member of the LEA gene family (CanLea34) are expressed in embryos depending on the developmental stage and the embryo cultivation in vitro. Walking stick (WS) and mature (M) cultivated and uncultivated embryos of C. sativa cultivars 'KC Dora' and 'USO 31' were analyzed. The RT-qPCR results indicated that for the development of immature (VH) embryos, the genes (IAA-1, IAA-2) are likely to be fundamental. Only an increased expression of the CanLea34 gene was characteristic of the fully maturated (M) embryos. In addition, this feature was significantly increased by cultivation. In conclusion, the cultivation led to the upsurge of expression of all studied genes.
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12
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Wu T, Alizadeh M, Lu B, Cheng J, Hoy R, Bu M, Laqua E, Tang D, He J, Go D, Gong Z, Song L. The transcriptional co-repressor SEED DORMANCY 4-LIKE (AtSDR4L) promotes the embryonic-to-vegetative transition in Arabidopsis thaliana. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2075-2096. [PMID: 36083579 DOI: 10.1111/jipb.13360] [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] [Received: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Repression of embryonic traits during the seed-to-seedling phase transition requires the inactivation of master transcription factors associated with embryogenesis. How the timing of such inactivation is controlled is unclear. Here, we report on a novel transcriptional co-repressor, Arabidopsis thaliana SDR4L, that forms a feedback inhibition loop with the master transcription factors LEC1 and ABI3 to repress embryonic traits post-imbibition. LEC1 and ABI3 regulate their own expression by inducing AtSDR4L during mid to late embryogenesis. AtSDR4L binds to sites upstream of LEC1 and ABI4, and these transcripts are upregulated in Atsdr4l seedlings. Atsdr4l seedlings phenocopy a LEC1 overexpressor. The embryonic traits of Atsdr4l can be partially rescued by impairing LEC1 or ABI3. The penetrance and expressivity of the Atsdr4l phenotypes depend on both developmental and external cues, demonstrating the importance of AtSDR4L in seedling establishment under suboptimal conditions.
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Affiliation(s)
- Ting Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Science, China Agricultural University, Beijing, 100193, China
| | - Milad Alizadeh
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Bailan Lu
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Jinkui Cheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Science, China Agricultural University, Beijing, 100193, China
| | - Ryan Hoy
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Miaoyu Bu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Science, China Agricultural University, Beijing, 100193, China
| | - Emma Laqua
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Dongxue Tang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Science, China Agricultural University, Beijing, 100193, China
| | - Junna He
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Science, China Agricultural University, Beijing, 100193, China
| | - Dongeun Go
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Science, China Agricultural University, Beijing, 100193, China
| | - Liang Song
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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13
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Zheng L, Otani M, Kanno Y, Seo M, Yoshitake Y, Yoshimoto K, Sugimoto K, Kawakami N. Seed dormancy 4 like1 of Arabidopsis is a key regulator of phase transition from embryo to vegetative development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:460-475. [PMID: 36036886 DOI: 10.1111/tpj.15959] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Seed dormancy is an adaptive trait that enables plants to survive adverse conditions and restart growth in a season and location suitable for vegetative and reproductive growth. Control of seed dormancy is also important for crop production and food quality because it can help induce uniform germination and prevent preharvest sprouting. Rice preharvest sprouting quantitative trait locus analysis has identified Seed dormancy 4 (Sdr4) as a positive regulator of dormancy development. Here, we analyzed the loss-of-function mutant of the Arabidopsis ortholog, Sdr4 Like1 (SFL1), and found that the sfl1-1 seeds showed precocious germination at the mid- to late-maturation stage similar to rice sdr4 mutant, but converted to become more dormant than the wild type during maturation drying. Coordinated with the dormancy levels, expression levels of the seed maturation and dormancy master regulator genes, ABI3, FUS3, and DOG1 in sfl1-1 seeds were lower than in wild type at early- and mid-maturation stages, but higher at the late-maturation stage. In addition to the seed dormancy phenotype, sfl1-1 seedlings showed a growth arrest phenotype and heterochronic expression of LAFL (LEC1, ABI3, FUS3, LEC2) and DOG1 in the seedlings. These data suggest that SFL1 is a positive regulator of initiation and termination of the seed dormancy program. We also found genetic interaction between SFL1 and the SFL2, SFL3, and SFL4 paralogs of SFL1, which impacts on the timing of the phase transition from embryo maturation to seedling growth.
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Affiliation(s)
- Lipeng Zheng
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Masahiko Otani
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Yuri Kanno
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yushi Yoshitake
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Kohki Yoshimoto
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Kazuhiko Sugimoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Naoto Kawakami
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
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14
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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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15
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Chen C, Du X. LEAFY COTYLEDONs: Connecting different stages of plant development. FRONTIERS IN PLANT SCIENCE 2022; 13:916831. [PMID: 36119568 PMCID: PMC9470955 DOI: 10.3389/fpls.2022.916831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The life of higher plants progresses successively through embryonic, juvenile, adult, and reproductive stages. LEAFY COTYLEDON (LEC) transcription factors, first discovered in Arabidopsis thaliana several decades ago, play a key role in regulating plant embryonic development, seed maturation, and subsequent growth. Existing studies have demonstrated that LECs together with other transcription factors form a huge and complex regulatory network to regulate many aspects of plant growth and development and respond to environmental stresses. Here, we focus on the role that has received little attention about the LECs linking different developmental stages and generational cycles in plants. We summarize the current fragmented research progress on the LECs role and molecular mechanism in connecting embryonic and vegetative growth periods and the reproductive stage. Furthermore, the possibility of LECs controlling the maintenance and transition of plant growth stages through epigenetic modifications is discussed.
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16
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Park ME, Kim HU. Applications and prospects of genome editing in plant fatty acid and triacylglycerol biosynthesis. FRONTIERS IN PLANT SCIENCE 2022; 13:969844. [PMID: 36119569 PMCID: PMC9471015 DOI: 10.3389/fpls.2022.969844] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/08/2022] [Indexed: 05/29/2023]
Abstract
Triacylglycerol (TAG), which is a neutral lipid, has a structure in which three molecules of fatty acid (FA) are ester-bonded to one molecule of glycerol. TAG is important energy source for seed germination and seedling development in plants. Depending on the FA composition of the TAG, it is used as an edible oil or industrial material for cosmetics, soap, and lubricant. As the demand for plant oil is rising worldwide, either the type of FA must be changed or the total oil content of various plants must be increased. In this review, we discuss the regulation of FA metabolism by Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, a recent genome-editing technology applicable to various plants. The development of plants with higher levels of oleic acid or lower levels of very long-chain fatty acids (VLCFAs) in seeds are discussed. In addition, the current status of research on acyltransferases, phospholipases, TAG lipases, and TAG synthesis in vegetative tissues is described. Finally, strategies for the application of CRISPR/Cas9 in lipid metabolism studies are mentioned.
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Affiliation(s)
- Mid-Eum Park
- Department of Molecular Biology, Sejong University, Seoul, South Korea
| | - Hyun Uk Kim
- Department of Molecular Biology, Sejong University, Seoul, South Korea
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, South Korea
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17
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Song J, Mavraganis I, Shen W, Yang H, Cram D, Xiang D, Patterson N, Zou J. Transcriptome dissection of candidate genes associated with lentil seed quality traits. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:815-826. [PMID: 35395134 DOI: 10.1111/plb.13426] [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: 01/11/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Lentils provide a rich plant-based protein source and staple food in many parts of the world. Despite numerous nutritional benefits, lentil seeds also possess undesirable elements, such as anti-nutritional factors. Understanding the genetic networks of seed metabolism is of great importance for improving the seed nutritional profile. We applied RNA sequencing analysis to survey the transcriptome of developing lentil seeds and compared this with that of the pod shells and leaves. In total, we identified 2622 genes differentially expressed among the tissues examined. Genes preferentially expressed in seeds were enriched in the Gene Ontology (GO) terms associated with development, nitrogen and carbon (N/C) metabolism and lipid synthesis. We further categorized seed preferentially expressed genes based on their involvement in storage protein production, starch accumulation, lipid and suberin metabolism, phytate, saponin and phenylpropanoid biosynthesis. The availability of transcript profile datasets on lentil seed metabolism and a roadmap of candidate genes presented here will be of great value for breeding strategies towards further improvement of lentil seed quality traits.
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Affiliation(s)
- J Song
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - I Mavraganis
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - W Shen
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - H Yang
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - D Cram
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - D Xiang
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - N Patterson
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - J Zou
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
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18
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Long Y, Yang Y, Pan G, Shen Y. New Insights Into Tissue Culture Plant-Regeneration Mechanisms. FRONTIERS IN PLANT SCIENCE 2022; 13:926752. [PMID: 35845646 PMCID: PMC9280033 DOI: 10.3389/fpls.2022.926752] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 05/31/2022] [Indexed: 05/08/2023]
Abstract
Plant regeneration occurs when plants repair or replace damaged structures based on the totipotency and pluripotency of their cells. Tissue culture is one of the most widely used regenerative technologies. Recently, a series of breakthroughs were made in the study of plant regeneration. This review summarizes two regenerative pathways in tissue culture: somatic embryogenesis and de novo organogenesis. Furthermore, we review the environmental factors influencing plant regeneration from explant sources, basal culture medium, plant growth regulators, and light/dark treatment. Additionally, we analyse the molecular mechanisms underlying two pathways. This knowledge will promote an understanding of the fundamental principles of plant regeneration from precursor cells and lay a solid foundation for applying plant micropropagation and genetic modification.
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Affiliation(s)
- Yun Long
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, China
| | - Yun Yang
- Nanchong Academy of Agricultural Sciences, Nanchong, China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
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19
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Rakpenthai A, Apodiakou A, Whitcomb SJ, Hoefgen R. In silico analysis of cis-elements and identification of transcription factors putatively involved in the regulation of the OAS cluster genes SDI1 and SDI2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1286-1304. [PMID: 35315155 DOI: 10.1111/tpj.15735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 02/09/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Arabidopsis thaliana sulfur deficiency-induced 1 and sulfur deficiency-induced 2 (SDI1 and SDI2) are involved in partitioning sulfur among metabolite pools during sulfur deficiency, and their transcript levels strongly increase in this condition. However, little is currently known about the cis- and trans-factors that regulate SDI expression. We aimed at identifying DNA sequence elements (cis-elements) and transcription factors (TFs) involved in regulating expression of the SDI genes. We performed in silico analysis of their promoter sequences cataloging known cis-elements and identifying conserved sequence motifs. We screened by yeast-one-hybrid an arrayed library of Arabidopsis TFs for binding to the SDI1 and SDI2 promoters. In total, 14 candidate TFs were identified. Direct association between particular cis-elements in the proximal SDI promoter regions and specific TFs was established via electrophoretic mobility shift assays: sulfur limitation 1 (SLIM1) was shown to bind SURE cis-element(s), the basic domain/leucine zipper (bZIP) core cis-element was shown to be important for HY5-homolog (HYH) binding, and G-box binding factor 1 (GBF1) was shown to bind the E box. Functional analysis of GBF1 and HYH using mutant and over-expressing lines indicated that these TFs promote a higher transcript level of SDI1 in vivo. Additionally, we performed a meta-analysis of expression changes of the 14 TF candidates in a variety of conditions that alter SDI expression. The presented results expand our understanding of sulfur pool regulation by SDI genes.
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Affiliation(s)
- Apidet Rakpenthai
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Anastasia Apodiakou
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Sarah J Whitcomb
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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20
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Nam JW, Lee HG, Do H, Kim HU, Seo PJ. Transcriptional regulation of triacylglycerol accumulation in plants under environmental stress conditions. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2905-2917. [PMID: 35560201 DOI: 10.1093/jxb/erab554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/15/2021] [Indexed: 06/15/2023]
Abstract
Triacylglycerol (TAG), a major energy reserve in lipid form, accumulates mainly in seeds. Although TAG concentrations are usually low in vegetative tissues because of the repression of seed maturation programs, these programs are derepressed upon the exposure of vegetative tissues to environmental stresses. Metabolic reprogramming of TAG accumulation is driven primarily by transcriptional regulation. A substantial proportion of transcription factors regulating seed TAG biosynthesis also participates in stress-induced TAG accumulation in vegetative tissues. TAG accumulation leads to the formation of lipid droplets and plastoglobules, which play important roles in plant tolerance to environmental stresses. Toxic lipid intermediates generated from environmental-stress-induced lipid membrane degradation are captured by TAG-containing lipid droplets and plastoglobules. This review summarizes recent advances in the transcriptional control of metabolic reprogramming underlying stress-induced TAG accumulation, and provides biological insight into the plant adaptive strategy, linking TAG biosynthesis with plant survival.
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Affiliation(s)
- Jeong-Won Nam
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Hong Gil Lee
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Hyungju Do
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, South Korea
| | - Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, South Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
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21
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Guo F, Zhang P, Wu Y, Lian G, Yang Z, Liu W, Buerte B, Zhou C, Zhang W, Li D, Han N, Tong Z, Zhu M, Xu L, Chen M, Bian H. Rice LEAFY COTYLEDON1 Hinders Embryo Greening During the Seed Development. FRONTIERS IN PLANT SCIENCE 2022; 13:887980. [PMID: 35620685 PMCID: PMC9128838 DOI: 10.3389/fpls.2022.887980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
LEAFY COTYLEDON1 (LEC1) is the central regulator of seed development in Arabidopsis, while its function in monocots is largely elusive. We generated Oslec1 mutants using CRISPR/Cas9 technology. Oslec1 mutant seeds lost desiccation tolerance and triggered embryo greening at the early development stage. Transcriptome analysis demonstrated that Oslec1 mutation altered diverse hormonal pathways and stress response in seed maturation, and promoted a series of photosynthesis-related genes. Further, genome-wide identification of OsLEC1-binding sites demonstrated that OsLEC1 bound to genes involved in photosynthesis, photomorphogenesis, as well as abscisic acid (ABA) and gibberellin (GA) pathways, involved in seed maturation. We illustrated an OsLEC1-regulating gene network during seed development, including the interconnection between photosynthesis and ABA/GA biosynthesis/signaling. Our findings suggested that OsLEC1 acts as not only a central regulator of seed maturation but also an inhibitor of embryo greening during rice seed development. This study would provide new understanding for the OsLEC1 regulatory mechanisms on photosynthesis in the monocot seed development.
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Affiliation(s)
- Fu Guo
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
| | - Peijing Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Centre, Hangzhou, China
| | - Yan Wu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Guiwei Lian
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhengfei Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - B. Buerte
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chun Zhou
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wenqian Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Dandan Li
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
| | - Ning Han
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zaikang Tong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, China
| | - Muyuan Zhu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hongwu Bian
- College of Life Sciences, Zhejiang University, Hangzhou, China
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22
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Yang Z, Liu X, Wang K, Li Z, Jia Q, Zhao C, Zhang M. ABA-INSENSITIVE 3 with or without FUSCA3 highly up-regulates lipid droplet proteins and activates oil accumulation. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2077-2092. [PMID: 34849730 DOI: 10.1093/jxb/erab524] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 11/26/2021] [Indexed: 05/25/2023]
Abstract
ABA-INSENSITIVE 3 (ABI3) has long been known for activation of storage protein accumulation. A role of ABI3 on oil accumulation was previously suggested based on a decrease of oil content in seeds of abi3 mutant. However, this conclusion could not exclude possibilities of indirect or pleiotropic effects, such as through mutual regulatory interactions with FUSCA3 (FUS3), an activator of oil accumulation. To identify that ABI3 functions independent of the effects of related seed transcription factors, we expressed ABI3 under the control of an inducible promoter in tobacco BY2 cells and Arabidopsis rosette leaves. Inducible expression of ABI3 activated oil accumulation in these non-seed cells, demonstrating a general role of ABI3 in regulation of oil biosynthesis. Further expressing ABI3 in rosette leaves of fus3 knockout mutant still caused up to 3-fold greater triacylglycerol accumulation, indicating ABI3 can activate lipid accumulation independently of FUS3. Transcriptome analysis revealed that LIPID DROPLET PROTEIN (LDP) genes, including OLEOSINs and CALEOSINs, were up-regulated up to 1000-fold by ABI3 in the absence of FUS3, while the expression of WRINKLED1 was doubled. Taken together, our results provide genetic evidence that ABI3 activates oil accumulation with or without FUS3, most likely through up-regulating LDPs and WRINKLED1.
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Affiliation(s)
- Zheng Yang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiangling Liu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Kai Wang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhuowei Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Qingli Jia
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Cuizhu Zhao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Meng Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
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23
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Chen Q, Zhang J, Li G. Dynamic epigenetic modifications in plant sugar signal transduction. TRENDS IN PLANT SCIENCE 2022; 27:379-390. [PMID: 34865981 DOI: 10.1016/j.tplants.2021.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/28/2021] [Accepted: 10/22/2021] [Indexed: 05/21/2023]
Abstract
In eukaryotes, dynamic chromatin states are closely related to changes in gene expression. Epigenetic modifications help plants adapt to their ever-changing environment by modulating gene expression via covalent modification at specific sites on DNA or histones. Sugars provide energy, but also function as signaling molecules to control plant growth and development. Various epigenetic modifications participate in sensing and transmitting sugar signals. Here we summarize recent progress in uncovering the epigenetic mechanisms involved in sugar signal transduction, including histone acetylation and deacetylation, histone methylation and demethylation, and DNA methylation. We also highlight changes in chromatin marks when crosstalk occurs between sugar signaling and the light, temperature, and phytohormone signaling pathways, and describe potential questions and approaches for future research.
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Affiliation(s)
- Qingshuai Chen
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, Shandong, China; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Jing Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China.
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24
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Maren NA, Duan H, Da K, Yencho GC, Ranney TG, Liu W. Genotype-independent plant transformation. HORTICULTURE RESEARCH 2022; 9:uhac047. [PMID: 35531314 PMCID: PMC9070643 DOI: 10.1093/hr/uhac047] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/11/2022] [Indexed: 05/26/2023]
Abstract
Plant transformation and regeneration remain highly species- and genotype-dependent. Conventional hormone-based plant regeneration via somatic embryogenesis or organogenesis is tedious, time-consuming, and requires specialized skills and experience. Over the last 40 years, significant advances have been made to elucidate the molecular mechanisms underlying embryogenesis and organogenesis. These pioneering studies have led to a better understanding of the key steps and factors involved in plant regeneration, resulting in the identification of crucial growth and developmental regulatory genes that can dramatically improve regeneration efficiency, shorten transformation time, and make transformation of recalcitrant genotypes possible. Co-opting these regulatory genes offers great potential to develop innovative genotype-independent genetic transformation methods for various plant species, including specialty crops. Further developing these approaches has the potential to result in plant transformation without the use of hormones, antibiotics, selectable marker genes, or tissue culture. As an enabling technology, the use of these regulatory genes has great potential to enable the application of advanced breeding technologies such as genetic engineering and gene editing for crop improvement in transformation-recalcitrant crops and cultivars. This review will discuss the recent advances in the use of regulatory genes in plant transformation and regeneration, and their potential to facilitate genotype-independent plant transformation and regeneration.
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Affiliation(s)
- Nathan A Maren
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27607, USA
| | - Hui Duan
- USDA-ARS, U.S. National Arboretum, Floral and Nursery Plants Research Unit, Beltsville Agricultural Research Center (BARC)-West, Beltsville, MD 20705, USA
| | - Kedong Da
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27607, USA
| | - G Craig Yencho
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27607, USA
| | - Thomas G Ranney
- Mountain Crop Improvement Lab, Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, NC 28759, USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27607, USA
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25
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Yin PP, Tang LP, Zhang XS, Su YH. Options for Engineering Apomixis in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:864987. [PMID: 35371148 PMCID: PMC8967160 DOI: 10.3389/fpls.2022.864987] [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: 01/29/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
In plants, embryogenesis and reproduction are not strictly dependent on fertilization. Several species can produce embryos in seeds asexually, a process known as apomixis. Apomixis is defined as clonal asexual reproduction through seeds, whereby the progeny is identical to the maternal genotype, and provides valuable opportunities for developing superior cultivars, as its induction in agricultural crops can facilitate the development and maintenance of elite hybrid genotypes. In this review, we summarize the current understanding of apomixis and highlight the successful introduction of apomixis methods into sexual crops. In addition, we discuss several genes whose overexpression can induce somatic embryogenesis as candidate genes to induce parthenogenesis, a unique reproductive method of gametophytic apomixis. We also summarize three schemes to achieve engineered apomixis, which will offer more opportunities for the realization of apomictic reproduction.
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Affiliation(s)
| | | | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai' an, China
| | - Ying Hua Su
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai' an, China
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26
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Molecular Aspects of Seed Development Controlled by Gibberellins and Abscisic Acids. Int J Mol Sci 2022; 23:ijms23031876. [PMID: 35163798 PMCID: PMC8837179 DOI: 10.3390/ijms23031876] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 11/16/2022] Open
Abstract
Plants have evolved seeds to permit the survival and dispersion of their lineages by providing nutrition for embryo growth and resistance to unfavorable environmental conditions. Seed formation is a complicated process that can be roughly divided into embryogenesis and the maturation phase, characterized by accumulation of storage compound, acquisition of desiccation tolerance, arrest of growth, and acquisition of dormancy. Concerted regulation of several signaling pathways, including hormonal and metabolic signals and gene networks, is required to accomplish seed formation. Recent studies have identified the major network of genes and hormonal signals in seed development, mainly in maturation. Gibberellin (GA) and abscisic acids (ABA) are recognized as the main hormones that antagonistically regulate seed development and germination. Especially, knowledge of the molecular mechanism of ABA regulation of seed maturation, including regulation of dormancy, accumulation of storage compounds, and desiccation tolerance, has been accumulated. However, the function of ABA and GA during embryogenesis still remains elusive. In this review, we summarize the current understanding of the sophisticated molecular networks of genes and signaling of GA and ABA in the regulation of seed development from embryogenesis to maturation.
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27
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Elhiti M, Stasolla C. Transduction of Signals during Somatic Embryogenesis. PLANTS (BASEL, SWITZERLAND) 2022; 11:178. [PMID: 35050066 PMCID: PMC8779037 DOI: 10.3390/plants11020178] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/30/2021] [Accepted: 01/07/2022] [Indexed: 05/05/2023]
Abstract
Somatic embryogenesis (SE) is an in vitro biological process in which bipolar structures (somatic embryos) can be induced to form from somatic cells and regenerate into whole plants. Acquisition of the embryogenic potential in culture is initiated when some competent cells within the explants respond to inductive signals (mostly plant growth regulators, PRGs), and de-differentiate into embryogenic cells. Such cells, "canalized" into the embryogenic developmental pathway, are able to generate embryos comparable in structure and physiology to their in vivo counterparts. Genomic and transcriptomic studies have identified several pathways governing the initial stages of the embryogenic process. In this review, the authors emphasize the importance of the developmental signals required for the progression of embryo development, starting with the de-differentiation of somatic cells and culminating with tissue patterning during the formation of the embryo body. The action and interaction of PGRs are highlighted, along with the participation of master regulators, mostly transcription factors (TFs), and proteins involved in stress responses and the signal transduction required for the initiation of the embryogenic process.
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Affiliation(s)
- Mohamed Elhiti
- Department of Botany, Faculty of Science, Tanta University, Tanta 31527, Egypt;
| | - Claudio Stasolla
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T2N2, Canada
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28
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Yang W, Hu J, Behera JR, Kilaru A, Yuan Y, Zhai Y, Xu Y, Xie L, Zhang Y, Zhang Q, Niu L. A Tree Peony Trihelix Transcription Factor PrASIL1 Represses Seed Oil Accumulation. FRONTIERS IN PLANT SCIENCE 2021; 12:796181. [PMID: 34956296 PMCID: PMC8702530 DOI: 10.3389/fpls.2021.796181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/22/2021] [Indexed: 05/31/2023]
Abstract
In many higher plants, seed oil accumulation is governed by complex multilevel regulatory networks including transcriptional regulation, which primarily affects fatty acid biosynthesis. Tree peony (Paeonia rockii), a perennial deciduous shrub endemic to China is notable for its seed oil that is abundant in unsaturated fatty acids. We discovered that a tree peony trihelix transcription factor, PrASIL1, localized in the nucleus, is expressed predominantly in developing seeds during maturation. Ectopic overexpression of PrASIL1 in Nicotiana benthamiana leaf tissue and Arabidopsis thaliana seeds significantly reduced total fatty acids and altered the fatty acid composition. These changes were in turn associated with the decreased expression of multitudinous genes involved in plastidial fatty acid synthesis and oil accumulation. Thus, we inferred that PrASIL1 is a critical transcription factor that represses oil accumulation by down-regulating numerous key genes during seed oil biosynthesis. In contrary, up-regulation of oil biosynthesis genes and a significant increase in total lipids and several major fatty acids were observed in PrASIL1-silenced tree peony leaves. Together, these results provide insights into the role of trihelix transcription factor PrASIL1 in controlling seed oil accumulation. PrASIL1 can be targeted potentially for oil enhancement in tree peony and other crops through gene manipulation.
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Affiliation(s)
- Weizong Yang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling, China
| | - Jiayuan Hu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling, China
| | - Jyoti R. Behera
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, United States
| | - Aruna Kilaru
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, United States
| | - Yanping Yuan
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling, China
| | - Yuhui Zhai
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling, China
| | - Yanfeng Xu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling, China
| | - Lihang Xie
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yanlong Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling, China
| | - Qingyu Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling, China
| | - Lixin Niu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling, China
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29
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Lu L, Wei W, Li QT, Bian XH, Lu X, Hu Y, Cheng T, Wang ZY, Jin M, Tao JJ, Yin CC, He SJ, Man WQ, Li W, Lai YC, Zhang WK, Chen SY, Zhang JS. A transcriptional regulatory module controls lipid accumulation in soybean. THE NEW PHYTOLOGIST 2021; 231:661-678. [PMID: 33864683 DOI: 10.1111/nph.17401] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/29/2021] [Indexed: 05/19/2023]
Abstract
Soybean (Glycine max) is one of the most important oilseed crops. However, the regulatory mechanism that governs the process of oil accumulation in soybean remains poorly understood. In this study, GmZF392, a tandem CCCH zinc finger (TZF) protein which was identified in our previous RNA-seq analysis of seed-preferred transcription factors, was found to function as a positive regulator of lipid production. GmZF392 promotes seed oil accumulation in both transgenic Arabidopsis and stable transgenic soybean plants by binding to a bipartite cis-element, containing TG- and TA-rich sequences, in promoter regions, activating the expression of genes in the lipid biosynthesis pathway. GmZF392 physically interacts with GmZF351, our previously identified transcriptional regulator of lipid biosynthesis, to synergistically promote downstream gene expression. Both GmZF392 and GmZF351 are further upregulated by GmNFYA, another transcription factor involved in lipid biosynthesis, directly (in the former case) and indirectly (in the latter case). Promoter sequence diversity analysis showed that the GmZF392 promoter may have been selected at the origin of the Glycine genus and further mildly selected during domestication from wild soybeans to cultivated soybeans. Our study reveals a regulatory module containing three transcription factors in the lipid biosynthesis pathway, and manipulation of the module may improve oil production in soybean and other oilseed crops.
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Affiliation(s)
- Long Lu
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Wei
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qing-Tian Li
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiao-Hua Bian
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiang Lu
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Hu
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tong Cheng
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhou-Ya Wang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng Jin
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Jun Tao
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cui-Cui Yin
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Si-Jie He
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei-Qun Man
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Wei Li
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yong-Cai Lai
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Wan-Ke Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shou-Yi Chen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jin-Song Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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30
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Song J, Xie X, Chen C, Shu J, Thapa RK, Nguyen V, Bian S, Kohalmi SE, Marsolais F, Zou J, Cui Y. LEAFY COTYLEDON1 expression in the endosperm enables embryo maturation in Arabidopsis. Nat Commun 2021; 12:3963. [PMID: 34172749 PMCID: PMC8233312 DOI: 10.1038/s41467-021-24234-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 06/03/2021] [Indexed: 11/09/2022] Open
Abstract
The endosperm provides nutrients and growth regulators to the embryo during seed development. LEAFY COTYLEDON1 (LEC1) has long been known to be essential for embryo maturation. LEC1 is expressed in both the embryo and the endosperm; however, the functional relevance of the endosperm-expressed LEC1 for seed development is unclear. Here, we provide genetic and transgenic evidence demonstrating that endosperm-expressed LEC1 is necessary and sufficient for embryo maturation. We show that endosperm-synthesized LEC1 is capable of orchestrating full seed maturation in the absence of embryo-expressed LEC1. Inversely, without LEC1 expression in the endosperm, embryo development arrests even in the presence of functional LEC1 alleles in the embryo. We further reveal that LEC1 expression in the endosperm begins at the zygote stage and the LEC1 protein is then trafficked to the embryo to activate processes of seed maturation. Our findings thus establish a key role for endosperm in regulating embryo development.
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Affiliation(s)
- Jingpu Song
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada. .,Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, SK, Canada. .,Department of Biology, Western University, London, ON, Canada.
| | - Xin Xie
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,Department of Biology, Western University, London, ON, Canada
| | - Chen Chen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,Department of Biology, Western University, London, ON, Canada.,Molecular Analysis and Genetic Improvement Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jie Shu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,Department of Biology, Western University, London, ON, Canada.,Molecular Analysis and Genetic Improvement Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Raj K Thapa
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,Department of Biology, Western University, London, ON, Canada
| | - Vi Nguyen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Shaomin Bian
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,College of Plant Science, Jilin University, Changchun, China
| | | | - Frédéric Marsolais
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.,Department of Biology, Western University, London, ON, Canada
| | - Jitao Zou
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, SK, Canada.
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada. .,Department of Biology, Western University, London, ON, Canada.
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31
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Ranade SS, Egertsdotter U. In silico characterization of putative gene homologues involved in somatic embryogenesis suggests that some conifer species may lack LEC2, one of the key regulators of initiation of the process. BMC Genomics 2021; 22:392. [PMID: 34039265 PMCID: PMC8157724 DOI: 10.1186/s12864-021-07718-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/12/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) is the process in which somatic embryos develop from somatic tissue in vitro on medium in most cases supplemented with growth regulators. Knowledge of genes involved in regulation of initiation and of development of somatic embryos is crucial for application of SE as an efficient tool to enable genetic improvement across genotypes by clonal propagation. RESULTS Current work presents in silico identification of putative homologues of central regulators of SE initiation and development in conifers focusing mainly on key transcription factors (TFs) e.g. BBM, LEC1, LEC1-LIKE, LEC2 and FUSCA3, based on sequence similarity using BLASTP. Protein sequences of well-characterised candidates genes from Arabidopsis thaliana were used to query the databases (Gymno PLAZA, Congenie, GenBank) including whole-genome sequence data from two representative species from the genus Picea (Picea abies) and Pinus (Pinus taeda), for finding putative conifer homologues, using BLASTP. Identification of corresponding conifer proteins was further confirmed by domain search (Conserved Domain Database), alignment (MUSCLE) with respective sequences of Arabidopsis thaliana proteins and phylogenetic analysis (Phylogeny.fr). CONCLUSIONS This in silico analysis suggests absence of LEC2 in Picea abies and Pinus taeda, the conifer species whose genomes have been sequenced. Based on available sequence data to date, LEC2 was also not detected in the other conifer species included in the study. LEC2 is one of the key TFs associated with initiation and regulation of the process of SE in angiosperms. Potential alternative mechanisms that might be functional in conifers to compensate the lack of LEC2 are discussed.
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Affiliation(s)
- Sonali Sachin Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center (UPSC), Swedish University of Agricultural Science (SLU), 901 83, Umeå, Sweden.
| | - Ulrika Egertsdotter
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center (UPSC), Swedish University of Agricultural Science (SLU), 901 83, Umeå, Sweden
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32
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Rikiishi K, Sugimoto M, Maekawa M. Transcriptomic analysis of developing seeds in a wheat ( Triticum aestivum L.) mutant RSD32 with reduced seed dormancy. BREEDING SCIENCE 2021; 71:155-166. [PMID: 34377063 PMCID: PMC8329890 DOI: 10.1270/jsbbs.20016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 10/11/2020] [Indexed: 06/13/2023]
Abstract
Seed dormancy, a major factor regulating pre-harvest sprouting, can severely hinder wheat cultivation. Reduced Seed Dormancy 32 (RSD32), a wheat (Triticum aestivum L.) mutant with reduced seed dormancy, is derived from the pre-harvest sprouting tolerant cultivar, 'Norin61'. RSD32 is regulated by a single recessive gene and mutant phenotype expressed in a seed-specific manner. Gene expressions in embryos of 'Norin61' and RSD32 were compared using RNA sequencing (RNA-seq) analysis at different developmental stages of 20, 30, and 40 days after pollination (DAP). Numbers of up-regulated genes in RSD32 are equivalent in all developmental stages. However, down-regulated genes in RSD32 are more numerous on DAP20 and DAP30 than on DAP40. In central components affecting the circadian clock, homologues to the morning-expressed genes are expressed at lower levels in RSD32. However, higher expressions of homologues acting as evening-expressed genes are observed in RSD32. Homologues of Ca2+ signaling pathway related genes are specifically expressed on DAP20 in 'Norin61'. Lower expression is shown in RSD32. These results suggest that RSD32 mutation expresses on DAP20 and earlier seed developmental stages and suggest that circadian clock regulation and Ca2+ signaling pathway are involved in the regulation of wheat seed dormancy.
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Affiliation(s)
- Kazuhide Rikiishi
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Manabu Sugimoto
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Masahiko Maekawa
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
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33
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Nalapalli S, Tunc-Ozdemir M, Sun Y, Elumalai S, Que Q. Morphogenic Regulators and Their Application in Improving Plant Transformation. Methods Mol Biol 2021; 2238:37-61. [PMID: 33471323 DOI: 10.1007/978-1-0716-1068-8_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Generation of plant lines with transgene or edited gene variants is the desired outcome of transformation technology. Conventional DNA-based plant transformation methods are the most commonly used technology but these approaches are limited to a small number of plant species with efficient transformation systems. The ideal transformation technologies are those that allow biotechnology applications across wide genetic background, especially within elite germplasm of major crop species. This chapter will briefly review key regulatory genes involved in plant morphogenesis with a focus on in vitro somatic embryogenesis and their application in improving plant transformation.
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Affiliation(s)
- Samson Nalapalli
- Seeds Research, Syngenta Crop Protection LLC, Research Triangle Park, NC, USA.
| | | | - Yuejin Sun
- Seeds Research, Syngenta Crop Protection LLC, Research Triangle Park, NC, USA
| | - Sivamani Elumalai
- Seeds Research, Syngenta Crop Protection LLC, Research Triangle Park, NC, USA
| | - Qiudeng Que
- Seeds Research, Syngenta Crop Protection LLC, Research Triangle Park, NC, USA
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34
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Su YH, Tang LP, Zhao XY, Zhang XS. Plant cell totipotency: Insights into cellular reprogramming. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:228-243. [PMID: 32437079 DOI: 10.1111/jipb.12972] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Plant cells have a powerful capacity in their propagation to adapt to environmental change, given that a single plant cell can give rise to a whole plant via somatic embryogenesis without the need for fertilization. The reprogramming of somatic cells into totipotent cells is a critical step in somatic embryogenesis. This process can be induced by stimuli such as plant hormones, transcriptional regulators and stress. Here, we review current knowledge on how the identity of totipotent cells is determined and the stimuli required for reprogramming of somatic cells into totipotent cells. We highlight key molecular regulators and associated networks that control cell fate transition from somatic to totipotent cells. Finally, we pose several outstanding questions that should be addressed to enhance our understanding of the mechanisms underlying plant cell totipotency.
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Affiliation(s)
- Ying Hua Su
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Li Ping Tang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiang Yu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
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Tian R, Paul P, Joshi S, Perry SE. Genetic activity during early plant embryogenesis. Biochem J 2020; 477:3743-3767. [PMID: 33045058 PMCID: PMC7557148 DOI: 10.1042/bcj20190161] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022]
Abstract
Seeds are essential for human civilization, so understanding the molecular events underpinning seed development and the zygotic embryo it contains is important. In addition, the approach of somatic embryogenesis is a critical propagation and regeneration strategy to increase desirable genotypes, to develop new genetically modified plants to meet agricultural challenges, and at a basic science level, to test gene function. We briefly review some of the transcription factors (TFs) involved in establishing primary and apical meristems during zygotic embryogenesis, as well as TFs necessary and/or sufficient to drive somatic embryo programs. We focus on the model plant Arabidopsis for which many tools are available, and review as well as speculate about comparisons and contrasts between zygotic and somatic embryo processes.
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Affiliation(s)
- Ran Tian
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Priyanka Paul
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Sanjay Joshi
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Sharyn E. Perry
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
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Chen N, Wang H, Abdelmageed H, Veerappan V, Tadege M, Allen RD. HSI2/VAL1 and HSL1/VAL2 function redundantly to repress DOG1 expression in Arabidopsis seeds and seedlings. THE NEW PHYTOLOGIST 2020; 227:840-856. [PMID: 32201955 PMCID: PMC7383879 DOI: 10.1111/nph.16559] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/16/2020] [Indexed: 05/21/2023]
Abstract
DELAY OF GERMINATION1 (DOG1) is a primary regulator of seed dormancy. Accumulation of DOG1 in seeds leads to deep dormancy and delayed germination in Arabidopsis. B3 domain-containing transcriptional repressors HSI2/VAL1 and HSL1/VAL2 silence seed dormancy and enable the subsequent germination and seedling growth. However, the roles of HSI2 and HSL1 in regulation of DOG1 expression and seed dormancy remain elusive. Seed dormancy was analysed by measurement of maximum germination percentage of freshly harvested Arabidopsis seeds. In vivo protein-protein interaction analysis, ChIP-qPCR and EMSA were performed and suggested that HSI2 and HSL1 can form dimers to directly regulate DOG1. HSI2 and HSL1 dimers interact with RY elements at DOG1 promoter. Both B3 and PHD-like domains are required for enrichment of HSI2 and HSL1 at the DOG1 promoter. HSI2 and HSL1 recruit components of polycomb-group proteins, including CURLY LEAF (CLF) and LIKE HETERCHROMATIN PROTEIN 1 (LHP1), for consequent deposition of H3K27me3 marks, leading to repression of DOG1 expression. Our findings suggest that HSI2- and HSL1-dependent histone methylation plays critical roles in regulation of seed dormancy during seed germination and early seedling growth.
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Affiliation(s)
- Naichong Chen
- Institute for Agricultural BiosciencesOklahoma State UniversityArdmoreOK73401USA
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwater74078OKUSA
| | - Hui Wang
- Institute for Agricultural BiosciencesOklahoma State UniversityArdmoreOK73401USA
| | - Haggag Abdelmageed
- Institute for Agricultural BiosciencesOklahoma State UniversityArdmoreOK73401USA
- Department of Agricultural BotanyFaculty of AgricultureCairo UniversityGiza12613Egypt
| | | | - Million Tadege
- Institute for Agricultural BiosciencesOklahoma State UniversityArdmoreOK73401USA
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Randy D. Allen
- Institute for Agricultural BiosciencesOklahoma State UniversityArdmoreOK73401USA
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwater74078OKUSA
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Cai G, Kim SC, Li J, Zhou Y, Wang X. Transcriptional Regulation of Lipid Catabolism during Seedling Establishment. MOLECULAR PLANT 2020; 13:984-1000. [PMID: 32334070 DOI: 10.1016/j.molp.2020.04.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/15/2020] [Accepted: 04/18/2020] [Indexed: 05/20/2023]
Abstract
Lipid catabolism in germinating seeds provides energy and substrates for initial seedling growth, but how this process is regulated is not well understood. Here, we show that an AT-hook motif-containing nuclear localized (AHL) protein regulates lipid mobilization and fatty acid β-oxidation during seed germination and seedling establishment. AHL4 was identified to directly interact with the lipid mediator phosphatidic acid (PA). Knockout (KO) of AHL4 enhanced, but overexpression (OE) of AHL4 attenuated, triacylglycerol (TAG) degradation and seedling growth. Normal seedling growth of the OE lines was restored by sucrose supplementation to the growth medium. AHL4-OE seedlings displayed decreased expression of genes involved in TAG hydrolysis and fatty acid oxidation, whereas the opposite was observed in AHL4-KOs. These genes contained AHL4-binding cis elements, and AHL4 was shown to bind to the promoter regions of genes encoding the TAG lipases SDP1 and DALL5 and acyl-thioesterase KAT5. These AHL4-DNA interactions were suppressed by PA species that bound to AHL4. These results indicate that AHL4 suppresses lipid catabolism by repressing the expression of specific genes involved in TAG hydrolysis and fatty acid oxidation, and that PA relieves AHL4-mediated suppression and promotes TAG degradation. Thus, AHL4 and PA together regulate lipid degradation during seed germination and seedling establishment.
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Affiliation(s)
- Guangqin Cai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Department of Biology, University of Missouri, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Sang-Chul Kim
- Department of Biology, University of Missouri, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Jianwu Li
- Department of Biology, University of Missouri, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuemin Wang
- Department of Biology, University of Missouri, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
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Regulation of cell reprogramming by auxin during somatic embryogenesis. ABIOTECH 2020; 1:185-193. [PMID: 36303566 PMCID: PMC9590521 DOI: 10.1007/s42994-020-00029-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/21/2020] [Indexed: 01/03/2023]
Abstract
How somatic cells develop into a whole plant is a central question in plant developmental biology. This powerful ability of plant cells is recognized as their totipotency. Somatic embryogenesis is an excellent example and a good research system for studying plant cell totipotency. However, very little is known about the molecular basis of cell reprogramming from somatic cells to totipotent cells in this process. During somatic embryogenesis from immature zygotic embryos in Arabidopsis, exogenous auxin treatment is required for embryonic callus formation, but removal of exogenous auxin inducing endogenous auxin biosynthesis is essential for somatic embryo (SE) induction. Ectopic expression of specific transcription factor genes, such as "LAFL" and BABY BOOM (BBM), can induce SEs without exogenous growth regulators. Somatic embryogenesis can also be triggered by stress, as well as by disruption of chromatin remodeling, including PRC2-mediated histone methylation, histone deacetylation, and PKL-related chromatin remodeling. It is evident that embryonic identity genes are required and endogenous auxin plays a central role for cell reprogramming during the induction of SEs. Thus, we focus on reviewing the regulation of cell reprogramming for somatic embryogenesis by auxin.
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Geleta M, Gustafsson C, Glaubitz JC, Ortiz R. High-Density Genetic Linkage Mapping of Lepidium Based on Genotyping-by-Sequencing SNPs and Segregating Contig Tag Haplotypes. FRONTIERS IN PLANT SCIENCE 2020; 11:448. [PMID: 32425961 PMCID: PMC7204607 DOI: 10.3389/fpls.2020.00448] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/26/2020] [Indexed: 05/09/2023]
Abstract
Lepidium campestre has been targeted for domestication as future oilseed and catch crop. Three hundred eighty plants comprising genotypes of L. campestre, Lepidium heterophyllum, and their interspecific F2 mapping population were genotyped using genotyping by sequencing (GBS), and the generated polymorphic markers were used for the construction of high-density genetic linkage map. TASSEL-GBS, a reference genome-based pipeline, was used for this analysis using a draft L. campestre whole genome sequence. The analysis resulted in 120,438 biallelic single-nucleotide polymorphisms (SNPs) with minor allele frequency (MAF) above 0.01. The construction of genetic linkage map was conducted using MSTMap based on phased SNPs segregating in 1:2:1 ratio for the F2 individuals, followed by genetic mapping of segregating contig tag haplotypes as dominant markers against the linkage map. The final linkage map consisted of eight linkage groups (LGs) containing 2,330 SNP markers and spanned 881 Kosambi cM. Contigs (10,302) were genetically mapped to the eight LGs, which were assembled into pseudomolecules that covered a total of ∼120.6 Mbp. The final size of the pseudomolecules ranged from 9.4 Mbp (LG-4) to 20.4 Mpb (LG-7). The following major correspondence between the eight Lepidium LGs (LG-1 to LG-8) and the five Arabidopsis thaliana (At) chromosomes (Atx-1-Atx-5) was revealed through comparative genomics analysis: LG-1&2_Atx-1, LG-3_Atx-2&3, LG-4_Atx-2, LG-5_Atx-2&Atx-3, LG-6_Atx-4&5, LG-7_Atx-4, and LG-8_Atx-5. This analysis revealed that at least 66% of the sequences of the LGs showed high collinearity with At chromosomes. The sequence identity between the corresponding regions of the LGs and At chromosomes ranged from 80.6% (LG-6) to 86.4% (LG-8) with overall mean of 82.9%. The map positions on Lepidium LGs of the homologs of 24 genes that regulate various traits in A. thaliana were also identified. The eight LGs revealed in this study confirm the previously reported (1) haploid chromosome number of eight in L. campestre and L. heterophyllum and (2) chromosomal fusion, translocation, and inversion events during the evolution of n = 8 karyotype in ancestral species shared by Lepidium and Arabidopsis to n = 5 karyotype in A. thaliana. This study generated highly useful genomic tools and resources for Lepidium that can be used to accelerate its domestication.
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Affiliation(s)
- Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Cecilia Gustafsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Jha P, Ochatt SJ, Kumar V. WUSCHEL: a master regulator in plant growth signaling. PLANT CELL REPORTS 2020; 39:431-444. [PMID: 31984435 DOI: 10.1007/s00299-020-02511-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/13/2020] [Indexed: 05/24/2023]
Abstract
This review summarizes recent knowledge on functions of WUS and WUS-related homeobox (WOX) transcription factors in diverse signaling pathways governing shoot meristem biology and several other aspects of plant dynamics. Transcription factors (TFs) are master regulators involved in controlling different cellular and biological functions as well as diverse signaling pathways in plant growth and development. WUSCHEL (WUS) is a homeodomain transcription factor necessary for the maintenance of the stem cell niche in the shoot apical meristem, the differentiation of lateral primordia, plant cell totipotency and other diverse cellular processes. Recent research about WUS has uncovered several unique features including the complex signaling pathways that further improve the understanding of vital network for meristem biology and crop productivity. In addition, several reports bridge the gap between WUS expression and plant signaling pathway by identifying different WUS and WUS-related homeobox (WOX) genes during the formation of shoot (apical and axillary) meristems, vegetative-to-embryo transition, genetic transformation, and other aspects of plant growth and development. In this respect, the WOX family of TFs comprises multiple members involved in diverse signaling pathways, but how these pathways are regulated remains to be elucidated. Here, we review the current status and recent discoveries on the functions of WUS and newly identified WOX family members in the regulatory network of various aspects of plant dynamics.
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Affiliation(s)
- Priyanka Jha
- Amity Institute of Biotechnology, Amity University, Major Arterial Road, Action Area II, Kolkata, West Bengal, India
| | - Sergio J Ochatt
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Vijay Kumar
- Plant Biotechnology Lab, Division of Research and Development, Lovely Professional University, Phagwara, Punjab, 144411, India.
- Department of Biotechnology, Lovely Faculty of Technology and Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India.
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Abstract
Seed development is a complex process and consists of two phases: embryo morphogenesis and seed maturation. LEAFY COTYLEDON (LEC) transcription factors, first discovered in
Arabidopsis thaliana several decades ago, are master regulators of seed development. Here, we first summarize molecular genetic mechanisms underlying the control of embryogenesis and seed maturation by
LECs and then provide a brief review of recent findings in the role of
LECs in embryonic resetting of the parental ‘memory of winter cold’ in Arabidopsis. In addition, we discuss various chromatin-based mechanisms underlying developmental silencing of
LEC genes throughout the post-embryonic development to terminate the embryonic developmental program.
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Affiliation(s)
- De Niu
- National Key Laboratory of Plant Molecular Genetics & Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai, China
| | - Yuehui He
- National Key Laboratory of Plant Molecular Genetics & Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai, China
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Pouvreau B, Blundell C, Vohra H, Zwart AB, Arndell T, Singh S, Vanhercke T. A Versatile High Throughput Screening Platform for Plant Metabolic Engineering Highlights the Major Role of ABI3 in Lipid Metabolism Regulation. FRONTIERS IN PLANT SCIENCE 2020; 11:288. [PMID: 32256511 PMCID: PMC7090168 DOI: 10.3389/fpls.2020.00288] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 02/26/2020] [Indexed: 05/16/2023]
Abstract
Traditional functional genetic studies in crops are time consuming, complicated and cannot be readily scaled up. The reason is that mutant or transformed crops need to be generated to study the effect of gene modifications on specific traits of interest. However, many crop species have a complex genome and a long generation time. As a result, it usually takes several months to over a year to obtain desired mutants or transgenic plants, which represents a significant bottleneck in the development of new crop varieties. To overcome this major issue, we are currently establishing a versatile plant genetic screening platform, amenable to high throughput screening in almost any crop species, with a unique workflow. This platform combines protoplast transformation and fluorescence activated cell sorting. Here we show that tobacco protoplasts can accumulate high levels of lipid if transiently transformed with genes involved in lipid biosynthesis and can be sorted based on lipid content. Hence, protoplasts can be used as a predictive tool for plant lipid engineering. Using this newly established strategy, we demonstrate the major role of ABI3 in plant lipid accumulation. We anticipate that this workflow can be applied to numerous highly valuable metabolic traits other than storage lipid accumulation. This new strategy represents a significant step toward screening complex genetic libraries, in a single experiment and in a matter of days, as opposed to years by conventional means.
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Affiliation(s)
- Benjamin Pouvreau
- Agriculture and Food, CSIRO, Canberra, ACT, Australia
- Synthetic Biology Future Science Platform, CSIRO, Canberra, ACT, Australia
- *Correspondence: Benjamin Pouvreau,
| | - Cheryl Blundell
- Agriculture and Food, CSIRO, Canberra, ACT, Australia
- Synthetic Biology Future Science Platform, CSIRO, Canberra, ACT, Australia
| | - Harpreet Vohra
- The John Curtin School of Medical Research, Australian National University College of Health and Medicine, Canberra, ACT, Australia
| | | | - Taj Arndell
- Agriculture and Food, CSIRO, Canberra, ACT, Australia
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Flores-Vergara MA, Oneal E, Costa M, Villarino G, Roberts C, De Luis Balaguer MA, Coimbra S, Willis J, Franks RG. Developmental Analysis of Mimulus Seed Transcriptomes Reveals Functional Gene Expression Clusters and Four Imprinted, Endosperm-Expressed Genes. FRONTIERS IN PLANT SCIENCE 2020; 11:132. [PMID: 32161609 PMCID: PMC7052496 DOI: 10.3389/fpls.2020.00132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/28/2020] [Indexed: 05/15/2023]
Abstract
The double fertilization of the female gametophyte initiates embryogenesis and endosperm development in seeds via the activation of genes involved in cell differentiation, organ patterning, and growth. A subset of genes expressed in endosperm exhibit imprinted expression, and the correct balance of gene expression between parental alleles is critical for proper endosperm and seed development. We use a transcriptional time series analysis to identify genes that are associated with key shifts in seed development, including genes associated with secondary cell wall synthesis, mitotic cell cycle, chromatin organization, auxin synthesis, fatty acid metabolism, and seed maturation. We relate these genes to morphological changes in Mimulus seeds. We also identify four endosperm-expressed transcripts that display imprinted (paternal) expression bias. The imprinted status of these four genes is conserved in other flowering plants, suggesting that they are functionally important in endosperm development. Our study explores gene regulatory dynamics in a species with ab initio cellular endosperm development, broadening the taxonomic focus of the literature on gene expression in seeds. Moreover, it is the first to validate genes with imprinted endosperm expression in Mimulus guttatus, and will inform future studies on the genetic causes of seed failure in this model system.
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Affiliation(s)
- Miguel A. Flores-Vergara
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Elen Oneal
- Department of Biology, Duke University, Durham, NC, United States
- *Correspondence: Elen Oneal,
| | - Mario Costa
- GreenUPorto, Sustainable Agrifood Production Research Centre, Biology Department, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Gonzalo Villarino
- Biology Department, San Diego State University, San Diego, CA, United States
| | - Caitlyn Roberts
- Department of Biology, Berea College, Berea, KY, United States
| | | | - Sílvia Coimbra
- GreenUPorto, Sustainable Agrifood Production Research Centre, Biology Department, Faculty of Sciences, University of Porto, Porto, Portugal
| | - John Willis
- Department of Biology, Duke University, Durham, NC, United States
| | - Robert G. Franks
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Kumar M, Kesawat MS, Ali A, Lee SC, Gill SS, Kim HU. Integration of Abscisic Acid Signaling with Other Signaling Pathways in Plant Stress Responses and Development. PLANTS (BASEL, SWITZERLAND) 2019; 8:E592. [PMID: 31835863 PMCID: PMC6963649 DOI: 10.3390/plants8120592] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 11/26/2019] [Accepted: 12/10/2019] [Indexed: 12/30/2022]
Abstract
Plants are immobile and, to overcome harsh environmental conditions such as drought, salt, and cold, they have evolved complex signaling pathways. Abscisic acid (ABA), an isoprenoid phytohormone, is a critical signaling mediator that regulates diverse biological processes in various organisms. Significant progress has been made in the determination and characterization of key ABA-mediated molecular factors involved in different stress responses, including stomatal closure and developmental processes, such as seed germination and bud dormancy. Since ABA signaling is a complex signaling network that integrates with other signaling pathways, the dissection of its intricate regulatory network is necessary to understand the function of essential regulatory genes involved in ABA signaling. In the present review, we focus on two aspects of ABA signaling. First, we examine the perception of the stress signal (abiotic and biotic) and the response network of ABA signaling components that transduce the signal to the downstream pathway to respond to stress tolerance, regulation of stomata, and ABA signaling component ubiquitination. Second, ABA signaling in plant development processes, such as lateral root growth regulation, seed germination, and flowering time regulation is investigated. Examining such diverse signal integration dynamics could enhance our understanding of the underlying genetic, biochemical, and molecular mechanisms of ABA signaling networks in plants.
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Affiliation(s)
- Manu Kumar
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea
| | | | - Asjad Ali
- Southern Cross Plant Science, Southern Cross University, East Lismore NSW 2480, Australia;
| | | | - Sarvajeet Singh Gill
- Stress Physiology and Molecular Biology Lab, Centre for Biotechnology, MD University, Rohtak 124001, India;
| | - Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea
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CRK5 Protein Kinase Contributes to the Progression of Embryogenesis of Arabidopsis thaliana. Int J Mol Sci 2019; 20:ijms20246120. [PMID: 31817249 PMCID: PMC6941128 DOI: 10.3390/ijms20246120] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/29/2019] [Accepted: 11/30/2019] [Indexed: 12/26/2022] Open
Abstract
The fine tuning of hormone (e.g., auxin and gibberellin) levels and hormone signaling is required for maintaining normal embryogenesis. Embryo polarity, for example, is ensured by the directional movement of auxin that is controlled by various types of auxin transporters. Here, we present pieces of evidence for the auxin-gibberellic acid (GA) hormonal crosstalk during embryo development and the regulatory role of the Arabidopsis thaliana Calcium-Dependent Protein Kinase-Related Kinase 5 (AtCRK5) in this regard. It is pointed out that the embryogenesis of the Atcrk5-1 mutant is delayed in comparison to the wild type. This delay is accompanied with a decrease in the levels of GA and auxin, as well as the abundance of the polar auxin transport (PAT) proteins PIN1, PIN4, and PIN7 in the mutant embryos. We have previously showed that AtCRK5 can regulate the PIN2 and PIN3 proteins either directly by phosphorylation or indirectly affecting the GA level during the root gravitropic and hypocotyl hook bending responses. In this manuscript, we provide evidence that the AtCRK5 protein kinase can in vitro phosphorylate the hydrophilic loops of additional PIN proteins that are important for embryogenesis. We propose that AtCRK5 can govern embryo development in Arabidopsis through the fine tuning of auxin-GA level and the accumulation of certain polar auxin transport proteins.
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A comprehensive analysis of the B3 superfamily identifies tissue-specific and stress-responsive genes in chickpea ( Cicer arietinum L.). 3 Biotech 2019; 9:346. [PMID: 31497464 DOI: 10.1007/s13205-019-1875-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/14/2019] [Indexed: 12/31/2022] Open
Abstract
The aim of this study was to provide a comprehensive analysis of the plant-specific B3 domain-containing transcription factors (TFs) in chickpea. Scanning of the chickpea genome resulted in the identification of 51 B3 domain-containing TFs that were located on seven out of eight chickpea chromosomes. Based on the presence of additional domains other than the B3 domain, the candidates were classified into four subfamilies, i.e., ARF (24), REM (19), LAV (6) and RAV (2). Phylogenetic analysis classified them into four groups in which members of the same group had similar intron-exon organization and motif composition. Genome duplication analysis of the candidate B3 genes revealed an event of segmental duplication that was instrumental in the expansion of the B3 gene family. Ka/Ks analysis showed that the B3 gene family was under purifying selection. Further, chickpea B3 genes showed maximum orthology with Medicago followed by soybean and Arabidopsis. Promoter analyses of the B3 genes led to the identification of several tissue-specific and stress-responsive cis-regulatory elements. Expression profiling of the candidate B3 genes using publicly available RNA-seq data of several chickpea tissues indicated their putative role in plant development and abiotic stress response. These findings were further validated by real-time expression analysis. Overall, this study provides a comprehensive analysis of the B3 domain-containing proteins in chickpea that would aid in devising strategies for crop manipulation in chickpea.
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Deng S, Mai Y, Shui L, Niu J. WRINKLED1 transcription factor orchestrates the regulation of carbon partitioning for C18:1 (oleic acid) accumulation in Siberian apricot kernel. Sci Rep 2019; 9:2693. [PMID: 30804440 PMCID: PMC6389899 DOI: 10.1038/s41598-019-39236-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/21/2019] [Indexed: 11/09/2022] Open
Abstract
WRINKLED1 (WRI1), an APETALA2 (AP2)-type transcription factor, has been shown to be required for the regulation of carbon partitioning into fatty acid (FA) synthesis in plant seeds. To our knowledge, the regulatory network of WRI1 remains unknown in Prunus sibirica kernel (PSK), a novel woody biodiesel feedstock in China. In this study, based on the transcriptional data from developing oilseeds of multiple plant species, we identified 161 WRI1-coexpressed genes using weighted gene co-expression network analysis (WGCNA). The major portion of WRI1-coexpressed genes was characterized to be involved in carbon partitioning and FA biosynthesis. Additionally, we detected the temporal patterns for oil content and FA compositions in developing PSK from two different germplasms (AS-85 and AS-86). The major differences between the two germplasms are higher contents of oil and C18:1 in AS-85 than in AS-86 at a mature stage. Thus, AS-85 and AS-86 are desirable materials to explore the molecular and metabolic mechanisms of oil accumulation in Siberian apricot. Expression analysis in developing PSK of AS-85 and AS-86 indicated that the expression level of P. sibirica WRI1 (PsWRI1) was closely correlated to accumulative rate of oil. Also, the comparison of expression profiles in developing PSK of AS-85 and AS-86 displayed that the pPK, E1-α, E2, TAL, BC, MCMT, BS, SAD and FAD2 have a high correlation with PsWRI1. Transient expression showed that ProSAD- and ProBS-driving GUS expression showed no substantial difference between AS-85 and AS-86, while the expression level of ProPEPCK-AS-85 driving GUS was significantly higher than that of ProPEPCK-AS-86 driving GUS. Additionally, transient co-transformation with PsWRI1 revealed that ProSAD, ProPEPCK and ProBS activity could be specifically up-regulated by PsWRI1. This regulatory mechanism of PsWRI1 may create a steep concentration difference, thereby facilitating carbon flux into C18:1 accumulation in developing PSK. Overall, all our findings imply a versatile mechanism of WRI1 to optimize carbon allocation for oil accumulation, which can provide reference for researching the woody biodiesel plants.
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Affiliation(s)
- Shuya Deng
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570228, China
| | - Yiting Mai
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570228, China
| | - Lanya Shui
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570228, China
| | - Jun Niu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570228, China.
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48
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Méndez-Hernández HA, Ledezma-Rodríguez M, Avilez-Montalvo RN, Juárez-Gómez YL, Skeete A, Avilez-Montalvo J, De-la-Peña C, Loyola-Vargas VM. Signaling Overview of Plant Somatic Embryogenesis. FRONTIERS IN PLANT SCIENCE 2019; 10:77. [PMID: 30792725 PMCID: PMC6375091 DOI: 10.3389/fpls.2019.00077] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/17/2019] [Indexed: 05/17/2023]
Abstract
Somatic embryogenesis (SE) is a means by which plants can regenerate bipolar structures from a somatic cell. During the process of cell differentiation, the explant responds to endogenous stimuli, which trigger the induction of a signaling response and, consequently, modify the gene program of the cell. SE is probably the most studied plant regeneration model, but to date it is the least understood due to the unclear mechanisms that occur at a cellular level. In this review, the authors seek to emphasize the importance of signaling on plant SE, highlighting the interactions between the different plant growth regulators (PGR), mainly auxins, cytokinins (CKs), ethylene and abscisic acid (ABA), during the induction of SE. The role of signaling is examined from the start of cell differentiation through the early steps on the embryogenic pathway, as well as its relation to a plant's tolerance of different types of stress. Furthermore, the role of genes encoded to transcription factors (TFs) during the embryogenic process such as the LEAFY COTYLEDON (LEC), WUSCHEL (WUS), BABY BOOM (BBM) and CLAVATA (CLV) genes, Arabinogalactan-proteins (AGPs), APETALA 2 (AP2) and epigenetic factors is discussed.
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Affiliation(s)
- Hugo A. Méndez-Hernández
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Maharshi Ledezma-Rodríguez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Randy N. Avilez-Montalvo
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Yary L. Juárez-Gómez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Analesa Skeete
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Johny Avilez-Montalvo
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Víctor M. Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
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49
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Roscoe TJ, Vaissayre V, Paszkiewicz G, Clavijo F, Kelemen Z, Michaud C, Lepiniec LC, Dubreucq B, Zhou DX, Devic M. Regulation of FUSCA3 Expression During Seed Development in Arabidopsis. PLANT & CELL PHYSIOLOGY 2019; 60:476-487. [PMID: 30462310 DOI: 10.1093/pcp/pcy224] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/18/2018] [Indexed: 06/09/2023]
Abstract
FUSCA3 (FUS3) is a master regulator of seed development important in establishing and maintaining embryonic identity whose expression is tightly regulated at genetic and epigenetic levels. Despite this prominent role, the control of FUS3 expression remains poorly understood. Promoter and functional complementation analyses provided insight into the regulation of FUS3. W-boxes present in the promoter proximal to the start of transcription are recognized by WRKY type-1 factors which are necessary for the activation of FUS3 expression. The RY motif, the binding site of B3 factors, is important for the activation of FUS3 in the embryo proper but not in the suspensor. The loss of a negative regulatory sequence (NRS) leads to preferential expression of FUS3 in the vasculature of vegetative tissues. Since the NRS includes the RY motif, mechanisms of activation and repression target adjacent or overlapping regions. These findings discriminate the regulation of FUS3 from that of LEAFY COTYLEDON2 by the control exerted by WRKY factors and by the presence of the RY motif, yet also confirm conservation of certain regulatory elements, thereby implicating potential regulation by BASIC PENTACYSTEINE (BPC) factors and POLYCOMB REPRESSIVE COMPLEX2 (PRC2).
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Affiliation(s)
| | - Virginie Vaissayre
- DIADE, ERL 5300 CNRS-IRD, Universit� de Montpellier, Montpellier, France
| | - Gael Paszkiewicz
- DIADE, ERL 5300 CNRS-IRD, Universit� de Montpellier, Montpellier, France
| | - Fernando Clavijo
- DIADE, ERL 5300 CNRS-IRD, Universit� de Montpellier, Montpellier, France
| | - Zsolt Kelemen
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles Cedex, France
| | - Caroline Michaud
- DIADE, ERL 5300 CNRS-IRD, Universit� de Montpellier, Montpellier, France
| | - Loï C Lepiniec
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles Cedex, France
| | - Bertrand Dubreucq
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles Cedex, France
| | - Dao-Xiu Zhou
- Universit� Paris-sud 11, Institut de Biologie des Plantes, CNRS, UMR8618, Saclay Plant Science, Orsay, France
| | - Martine Devic
- DIADE, ERL 5300 CNRS-IRD, Universit� de Montpellier, Montpellier, France
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50
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Brand A, Quimbaya M, Tohme J, Chavarriaga-Aguirre P. Arabidopsis LEC1 and LEC2 Orthologous Genes Are Key Regulators of Somatic Embryogenesis in Cassava. FRONTIERS IN PLANT SCIENCE 2019; 10:673. [PMID: 31191582 PMCID: PMC6541005 DOI: 10.3389/fpls.2019.00673] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 05/03/2019] [Indexed: 05/22/2023]
Abstract
High genotype-dependent variation in friable embryogenic callus (FEC) induction and subsequent somaclonal variation constitute bottlenecks for the application and scaling of genetic transformation (GT) technology to more farmer- and industry-preferred cassava varieties. The understanding and identification of molecular factors underlying embryogenic development in cassava may help to overcome these constraints. Here, we described the Arabidopsis thaliana LEAFY COTYLEDON (LEC) LEC1 and LEC2 orthologous genes in cassava, designated as MeLEC1 and MeLEC2, respectively. Expression analyses showed that both, MeLEC1 and MeLEC2, are expressed at higher levels in somatic embryogenic (SE) tissues in contrast with differentiated mature tissues. The rapid expression increase of MeLEC genes at early SE induction times strongly suggests that they are involved in the transition from a somatic to an embryonic state, and probably, in the competence acquisition for SE development in cassava. The independent overexpression of the MeLEC genes resulted in different regenerated events with embryogenic characteristics such as MeLEC1OE plants with cotyledon-like leaves and MeLEC2OE plants with somatic-like embryos that emerged over the surface of mature leaves. Transcript increases of other embryo-specific regulating factors were also detected in MeLECOE plants, supporting their mutual interaction in the embryo development coordination. The single overexpression of MeLEC2 was enough to reprogram the vegetative cells and induce direct somatic embryogenesis, which converts this gene into a tool that could improve the recovery of transformed plants of recalcitrant genotypes. The identification of MeLEC genes contributes not only to improve our understanding of SE process in cassava, but also provides viable alternatives to optimize GT and advance in gene editing in this crop, through the development of genotype-independent protocols.
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Affiliation(s)
- Alejandro Brand
- International Center for Tropical Agriculture, Cali, Colombia
| | - Mauricio Quimbaya
- Department of Natural Sciences and Mathematics, Pontificia Universidad Javeriana Cali, Cali, Colombia
| | - Joe Tohme
- International Center for Tropical Agriculture, Cali, Colombia
| | - Paul Chavarriaga-Aguirre
- International Center for Tropical Agriculture, Cali, Colombia
- *Correspondence: Paul Chavarriaga-Aguirre,
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