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Zhang C, Li S, Wang Y, Long J, Li X, Ke L, Xu R, Wu Z, Pi Z. Vernalization promotes bolting in sugar beet by inhibiting the transcriptional repressors of BvGI. PLANT MOLECULAR BIOLOGY 2024; 114:67. [PMID: 38836995 DOI: 10.1007/s11103-024-01460-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 04/26/2024] [Indexed: 06/06/2024]
Abstract
Sugar beet (Beta vulgaris L.), a biennial sugar crop, contributes about 16% of the world's sugar production. The transition from vegetative growth, during which sugar accumulated in beet, to reproductive growth, during which sugar exhausted in beet, is determined by vernalization and photoperiod. GIGANTEA (GI) is a key photoperiodic flowering gene that is induced by vernalization in sugar beet. To identify the upstream regulatory factors of BvGI, candidate transcription factors (TF) that were co-expressed with BvGI and could bind to the BvGI promoter were screened based on weighted gene co-expression network analysis (WGCNA) and TF binding site prediction. Subsequently, their transcriptional regulatory role on the BvGI was validated through subcellular localization, dual-luciferase assays and yeast transformation tests. A total of 7,586 differentially expressed genes were identified after vernalization and divided into 18 co-expression modules by WGCNA, of which one (MEcyan) and two (MEdarkorange2 and MEmidnightblue) modules were positively and negatively correlated with the expression of BvGI, respectively. TF binding site predictions using PlantTFDB enabled the screening of BvLHY, BvTCP4 and BvCRF4 as candidate TFs that negatively regulated the expression of BvGI by affecting its transcription. Subcellular localization showed that BvLHY, BvTCP4 and BvCRF4 were localized to the nucleus. The results of dual-luciferase assays and yeast transformation tests showed that the relative luciferase activity and expression of HIS3 was reduced in the BvLHY, BvTCP4 and BvCRF4 transformants, which suggested that the three TFs inhibited the BvGI promoter. In addition, real-time quantitative reverse transcription PCR showed that BvLHY and BvTCP4 exhibited rhythmic expression characteristics similar to that of BvGI, while BvCRF4 did not. Our results revealed that vernalization crosstalked with the photoperiod pathway to initiate bolting in sugar beet by inhibiting the transcriptional repressors of BvGI.
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Affiliation(s)
- Chunxue Zhang
- Academy of Modern Agriculture and Ecological Environment, Heilongjiang University, 150080, Harbin, China
| | - Shengnan Li
- Academy of Modern Agriculture and Ecological Environment, Heilongjiang University, 150080, Harbin, China
| | - Yuguang Wang
- Academy of Modern Agriculture and Ecological Environment, Heilongjiang University, 150080, Harbin, China
| | - Jiali Long
- College of Life Sciences, Heilongjiang University, 150080, Harbin, China
| | - Xinru Li
- Academy of Modern Agriculture and Ecological Environment, Heilongjiang University, 150080, Harbin, China
| | - Lixun Ke
- Academy of Modern Agriculture and Ecological Environment, Heilongjiang University, 150080, Harbin, China
| | - Rui Xu
- Academy of Modern Agriculture and Ecological Environment, Heilongjiang University, 150080, Harbin, China
| | - Zedong Wu
- Academy of Modern Agriculture and Ecological Environment, Heilongjiang University, 150080, Harbin, China.
| | - Zhi Pi
- Academy of Modern Agriculture and Ecological Environment, Heilongjiang University, 150080, Harbin, China.
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Gao Z, He Y. Molecular epigenetic understanding of winter memory in Arabidopsis. PLANT PHYSIOLOGY 2024; 194:1952-1961. [PMID: 37950890 DOI: 10.1093/plphys/kiad597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 10/13/2023] [Accepted: 11/03/2023] [Indexed: 11/13/2023]
Affiliation(s)
- Zheng Gao
- National Key Laboratory of Wheat Improvement, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yuehui He
- National Key Laboratory of Wheat Improvement, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
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Mahmood T, He S, Abdullah M, Sajjad M, Jia Y, Ahmar S, Fu G, Chen B, Du X. Epigenetic insight into floral transition and seed development in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111926. [PMID: 37984609 DOI: 10.1016/j.plantsci.2023.111926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/20/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Seasonal changes are crucial in shifting the developmental stages from the vegetative phase to the reproductive phase in plants, enabling them to flower under optimal conditions. Plants grown at different latitudes sense and interpret these seasonal variations, such as changes in day length (photoperiod) and exposure to cold winter temperatures (vernalization). These environmental factors influence the expression of various genes related to flowering. Plants have evolved to stimulate a rapid response to environmental conditions through genetic and epigenetic mechanisms. Multiple epigenetic regulation systems have emerged in plants to interpret environmental signals. During the transition to the flowering phase, changes in gene expression are facilitated by chromatin remodeling and small RNAs interference, particularly in annual and perennial plants. Key flowering regulators, such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT), interact with various factors and undergo chromatin remodeling in response to seasonal cues. The Polycomb silencing complex (PRC) controls the expression of flowering-related genes in photoperiodic flowering regulation. Under vernalization-dependent flowering, FLC acts as a potent flowering suppressor by downregulating the gene expression of various flower-promoting genes. Eventually, PRCs are critically involved in the regulation of FLC and FT locus interacting with several key genes in photoperiod and vernalization. Subsequently, PRCs also regulate Epigenetical events during gametogenesis and seed development as a driving force. Furthermore, DNA methylation in the context of CHG, CG, and CHH methylation plays a critical role in embryogenesis. DNA glycosylase DME (DEMETER) is responsible for demethylation during seed development. Thus, the review briefly discusses flowering regulation through light signaling, day length variation, temperature variation and seed development in plants.
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Affiliation(s)
- Tahir Mahmood
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Muhammad Abdullah
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Muhammad Sajjad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Guoyong Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Baojun Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China.
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Lee SW, Nugroho ABD, Park M, Moon H, Kim J, Kim DH. Identification of vernalization-related genes and cold memory element (CME) required for vernalization response in radish (Raphanus sativus L.). PLANT MOLECULAR BIOLOGY 2024; 114:5. [PMID: 38227117 DOI: 10.1007/s11103-023-01412-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024]
Abstract
Floral transition is accelerated by exposure to long-term cold like winter in plants, which is called as vernalization. Acceleration of floral transition by vernalization is observed in a diversity of biennial and perennial plants including Brassicaceae family plants. Scientific efforts to understand molecular mechanism underlying vernalization-mediated floral transition have been intensively focused in model plant Arabidopsis thaliana. To get a better understanding on floral transition by vernalization in radish (Raphanus sativus L.), we investigated transcriptomic changes taking place during vernalization in radish. Thousands of genes were differentially regulated along time course of vernalization compared to non-vernalization (NV) sample. Twelve major clusters of DEGs were identified based on distinctive expression profiles during vernalization. Radish FLC homologs were shown to exert an inhibition of floral transition when transformed into Arabidopsis plants. In addition, DNA region containing RY motifs located within a Raphanus sativus FLC homolog, RsFLC1 was found to be required for repression of RsFLC1 by vernalization. Transgenic plants harboring disrupted RY motifs were impaired in the enrichment of H3K27me3 on RsFLC1 chromatin, thus resulting in the delayed flowering in Arabidopsis. Taken together, we report transcriptomic profiles of radish during vernalization and demonstrate the requirement of RY motif for vernalization-mediated repression of RsFLC homologs in radish (Raphanus sativus L.).
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Affiliation(s)
- Sang Woo Lee
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | | | | | - Heewon Moon
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Jun Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Dong-Hwan Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea.
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Yu Y, Wang S, Wang Z, Gao R, Lee J. Arabidopsis thaliana: a powerful model organism to explore histone modifications and their upstream regulations. Epigenetics 2023; 18:2211362. [PMID: 37196184 DOI: 10.1080/15592294.2023.2211362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 04/07/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Histones are subjected to extensive covalent modifications that affect inter-nucleosomal interactions as well as alter chromatin structure and DNA accessibility. Through switching the corresponding histone modifications, the level of transcription and diverse downstream biological processes can be regulated. Although animal systems are widely used in studying histone modifications, the signalling processes that occur outside the nucleus prior to histone modifications have not been well understood due to the limitations including non viable mutants, partial lethality, and infertility of survivors. Here, we review the benefits of using Arabidopsis thaliana as the model organism to study histone modifications and their upstream regulations. Similarities among histones and key histone modifiers such as the Polycomb group (PcG) and Trithorax group (TrxG) in Drosophila, Human, and Arabidopsis are examined. Furthermore, prolonged cold-induced vernalization system has been well-studied and revealed the relationship between the controllable environment input (duration of vernalization), its chromatin modifications of FLOWERING LOCUS C (FLC), following gene expression, and the corresponding phenotypes. Such evidence suggests that research on Arabidopsis can bring insights into incomplete signalling pathways outside of the histone box, which can be achieved through viable reverse genetic screenings based on the phenotypes instead of direct monitoring of histone modifications among individual mutants. The potential upstream regulators in Arabidopsis can provide cues or directions for animal research based on the similarities between them.
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Affiliation(s)
- Yang Yu
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Sihan Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Ziqin Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Renwei Gao
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Joohyun Lee
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
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Shemesh-Mayer E, Faigenboim A, Sherman A, Gao S, Zeng Z, Liu T, Kamenetsky-Goldstein R. Deprivation of Sexual Reproduction during Garlic Domestication and Crop Evolution. Int J Mol Sci 2023; 24:16777. [PMID: 38069099 PMCID: PMC10706073 DOI: 10.3390/ijms242316777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Garlic, originating in the mountains of Central Asia, has undergone domestication and subsequent widespread introduction to diverse regions. Human selection for adaptation to various climates has resulted in the development of numerous garlic varieties, each characterized by specific morphological and physiological traits. However, this process has led to a loss of fertility and seed production in garlic crops. In this study, we conducted morpho-physiological and transcriptome analyses, along with whole-genome resequencing of 41 garlic accessions from different regions, in order to assess the variations in reproductive traits among garlic populations. Our findings indicate that the evolution of garlic crops was associated with mutations in genes related to vernalization and the circadian clock. The decline in sexual reproduction is not solely attributed to a few mutations in specific genes, but is correlated with extensive alterations in the genetic regulation of the annual cycle, stress adaptations, and environmental requirements. The regulation of flowering ability, stress response, and metabolism occurs at both the genetic and transcriptional levels. We conclude that the migration and evolution of garlic crops involve substantial and diverse changes across the entire genome landscape. The construction of a garlic pan-genome, encompassing genetic diversity from various garlic populations, will provide further insights for research into and the improvement of garlic crops.
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Affiliation(s)
- Einat Shemesh-Mayer
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel; (E.S.-M.); (A.F.); (A.S.)
| | - Adi Faigenboim
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel; (E.S.-M.); (A.F.); (A.S.)
| | - Amir Sherman
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel; (E.S.-M.); (A.F.); (A.S.)
| | - Song Gao
- College of Horticulture and Landscape Architecture, Yangzhou University, Hanjiang District, Yangzhou 225012, China; (S.G.); (Z.Z.); (T.L.)
| | - Zheng Zeng
- College of Horticulture and Landscape Architecture, Yangzhou University, Hanjiang District, Yangzhou 225012, China; (S.G.); (Z.Z.); (T.L.)
| | - Touming Liu
- College of Horticulture and Landscape Architecture, Yangzhou University, Hanjiang District, Yangzhou 225012, China; (S.G.); (Z.Z.); (T.L.)
| | - Rina Kamenetsky-Goldstein
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel; (E.S.-M.); (A.F.); (A.S.)
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Karami O, Mueller-Roeber B, Rahimi A. The central role of stem cells in determining plant longevity variation. PLANT COMMUNICATIONS 2023; 4:100566. [PMID: 36840355 PMCID: PMC10504568 DOI: 10.1016/j.xplc.2023.100566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/10/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Vascular plants display a huge variety of longevity patterns, from a few weeks for several annual species up to thousands of years for some perennial species. Understanding how longevity variation is structured has long been considered a fundamental aspect of the life sciences in view of evolution, species distribution, and adaptation to diverse environments. Unlike animals, whose organs are typically formed during embryogenesis, vascular plants manage to extend their life by continuously producing new tissues and organs in apical and lateral directions via proliferation of stem cells located within specialized tissues called meristems. Stem cells are the main source of plant longevity. Variation in plant longevity is highly dependent on the activity and fate identity of stem cells. Multiple developmental factors determine how stem cells contribute to variation in plant longevity. In this review, we provide an overview of the genetic mechanisms, hormonal signaling, and environmental factors involved in controlling plant longevity through long-term maintenance of stem cell fate identity.
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Affiliation(s)
- Omid Karami
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
| | - Bernd Mueller-Roeber
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam, Germany
| | - Arezoo Rahimi
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
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Kim JH, Jung WJ, Kim MS, Seo YW. The wheat TaF-box3, SCF ubiquitin ligase component, participates in the regulation of flowering time in transgenic Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 331:111668. [PMID: 36858206 DOI: 10.1016/j.plantsci.2023.111668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/21/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Histone methylation is actively involved in plant flowering time and is regulated by a myriad of genetic pathways that integrate endogenous and exogenous signals. We identified an F-box gene from wheat (Triticum aestivum L.) and named it TaF-box3. Transcript expression analysis showed that TaF-box3 expression was gradually induced during the floret development and anthesis stages (WS2.5-10). Furthermore, ubiquitination assays have shown that TaF-box3 is a key component of the SCF ubiquitin ligase complex. TaF-box3 overexpression in Arabidopsis resulted in an early flowering phenotype and different cell sizes in leaves compared to the WT. Furthermore, the transcript level of a flowering time-related gene was significantly reduced in TaF-box3 overexpressing plants, which was linked with lower histone H3 Lys4 trimethylation (H3K4me3) and H3 Lys36 trimethylation (H3K36me3). Overexpression of TaF-box3 in Arabidopsis was shown to be involved in the regulation of flowering time by demethylating FLC chromatin, according to ChIP experiments. Protein analysis confirmed that TaMETS interacts with TaF-box3 and is ubiquitinated and degraded in a TaF-box3-dependnent manner. Based on these findings, we propose that TaF-box3 has a positive role in flowering time, which leads to a better understanding of TaF-box3 physiological mechanism in Arabidopsis.
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Affiliation(s)
- Jae Ho Kim
- Department of Plant Biotechnology, Korea University, Seoul, the Republic of Korea; Institute of Animal Molecular Biotechnology, Korea University, Seoul, the Republic of Korea
| | - Woo Joo Jung
- Institute of Life Science and Natural Resources, Korea University, Seoul, the Republic of Korea
| | - Moon Seok Kim
- Department of Plant Biotechnology, Korea University, Seoul, the Republic of Korea
| | - Yong Weon Seo
- Department of Plant Biotechnology, Korea University, Seoul, the Republic of Korea; Ojeong Plant Breeding Research Center, Korea University, Seoul, the Republic of Korea.
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Liang C, Liu L, Zhang Z, Ze S, Pei L, Feng L, Ji M, Yang B, Zhao N. Transcriptome analysis of critical genes related to flowering in Mikania micrantha at different altitudes provides insights for a potential control. BMC Genomics 2023; 24:14. [PMID: 36627560 PMCID: PMC9832669 DOI: 10.1186/s12864-023-09108-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/02/2023] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Mikania micrantha is a vine with strong invasion ability, and its strong sexual reproduction ability is not only the main factor of harm, but also a serious obstacle to control. M. micrantha spreads mainly through seed production. Therefore, inhibiting the flowering and seed production of M. micrantha is an effective strategy to prevent from continuing to spread. RESULT The flowering number of M. micrantha is different at different altitudes. A total of 67.01 Gb of clean data were obtained from nine cDNA libraries, and more than 83.47% of the clean reads were mapped to the reference genome. In total, 5878 and 7686 significantly differentially expressed genes (DEGs) were found in E2 vs. E9 and E13 vs. E9, respectively. Based on the background annotation and gene expression, some candidate genes related to the flowering pathway were initially screened, and their expression levels in the three different altitudes in flower bud differentiation showed the same trend. That is, at an altitude of 1300 m, the flower integration gene and flower meristem gene were downregulated (such as SOC1 and AP1), and the flowering inhibition gene was upregulated (such as FRI and SVP). Additionally, the results showed that there were many DEGs involved in the hormone signal transduction pathway in the flower bud differentiation of M. micrantha at different altitudes. CONCLUSIONS Our results provide abundant sequence resources for clarifying the underlying mechanisms of flower bud differentiation and mining the key factors inhibiting the flowering and seed production of M. micrantha to provide technical support for the discovery of an efficient control method.
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Affiliation(s)
- Chen Liang
- grid.412720.20000 0004 1761 2943College of Life Sciences, Southwest Forestry University, Kunming, 650224 China
| | - Ling Liu
- grid.464490.b0000 0004 1798 048XYunnan Academy of Forestry and Grassland, Kunming, 650201 China
| | - Zhixiao Zhang
- grid.464490.b0000 0004 1798 048XYunnan Academy of Forestry and Grassland, Kunming, 650201 China
| | - Sangzi Ze
- Yunnan Forestry and Grassland Pest Control and Quarantine Bureau, Kunming, 650051 China
| | - Ling Pei
- grid.412720.20000 0004 1761 2943College of Life Sciences, Southwest Forestry University, Kunming, 650224 China
| | - Lichen Feng
- grid.412720.20000 0004 1761 2943College of Life Sciences, Southwest Forestry University, Kunming, 650224 China
| | - Mei Ji
- grid.464490.b0000 0004 1798 048XYunnan Academy of Forestry and Grassland, Kunming, 650201 China
| | - Bin Yang
- grid.412720.20000 0004 1761 2943Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, 650224 China
| | - Ning Zhao
- grid.412720.20000 0004 1761 2943College of Life Sciences, Southwest Forestry University, Kunming, 650224 China ,grid.412720.20000 0004 1761 2943Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, 650224 China
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Xu G, Tao Z, He Y. Embryonic reactivation of FLOWERING LOCUS C by ABSCISIC ACID-INSENSITIVE 3 establishes the vernalization requirement in each Arabidopsis generation. THE PLANT CELL 2022; 34:2205-2221. [PMID: 35234936 PMCID: PMC9134069 DOI: 10.1093/plcell/koac077] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
Many over-wintering plants grown in temperate climate acquire competence to flower upon prolonged cold exposure in winter, through vernalization. In Arabidopsis thaliana, prolonged cold exposure induces the silencing of the potent floral repressor FLOWERING LOCUS C (FLC) through repressive chromatin modifications by Polycomb proteins. This repression is maintained to enable flowering after return to warmth, but is reset during seed development. Here, we show that embryonic FLC reactivation occurs in two phases: resetting of cold-induced FLC silencing during embryogenesis and further FLC activation during embryo maturation. We found that the B3 transcription factor (TF) ABSCISIC ACID-INSENSITIVE 3 (ABI3) mediates both FLC resetting in embryogenesis and further activation of FLC expression in embryo maturation. ABI3 binds to the cis-acting cold memory element at FLC and recruits a scaffold protein with active chromatin modifiers to reset FLC chromatin into an active state in late embryogenesis. Moreover, in response to abscisic acid (ABA) accumulation during embryo maturation, ABI3, together with the basic leucine zipper TF ABI5, binds to an ABA-responsive cis-element to further activate FLC expression to high level. Therefore, we have uncovered the molecular circuitries underlying embryonic FLC reactivation following parental vernalization, which ensures that each generation must experience winter cold prior to flowering.
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Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis). BMC Genomics 2021; 22:819. [PMID: 34773977 PMCID: PMC8590779 DOI: 10.1186/s12864-021-08110-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/18/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The transition from vegetative growth to reproductive growth involves various pathways. Vernalization is a crucial process for floral organ formation and regulation of flowering time that is widely utilized in plant breeding. In this study, we aimed to identify the global landscape of mRNAs, microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) related to vernalization in Chinese cabbage. These data were then used to construct a competitive endogenous RNA (ceRNA) network that provides valuable information to better understand the vernalization response. RESULTS In this study, seeds sampled from the Chinese cabbage doubled haploid (DH) line 'FT' with or without vernalization treatment were used for whole-transcriptome sequencing. A total of 2702 differentially expressed (DE) mRNAs, 151 DE lncRNAs, 16 DE circRNAs, and 233 DE miRNAs were identified in the vernalization-treated seeds. Various transcription factors, such as WRKY, MYB, NAC, bHLH, MADS-box, zinc finger protein CONSTANS-like gene, and B3 domain protein, and regulatory proteins that play important roles in the vernalization pathway were identified. Additionally, we constructed a vernalization-related ceRNA-miRNA-target gene network and obtained 199 pairs of ceRNA relationships, including 108 DEmiRNA‒DEmRNA, 67 DEmiRNA‒DElncRNA, and 12 DEmiRNA‒DEcircRNA interactions, in Chinese cabbage. Furthermore, several important vernalization-related genes and their interacting lncRNAs, circRNAs, and miRNAs, which are involved in the regulation of flowering time, floral organ formation, bolting, and flowering, were identified. CONCLUSIONS Our results reveal the potential mRNA and non-coding RNAs involved in vernalization, providing a foundation for further studies on the molecular mechanisms underlying vernalization in Chinese cabbage.
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Hirsz D, Dixon LE. The Roles of Temperature-Related Post-Transcriptional Regulation in Cereal Floral Development. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112230. [PMID: 34834593 PMCID: PMC8620327 DOI: 10.3390/plants10112230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/02/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Temperature is a critical environmental signal in the regulation of plant growth and development. The temperature signal varies across a daily 24 h period, between seasons and stochastically depending on local environmental events. Extracting important information from these complex signals has led plants to evolve multiple temperature responsive regulatory mechanisms at the molecular level. In temperate cereals, we are starting to identify and understand these molecular mechanisms. In addition, we are developing an understanding of how this knowledge can be used to increase the robustness of crop yield in response to significant changes in local and global temperature patterns. To enable this, it is becoming apparent that gene regulation, regarding expression and post-transcriptional regulation, is crucial. Large transcriptomic studies are identifying global changes in spliced transcript variants and regulatory non-coding RNAs in response to seasonal and stress temperature signals in many of the cereal crops. Understanding the functions of these variants and targets of the non-coding RNAs will greatly increase how we enable the adaptation of crops. This review considers our current understanding and areas for future development.
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The Regulation of Plant Vegetative Phase Transition and Rejuvenation: miRNAs, a Key Regulator. EPIGENOMES 2021; 5:epigenomes5040024. [PMID: 34968248 PMCID: PMC8715473 DOI: 10.3390/epigenomes5040024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/13/2023] Open
Abstract
In contrast to animals, adult organs in plants are not formed during embryogenesis but generated from meristematic cells as plants advance through development. Plant development involves a succession of different phenotypic stages and the transition between these stages is termed phase transition. Phase transitions need to be tightly regulated and coordinated to ensure they occur under optimal seasonal, environmental conditions. Polycarpic perennials transition through vegetative stages and the mature, reproductive stage many times during their lifecycles and, in both perennial and annual species, environmental factors and culturing methods can reverse the otherwise unidirectional vector of plant development. Epigenetic factors regulating gene expression in response to internal cues and external (environmental) stimuli influencing the plant’s phenotype and development have been shown to control phase transitions. How developmental and environmental cues interact to epigenetically alter gene expression and influence these transitions is not well understood, and understanding this interaction is important considering the current climate change scenarios, since epigenetic maladaptation could have catastrophic consequences for perennial plants in natural and agricultural ecosystems. Here, we review studies focusing on the epigenetic regulators of the vegetative phase change and highlight how these mechanisms might act in exogenously induced plant rejuvenation and regrowth following stress.
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Yuan C, Xu J, Chen Q, Liu Q, Hu Y, Jin Y, Qin C. C-terminal domain phosphatase-like 1 (CPL1) is involved in floral transition in Arabidopsis. BMC Genomics 2021; 22:642. [PMID: 34482814 PMCID: PMC8418720 DOI: 10.1186/s12864-021-07966-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RNA polymerase II plays critical roles in transcription in eukaryotic organisms. C-terminal Domain Phosphatase-like 1 (CPL1) regulates the phosphorylation state of the C-terminal domain of RNA polymerase II subunit B1, which is critical in determining RNA polymerase II activity. CPL1 plays an important role in miRNA biogenesis, plant growth and stress responses. Although cpl1 mutant showes delayed-flowering phenotype, the molecular mechanism behind CPL1's role in floral transition is still unknown. RESULTS To study the role of CPL1 during the floral transition, we first tested phenotypes of cpl1-3 mutant, which harbors a point-mutation. The cpl1-3 mutant contains a G-to-A transition in the second exon, which results in an amino acid substitution from Glu to Lys (E116K). Further analyses found that the mutated amino acid (Glu) was conserved in these species. As a result, we found that the cpl1-3 mutant experienced delayed flowering under both long- and short-day conditions, and CPL1 is involved in the vernalization pathway. Transcriptome analysis identified 109 genes differentially expressed in the cpl1 mutant, with 2 being involved in floral transition. Differential expression of the two flowering-related DEGs was further validated by qRT-PCR. CONCLUSIONS Flowering genetic pathways analysis coupled with transciptomic analysis provides potential genes related to floral transition in the cpl1-3 mutant, and a framework for future studies of the molecular mechanisms behind CPL1's role in floral transition.
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Affiliation(s)
- Chen Yuan
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Jingya Xu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Qianqian Chen
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Qinggang Liu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Yikai Hu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Yicheng Jin
- Division of Research and Development, Oriomics Inc, 310018, Hangzhou, China
| | - Cheng Qin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China.
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Zong W, Zhao B, Xi Y, Bordiya Y, Mun H, Cerda NA, Kim DH, Sung S. DEK domain-containing proteins control flowering time in Arabidopsis. THE NEW PHYTOLOGIST 2021; 231:182-192. [PMID: 33774831 PMCID: PMC8985477 DOI: 10.1111/nph.17366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/20/2021] [Indexed: 05/07/2023]
Abstract
Evolutionarily conserved DEK domain-containing proteins have been implicated in multiple chromatin-related processes, mRNA splicing and transcriptional regulation in eukaryotes. Here, we show that two DEK proteins, DEK3 and DEK4, control the floral transition in Arabidopsis. DEK3 and DEK4 directly associate with chromatin of related flowering repressors, FLOWERING LOCUS C (FLC), and its two homologs, MADS AFFECTING FLOWERING4 (MAF4) and MAF5, to promote their expression. The binding of DEK3 and DEK4 to a histone octamer in vivo affects histone modifications at FLC, MAF4 and MAF5 loci. In addition, DEK3 and DEK4 interact with RNA polymerase II and promote the association of RNA polymerase II with FLC, MAF4 and MAF5 chromatin to promote their expression. Our results show that DEK3 and DEK4 directly interact with chromatin to facilitate the transcription of key flowering repressors and thus prevent precocious flowering in Arabidopsis.
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Affiliation(s)
- Wei Zong
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Bo Zhao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yanpeng Xi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yogendra Bordiya
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Hyungwon Mun
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Nicholas A Cerda
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Dong-Hwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
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Dai Y, Sun X, Wang C, Li F, Zhang S, Zhang H, Li G, Yuan L, Chen G, Sun R, Zhang S. Gene co-expression network analysis reveals key pathways and hub genes in Chinese cabbage (Brassica rapa L.) during vernalization. BMC Genomics 2021; 22:236. [PMID: 33823810 PMCID: PMC8022416 DOI: 10.1186/s12864-021-07510-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 03/05/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Vernalization is a type of low temperature stress used to promote rapid bolting and flowering in plants. Although rapid bolting and flowering promote the reproduction of Chinese cabbages (Brassica rapa L. ssp. pekinensis), this process causes their commercial value to decline. Clarifying the mechanisms of vernalization is essential for its further application. We performed RNA sequencing of gradient-vernalization in order to explore the reasons for the different bolting process of two Chinese cabbage accessions during vernalization. RESULTS There was considerable variation in gene expression between different-bolting Chinese cabbage accessions during vernalization. Comparative transcriptome analysis and weighted gene co-expression network analysis (WGCNA) were performed for different-bolting Chinese cabbage during different vernalization periods. The biological function analysis and hub gene annotation of highly relevant modules revealed that shoot system morphogenesis and polysaccharide and sugar metabolism caused early-bolting 'XBJ' to bolt and flower faster; chitin, ABA and ethylene-activated signaling pathways were enriched in late-bolting 'JWW'; and leaf senescence and carbohydrate metabolism enrichment were found in the two Chinese cabbage-related modules, indicating that these pathways may be related to bolting and flowering. The high connectivity of hub genes regulated vernalization, including MTHFR2, CPRD49, AAP8, endoglucanase 10, BXLs, GATLs, and WRKYs. Additionally, five genes related to flower development, BBX32 (binds to the FT promoter), SUS1 (increases FT expression), TSF (the closest homologue of FT), PAO and NAC029 (plays a role in leaf senescence), were expressed in the two Chinese cabbage accessions. CONCLUSION The present work provides a comprehensive overview of vernalization-related gene networks in two different-bolting Chinese cabbages during vernalization. In addition, the candidate pathways and hub genes related to vernalization identified here will serve as a reference for breeders in the regulation of Chinese cabbage production.
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Affiliation(s)
- Yun Dai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Changjiang West Road, NO.130, Hefei, 230036, Anhui, China
| | - Xiao Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chenggang Wang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Changjiang West Road, NO.130, Hefei, 230036, Anhui, China
| | - Fei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shifan Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guoliang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lingyun Yuan
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Changjiang West Road, NO.130, Hefei, 230036, Anhui, China
| | - Guohu Chen
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Changjiang West Road, NO.130, Hefei, 230036, Anhui, China
| | - Rifei Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shujiang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Dai GY, Chen DK, Sun YP, Liang WY, Liu Y, Huang LQ, Li YK, He JF, Yao N. The Arabidopsis KH-domain protein FLOWERING LOCUS Y delays flowering by upregulating FLOWERING LOCUS C family members. PLANT CELL REPORTS 2020; 39:1705-1717. [PMID: 32948902 DOI: 10.1007/s00299-020-02598-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
We identified FLY as a previously uncharacterized RNA-binding-family protein that controls flowering time by positively regulating the expression of FLC clade members. The ability of flowering plants to adjust the timing of the floral transition based on endogenous and environmental signals contributes to their adaptive success. In Arabidopsis thaliana, the MADS-domain protein FLOWERING LOCUS C (FLC) and the FLC clade members FLOWERING LOCUS M/MADS AFFECTING FLOWERING1 (FLM/MAF1), MAF2, MAF3, MAF4, and MAF5 form nuclear complexes that repress flowering under noninductive conditions. However, how FLM/MAF genes are regulated requires further study. Using a genetic strategy, we showed that the previously uncharacterized K-homology (KH) domain protein FLOWERING LOCUS Y (FLY) modulates flowering time. The fly-1 knockout mutant and FLY artificial microRNA knockdown line flowered earlier than the wild type under long- and short-day conditions. The knockout fly-1 allele, a SALK T-DNA insertion mutant, contains an ~ 110-kb genomic deletion induced by T-DNA integration. FLC clade members were downregulated in the fly-1 mutants and FLY artificial microRNA knockdown line, whereas the level of the FLC antisense transcript COOLAIR was similar to that of the wild type. Our results identify FLY as a regulator that affects flowering time through upregulation of FLC clade members.
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Affiliation(s)
- Guang-Yi Dai
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ding-Kang Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yun-Peng Sun
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wei-Yi Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yu Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Li-Qun Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yong-Kang Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jia-Fan He
- School of Agriculture, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Nan Yao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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Golicz AA, Steinfort U, Arya H, Singh MB, Bhalla PL. Analysis of the quinoa genome reveals conservation and divergence of the flowering pathways. Funct Integr Genomics 2020; 20:245-258. [PMID: 31515641 PMCID: PMC7018680 DOI: 10.1007/s10142-019-00711-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 07/19/2019] [Accepted: 08/14/2019] [Indexed: 01/09/2023]
Abstract
Quinoa (Chenopodium quinoa Willd.) is a grain crop grown in the Andes renowned as a highly nutritious plant exhibiting tolerance to abiotic stress such as drought, cold and high salinity. Quinoa grows across a range of latitudes corresponding to differing day lengths, suggesting regional adaptations of flowering regulation. Improved understanding and subsequent modification of the flowering process, including flowering time, ensuring high yields, is one of the key factors behind expansion of cultivation zones and goals of the crop improvement programs worldwide. However, our understanding of the molecular basis of flower initiation and development in quinoa is limited. Here, we use a computational approach to perform genome-wide identification and analysis of 611 orthologues of the Arabidopsis thaliana flowering genes. Conservation of the genes belonging to the photoperiod, gibberellin and autonomous pathways was observed, while orthologues of the key genes found in the vernalisation pathway (FRI, FLC) were absent from the quinoa genome. Our analysis indicated that on average each Arabidopsis flowering gene has two orthologous copies in quinoa. Several genes including orthologues of MIF1, FT and TSF were identified as homologue-rich genes in quinoa. We also identified 459 quinoa-specific genes uniquely expressed in the flower and/or meristem, with no known orthologues in other species. The genes identified provide a resource and framework for further studies of flowering in quinoa and related species. It will serve as valuable resource for plant biologists, crop physiologists and breeders to facilitate further research and establishment of modern breeding programs for quinoa.
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Affiliation(s)
- Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia.
| | - Ursula Steinfort
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Hina Arya
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
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19
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He Y, Chen T, Zeng X. Genetic and Epigenetic Understanding of the Seasonal Timing of Flowering. PLANT COMMUNICATIONS 2020; 1:100008. [PMID: 33404547 PMCID: PMC7747966 DOI: 10.1016/j.xplc.2019.100008] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The developmental transition to flowering in many plants is timed by changing seasons, which enables plants to flower at a season that is favorable for seed production. Many plants grown at high latitudes perceive the seasonal cues of changing day length and/or winter cold (prolonged cold exposure), to regulate the expression of flowering-regulatory genes through the photoperiod pathway and/or vernalization pathway, and thus align flowering with a particular season. Recent studies in the model flowering plant Arabidopsis thaliana have revealed that diverse transcription factors engage various chromatin modifiers to regulate several key flowering-regulatory genes including FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT) in response to seasonal signals. Here, we summarize the current understanding of molecular and chromatin-regulatory or epigenetic mechanisms underlying the vernalization response and photoperiodic control of flowering in Arabidopsis. Moreover, the conservation and divergence of regulatory mechanisms for seasonal flowering in crops and other plants are briefly discussed.
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20
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McKeown P, Spillane C. An Overview of Current Research in Plant Epigenetic and Epigenomic Phenomena. Methods Mol Biol 2020; 2093:3-13. [PMID: 32088885 DOI: 10.1007/978-1-0716-0179-2_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: 06/10/2023]
Abstract
Biological phenomena defined as having an "epigenetic" component (according to various definitions) have been extensively studied in plant systems and illuminated many mechanisms by which gene expression is regulated and patterns of expression inherited through cell divisions. This second volume of Plant Epigenetics and Epigenomics: Methods in Molecular Biology builds on the work of its predecessor to describe cutting-edge tools for plant epigenetic and epigenomic research, and embrace crop and forestry species as well as natural populations and further insights from model species. In this chapter, the historical background to plant epigenetic and epigenomic research is summarized, and key considerations for the interpretation of current data are outlined.
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Affiliation(s)
- Peter McKeown
- Plant and Agribiosciences Research Centre, Ryan Institute, National University of Ireland Galway (NUI Galway), Galway, Ireland.
| | - Charles Spillane
- Plant and Agribiosciences Research Centre, Ryan Institute, National University of Ireland Galway (NUI Galway), Galway, Ireland
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21
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Testone G, Sobolev A, Gonnella M, Renna M, Mannina L, Capitani D, Arnesi G, Biancari T, Giannino D. Insights into sucrose pathway of chicory stems by integrative transcriptomic and metabolic analyses. PHYTOCHEMISTRY 2019; 167:112086. [PMID: 31450092 DOI: 10.1016/j.phytochem.2019.112086] [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: 01/11/2019] [Revised: 06/21/2019] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
The worldwide-cultivated chicory (Cichorium intybus L.) produces food and beneficial compounds, and young pre-flowering inflorescence stems are newly marketed vegetables. These sink-organs undergo growth by metabolizing sugars of leaf origin; the carbohydrate content and sweetness are crucial aspects for consumers' nutrition and acceptance. NMR profiling of 31 hydrosoluble phytochemicals showed that stem contents varied as influenced by genotype, environment and interaction, and that higher sucrose levels were associated with the sweeter of two landraces. Integrative analyses of metabolic and transcriptomic profile variations allowed the dissection of sucrose pathway. Overall, 427 and 23 unigenes respectively fell into the categories of sucrose metabolism and sugar carriers. Among 10 differentially expressed genes, the 11474/sucrose synthase, 53458/fructokinase, 9306 and 17035/hexokinases, and 20171/SWEET-type genes significantly associated to sugar content variation, and deduced proteins were characterised in silico. Correlation analyses encompassing sugar level variation, expressions of the former genes and of computationally assigned transcription factors (10938/NAC, 14712/bHLH, 40133/TALE and 17846/MIKC) revealed a gene network. The latter was minimally affected by the environment and accomplished with markers, representing a resource for biological studies and breeding.
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Affiliation(s)
- Giulio Testone
- Institute of Agricultural Biology and Biotechnology - Unit of Rome, National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, Rome, Italy
| | - Anatoly Sobolev
- Institute for Biological Systems, "Annalaura Segre" Magnetic Resonance Laboratory, CNR, Via Salaria Km 29,300, 00015, Monterotondo, Rome, Italy
| | - Maria Gonnella
- Institute of Sciences of Food Production, CNR, Via G. Amendola 122/O, 70126, Bari, Italy
| | - Massimiliano Renna
- Institute of Sciences of Food Production, CNR, Via G. Amendola 122/O, 70126, Bari, Italy; Department of Agricultural and Environmental Science, University of Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Luisa Mannina
- Institute for Biological Systems, "Annalaura Segre" Magnetic Resonance Laboratory, CNR, Via Salaria Km 29,300, 00015, Monterotondo, Rome, Italy; Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Donatella Capitani
- Institute for Biological Systems, "Annalaura Segre" Magnetic Resonance Laboratory, CNR, Via Salaria Km 29,300, 00015, Monterotondo, Rome, Italy
| | - Giuseppe Arnesi
- Enza Zaden Italia, Strada Statale Aurelia km. 96.400, 01016, Tarquinia, Viterbo, Italy
| | - Tiziano Biancari
- Enza Zaden Italia, Strada Statale Aurelia km. 96.400, 01016, Tarquinia, Viterbo, Italy
| | - Donato Giannino
- Institute of Agricultural Biology and Biotechnology - Unit of Rome, National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, Rome, Italy.
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22
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A-L LG, C LP, A D, S M. Developmental, genetic and environmental variations of global DNA methylation in the first leaves emerging from the shoot apical meristem in poplar trees. PLANT SIGNALING & BEHAVIOR 2019; 14:1596717. [PMID: 30915897 PMCID: PMC6546136 DOI: 10.1080/15592324.2019.1596717] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
In the context of climate changes, clarifying the causes underlying tree phenotypic plasticity and adaptation is crucial. Studies suggest a role of epigenetic mechanisms in response to external stimuli, raising the question whether such processes can promote acclimation of trees exposed to adverse climate conditions. Recently, we revealed an environmental epigenetic footprint in the shoot apical meristem (SAM) which could partially be transmitted mitotically, for several months, up until the winter-dormant bud in field conditions. Here, we extended our previous analysis to the leaves of the same P. deltoides×P. nigra clones. We aimed at estimating the range of developmentally, genetically, and environmentally induced variations on DNA methylation. We showed that only the first leaves emerging from the SAM displayed variations of DNA methylation under changing water conditions. We also found that these variations are genotype- and pedoclimatic site-dependent. Altogether, our data raised questions and perspectives on the direct acquisition, the maintenance of environmentally induced DNA methylation changes, and their mitotic transmission from the SAM to the first emerging leaves.
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Affiliation(s)
- Le Gac A-L
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC 1328 INRA, Université d’Orléans, Orléans, France
- Institute for Biology III, University of Freiburg, Freiburg, Germany
- CONTACT Maury S Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC 1328 INRA, Université d’Orléans, Orléans 45067, France
| | - Lafon-Placette C
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC 1328 INRA, Université d’Orléans, Orléans, France
- Department of Botany, Charles University, Prague, Czech Republic
| | - Delaunay A
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC 1328 INRA, Université d’Orléans, Orléans, France
| | - Maury S
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC 1328 INRA, Université d’Orléans, Orléans, France
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23
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Gómez R, Méndez-Vigo B, Marcer A, Alonso-Blanco C, Picó FX. Quantifying temporal change in plant population attributes: insights from a resurrection approach. AOB PLANTS 2018; 10:ply063. [PMID: 30370042 PMCID: PMC6198925 DOI: 10.1093/aobpla/ply063] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 10/05/2018] [Indexed: 05/11/2023]
Abstract
Rapid evolution in annual plants can be quantified by comparing phenotypic and genetic changes between past and contemporary individuals from the same populations over several generations. Such knowledge will help understand the response of plants to rapid environmental shifts, such as the ones imposed by global climate change. To that end, we undertook a resurrection approach in Spanish populations of the annual plant Arabidopsis thaliana that were sampled twice over a decade. Annual weather records were compared to their historical records to extract patterns of climatic shifts over time. We evaluated the differences between samplings in flowering time, a key life-history trait with adaptive significance, with a field experiment. We also estimated genetic diversity and differentiation based on neutral nuclear markers and nucleotide diversity in candidate flowering time (FRI and FLC) and seed dormancy (DOG1) genes. The role of genetic drift was estimated by computing effective population sizes with the temporal method. Overall, two climatic scenarios were detected: intense warming with increased precipitation and moderate warming with decreased precipitation. The average flowering time varied little between samplings. Instead, within-population variation in flowering time exhibited a decreasing trend over time. Substantial temporal changes in genetic diversity and differentiation were observed with both nuclear microsatellites and candidate genes in all populations, which were interpreted as the result of natural demographic fluctuations. We conclude that drought stress caused by moderate warming with decreased precipitation may have the potential to reduce within-population variation in key life-cycle traits, perhaps as a result of stabilizing selection on them, and to constrain the genetic differentiation over time. Besides, the demographic behaviour of populations probably accounts for the substantial temporal patterns of genetic variation, while keeping rather constant those of phenotypic variation.
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Affiliation(s)
- Rocío Gómez
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Arnald Marcer
- CREAF, Cerdanyola del Vallès, Spain
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
- Corresponding author’s e-mail address:
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Huan Q, Mao Z, Chong K, Zhang J. Global analysis of H3K4me3/H3K27me3 in Brachypodium distachyon reveals VRN3 as critical epigenetic regulation point in vernalization and provides insights into epigenetic memory. THE NEW PHYTOLOGIST 2018; 219:1373-1387. [PMID: 30063801 DOI: 10.1111/nph.15288] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 05/20/2018] [Indexed: 05/21/2023]
Abstract
Vernalization, the requirement of plants for long-term exposure to low environmental temperature for flowering, is an epigenetic phenomenon. Histone modification regulation has been revealed in vernalization, but is limited to key genes. Now, we know that VRN1 is epigenetically critical for monocots. Genome-wide analysis is still unavailable, however. We performed chromatin immunoprecipitation-sequencing for H3K4me3/H3K27me3 in Brachypodium distachyon to obtain a global view of histone modifications in vernalization on a genome-wide scale and for different pathways/genes. Our data showed that H3K4me3 and H3K27me3 play distinct roles in vernalization. Unlike H3K4me3, H3K27me3 exhibited regional regulation, showed main regulation targets in vernalization and contributed to epigenetic memory. For genes in four flowering regulation pathways, only FT2 (functional ortholog of VRN3 in B. distachyon) and VRN1 showed coordinated changes in H3K4me3/H3K27me3. The epigenetic response at VRN3 was weaker under short-day than under long-day conditions. VRN3 was revealed as an epigenetic regulation point integrating vernalization and day length signals. We globally identified genes maintaining vernalization-induced epigenetic changes. Most of these genes showed dose-dependent vernalization responses, revealing a quantitative 'recording system' for vernalization. Our studies shed light on the epigenetic role of VRN3 and H3K4me3/H3K27me3 in vernalization and reveal genes underlying epigenetic memory, laying the foundation for further study.
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Affiliation(s)
- Qing Huan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhiwei Mao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jingyu Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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25
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Meller B, Kuźnicki D, Arasimowicz-Jelonek M, Deckert J, Floryszak-Wieczorek J. BABA-Primed Histone Modifications in Potato for Intergenerational Resistance to Phytophthora infestans. FRONTIERS IN PLANT SCIENCE 2018; 9:1228. [PMID: 30233606 PMCID: PMC6135045 DOI: 10.3389/fpls.2018.01228] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/02/2018] [Indexed: 05/23/2023]
Abstract
In this paper we analyzed β-aminobutyric acid (BABA)-primed epigenetic adjustment of potato cv. "Sarpo Mira" to Phytophthora infestans. The first stress-free generation of the potato genotype obtained from BABA-primed parent plants via tubers and seeds showed pronounced resistance to the pathogen, which was tuned with the transcriptional memory of SA-responsive genes. During the early priming phase before the triggering stress, we found robust bistable deposition of histone marks (H3K4me2 and H3K27me3) on the NPR1 (Non-expressor of PR genes) and the SNI1 gene (Suppressor of NPR1, Inducible), in which transcription antagonized silencing. Switchable chromatin states of these adverse systemic acquired resistance (SAR) regulators probably reprogrammed responsiveness of the PR1 and PR2 genes and contributed to stress imprinting. The elevated levels of heritable H3K4me2 tag in the absence of transcription on SA-dependent genes in BABA-primed (F0) and its vegetative and generative progeny (F1) before pathogen challenge provided evidence for the epigenetic mark for intergenerational memory in potato. Moreover, our study revealed that histone acetylation was not critical for maintaining BABA-primed defense information until the plants were triggered with the virulent pathogen when rapid and boosted PRs gene expression probably required histone acetyltransferase (HAT) activity both in F0 and F1 progeny.
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Affiliation(s)
- Barbara Meller
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | - Daniel Kuźnicki
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | | | - Joanna Deckert
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
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Epigenetic Environmental Memories in Plants: Establishment, Maintenance, and Reprogramming. Trends Genet 2018; 34:856-866. [PMID: 30144941 DOI: 10.1016/j.tig.2018.07.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/15/2018] [Accepted: 07/19/2018] [Indexed: 12/21/2022]
Abstract
Plants are immobile and must respond to or endure fluctuating surroundings and diverse environmental challenges. Environmental inputs often induce chromatin modifications at various responsive genes and consequent changes in their expression. Environment-induced chromatin marks at certain loci are transmittable through cell divisions after relief from the original external signals, leading to acquired 'memorization' of environmental experiences in plants, namely epigenetic environmental memories, which enable plants to adapt to environmental changes or to perform better when events recur. Here, we review recent progress in epigenetic or chromatin-mediated environmental memories in plants, including defense priming, stress memories, and 'epigenetic memory of winter cold' or vernalization. Various advances in epigenetic mechanisms underlying plant-environment interactions highlight that plant environmental epigenetics is emerging as an important area in plant biology.
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27
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28
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Schilling S, Pan S, Kennedy A, Melzer R. MADS-box genes and crop domestication: the jack of all traits. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1447-1469. [PMID: 29474735 DOI: 10.1093/jxb/erx479] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/10/2018] [Indexed: 05/25/2023]
Abstract
MADS-box genes are key regulators of virtually every aspect of plant reproductive development. They play especially prominent roles in flowering time control, inflorescence architecture, floral organ identity determination, and seed development. The developmental and evolutionary importance of MADS-box genes is widely acknowledged. However, their role during flowering plant domestication is less well recognized. Here, we provide an overview illustrating that MADS-box genes have been important targets of selection during crop domestication and improvement. Numerous examples from a diversity of crop plants show that various developmental processes have been shaped by allelic variations in MADS-box genes. We propose that new genomic and genome editing resources provide an excellent starting point for further harnessing the potential of MADS-box genes to improve a variety of reproductive traits in crops. We also suggest that the biophysics of MADS-domain protein-protein and protein-DNA interactions, which is becoming increasingly well characterized, makes them especially suited to exploit coding sequence variations for targeted breeding approaches.
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Affiliation(s)
- Susanne Schilling
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Sirui Pan
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Alice Kennedy
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Rainer Melzer
- School of Biology and Environmental Science, University College Dublin, Irel
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29
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Zhong J, Robbett M, Poire A, Preston JC. Successive evolutionary steps drove Pooideae grasses from tropical to temperate regions. THE NEW PHYTOLOGIST 2018; 217:925-938. [PMID: 29091285 DOI: 10.1111/nph.14868] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/22/2017] [Indexed: 06/07/2023]
Abstract
Angiosperm adaptations to seasonally cold climates have occurred multiple times independently. However, the observation that less than half of all angiosperm families are represented in temperate latitudes suggests internal constraints on the evolution of cold tolerance/avoidance strategies. Similar to angiosperms as a whole, grasses are primarily tropical, but one major clade, subfamily Pooideae, radiated extensively within temperate regions. It is posited that this Pooideae niche transition was facilitated by an early origin of long-term cold responsiveness around the base of the subfamily, and that a set of more ancient pathways enabled evolution of seasonal cold tolerance. To test this, we compared transcriptome-level responses of disparate Pooideae to short-/long-term cold and with those previously known in the subtropical grass rice (Ehrhartoideae). Analyses identified several highly conserved cold-responsive 'orthogroups' within our focal Pooideae species that originated successively during the diversification of land plants, predominantly via gene duplication. The majority of conserved Pooideae cold-responsive genes appear to have ancient roles in stress responses, with most of the orthogroups also being sensitive to cold in rice. However, a subgroup of genes was likely co-opted de novo early in the Pooideae. These results highlight a plausible stepwise evolutionary trajectory for cold adaptations across Pooideae.
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Affiliation(s)
- Jinshun Zhong
- Department of Plant Biology, University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT, 05405, USA
| | - Meghan Robbett
- Department of Plant Biology, University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT, 05405, USA
| | - Alfonso Poire
- Department of Plant Biology, University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT, 05405, USA
| | - Jill C Preston
- Department of Plant Biology, University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT, 05405, USA
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Kim DH, Xi Y, Sung S. Modular function of long noncoding RNA, COLDAIR, in the vernalization response. PLoS Genet 2017; 13:e1006939. [PMID: 28759577 PMCID: PMC5552341 DOI: 10.1371/journal.pgen.1006939] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 08/10/2017] [Accepted: 07/21/2017] [Indexed: 12/14/2022] Open
Abstract
The long noncoding RNA COLDAIR is necessary for the repression of a floral repressor FLOWERING LOCUS C (FLC) during vernalization in Arabidopsis thaliana. The repression of FLC is mediated by increased enrichment of Polycomb Repressive Complex 2 (PRC2) and subsequent trimethylation of Histone H3 Lysine 27 (H3K27me3) at FLC chromatin. In this study we found that the association of COLDAIR with chromatin occurs only at the FLC locus and that the central region of the COLDAIR transcript is critical for this interaction. A modular motif in COLDAIR is responsible for the association with PRC2 in vitro, and the mutations within the motif that reduced the association of COLDAIR with PRC2 resulted in vernalization insensitivity. The vernalization insensitivity caused by mutant COLDAIR was rescued by the ectopic expression of the wild-type COLDAIR. Our study reveals the molecular framework in which COLDAIR lncRNA mediates the PRC2-mediated repression of FLC during vernalization.
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Affiliation(s)
- Dong-Hwan Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, the University of Texas at Austin, TX, United States of America
| | - Yanpeng Xi
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, the University of Texas at Austin, TX, United States of America
| | - Sibum Sung
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, the University of Texas at Austin, TX, United States of America
- * E-mail:
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31
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Liu C, Wang S, Xu W, Liu X. Genome-wide transcriptome profiling of radish (Raphanus sativus L.) in response to vernalization. PLoS One 2017; 12:e0177594. [PMID: 28498850 PMCID: PMC5428929 DOI: 10.1371/journal.pone.0177594] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 04/28/2017] [Indexed: 11/21/2022] Open
Abstract
Vernalization is a key process for premature bolting. Although many studies on vernalization have been reported, the molecular mechanism of vernalization is still largely unknown in radish. In this study, we sequenced the transcriptomes of radish seedlings at three different time points during vernalization. More than 36 million clean reads were generated for each sample and the portions mapped to the reference genome were all above 67.0%. Our results show that the differentially expressed genes (DEGs) between room temperature and the early stage of vernalization (4,845) are the most in all treatments pairs. A series of vernalization related genes, including two FLOWERING LOCUS C (FLC) genes, were screened according to the annotations. A total of 775 genes were also filtered as the vernalization related candidates based on their expression profiles. Cold stress responsive genes were also analyzed to further confirm the sequencing result. Several key genes in vernalization or cold stress response were validated by quantitative RT-PCR (RT-qPCR). This study identified a number of genes that may be involved in vernalization, which are useful for other functional genomics research in radish.
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Affiliation(s)
- Chen Liu
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Jinan, Shandong, People's Republic of China
| | - Shufen Wang
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Jinan, Shandong, People's Republic of China
- * E-mail:
| | - Wenling Xu
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Jinan, Shandong, People's Republic of China
| | - Xianxian Liu
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Jinan, Shandong, People's Republic of China
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32
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Yan Q, Xia X, Sun Z, Fang Y. Depletion of Arabidopsis SC35 and SC35-like serine/arginine-rich proteins affects the transcription and splicing of a subset of genes. PLoS Genet 2017; 13:e1006663. [PMID: 28273088 PMCID: PMC5362245 DOI: 10.1371/journal.pgen.1006663] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 03/22/2017] [Accepted: 02/28/2017] [Indexed: 12/23/2022] Open
Abstract
Serine/arginine-rich (SR) proteins are important splicing factors which play significant roles in spliceosome assembly and splicing regulation. However, little is known regarding their biological functions in plants. Here, we analyzed the phenotypes of mutants upon depleting different subfamilies of Arabidopsis SR proteins. We found that loss of the functions of SC35 and SC35-like (SCL) proteins cause pleiotropic changes in plant morphology and development, including serrated leaves, late flowering, shorter roots and abnormal silique phyllotaxy. Using RNA-seq, we found that SC35 and SCL proteins play roles in the pre-mRNA splicing. Motif analysis revealed that SC35 and SCL proteins preferentially bind to a specific RNA sequence containing the AGAAGA motif. In addition, the transcriptions of a subset of genes are affected by the deletion of SC35 and SCL proteins which interact with NRPB4, a specific subunit of RNA polymerase II. The splicing of FLOWERING LOCUS C (FLC) intron1 and transcription of FLC were significantly regulated by SC35 and SCL proteins to control Arabidopsis flowering. Therefore, our findings provide mechanistic insight into the functions of plant SC35 and SCL proteins in the regulation of splicing and transcription in a direct or indirect manner to maintain the proper expression of genes and development. SR proteins were identified to be important splicing factors. This work generated mutants of different subfamilies of the classic Arabidopsis SR proteins. Genetic analysis revealed that loss of the function of SC35/SCL proteins influences the plant development. This study revealed SC35/SCL proteins regulate alternative splicing, preferentially bind a specific RNA motif, interact with NRPB4, and affect the transcription of a subset of genes. This study further revealed that SC35/SCL proteins control flowering by regulating the splicing and transcription of FLC. These results shed light on the functions of SR proteins in plants.
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Affiliation(s)
- Qingqing Yan
- National key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Xi Xia
- National key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Zhenfei Sun
- National key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Yuda Fang
- National key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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33
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Bouché F, Woods DP, Amasino RM. Winter Memory throughout the Plant Kingdom: Different Paths to Flowering. PLANT PHYSIOLOGY 2017; 173:27-35. [PMID: 27756819 PMCID: PMC5210730 DOI: 10.1104/pp.16.01322] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 09/21/2016] [Indexed: 05/18/2023]
Abstract
Molecular mechanisms contribute to the memory of winter in different plant groups.
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Affiliation(s)
- Frédéric Bouché
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706 (F.B., D.P.W., R.M.A.); and
- United States Department of Energy Great Lakes Bioenergy Research Center, Madison, Wisconsin 53726 (D.P.W., R.M.A.)
| | - Daniel P Woods
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706 (F.B., D.P.W., R.M.A.); and
- United States Department of Energy Great Lakes Bioenergy Research Center, Madison, Wisconsin 53726 (D.P.W., R.M.A.)
| | - Richard M Amasino
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706 (F.B., D.P.W., R.M.A.); and
- United States Department of Energy Great Lakes Bioenergy Research Center, Madison, Wisconsin 53726 (D.P.W., R.M.A.)
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34
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Gong X, Shen L, Peng YZ, Gan Y, Yu H. DNA Topoisomerase Iα Affects the Floral Transition. PLANT PHYSIOLOGY 2017; 173:642-654. [PMID: 27837087 PMCID: PMC5210759 DOI: 10.1104/pp.16.01603] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/08/2016] [Indexed: 05/16/2023]
Abstract
DNA topoisomerases modulate DNA topology to maintain chromosome superstructure and genome integrity, which is indispensable for DNA replication and RNA transcription. Their function in plant development still remains largely unknown. Here, we report a hitherto unidentified role of Topoisomerase Iα (TOP1α) in controlling flowering time in Arabidopsis (Arabidopsis thaliana). Loss of function of TOP1α results in early flowering under both long and short days. This is attributed mainly to a decrease in the expression of a central flowering repressor, FLOWERING LOCUS C (FLC), and its close homologs, MADS AFFECTING FLOWERING4 (MAF4) and MAF5, during the floral transition. TOP1α physically binds to the genomic regions of FLC, MAF4, and MAF5 and promotes the association of RNA polymerase II complexes to their transcriptional start sites. These correlate with the changes in histone modifications but do not directly affect nucleosome occupancy at these loci. Our results suggest that TOP1α mediates DNA topology to facilitate the recruitment of RNA polymerase II at FLC, MAF4, and MAF5 in conjunction with histone modifications, thus facilitating the expression of these key flowering repressors to prevent precocious flowering in Arabidopsis.
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Affiliation(s)
- Ximing Gong
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| | - Lisha Shen
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| | - Ya Zhi Peng
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| | - Yinbo Gan
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| | - Hao Yu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
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35
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Susila H, Jin S, Ahn JH. Light Intensity and Floral Transition: Chloroplast Says "Time to Flower!". MOLECULAR PLANT 2016; 9:1551-1553. [PMID: 27793786 DOI: 10.1016/j.molp.2016.10.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 10/06/2016] [Accepted: 10/21/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Hendry Susila
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, South Korea
| | - Suhyun Jin
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, South Korea
| | - Ji Hoon Ahn
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, South Korea.
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Abstract
Light is a major environmental factor regulating flowering time, thus ensuring reproductive success of higher plants. In contrast to our detailed understanding of light quality and photoperiod mechanisms involved, the molecular basis underlying high light-promoted flowering remains elusive. Here we show that, in Arabidopsis, a chloroplast-derived signal is critical for high light-regulated flowering mediated by the FLOWERING LOCUS C (FLC). We also demonstrate that PTM, a PHD transcription factor involved in chloroplast retrograde signaling, perceives such a signal and mediates transcriptional repression of FLC through recruitment of FVE, a component of the histone deacetylase complex. Thus, our data suggest that chloroplasts function as essential sensors of high light to regulate flowering and adaptive responses by triggering nuclear transcriptional changes at the chromatin level.
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37
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Schaker PDC, Palhares AC, Taniguti LM, Peters LP, Creste S, Aitken KS, Van Sluys MA, Kitajima JP, Vieira MLC, Monteiro-Vitorello CB. RNAseq Transcriptional Profiling following Whip Development in Sugarcane Smut Disease. PLoS One 2016; 11:e0162237. [PMID: 27583836 PMCID: PMC5008620 DOI: 10.1371/journal.pone.0162237] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/21/2016] [Indexed: 11/25/2022] Open
Abstract
Sugarcane smut disease is caused by the biotrophic fungus Sporisorium scitamineum. The disease is characterized by the development of a whip-like structure from the primary meristems, where billions of teliospores are produced. Sugarcane smut also causes tillering and low sucrose and high fiber contents, reducing cane productivity. We investigated the biological events contributing to disease symptoms in a smut intermediate-resistant sugarcane genotype by examining the transcriptional profiles (RNAseq) shortly after inoculating the plants and immediately after whip emission. The overall picture of disease progression suggests that premature transcriptional reprogramming of the shoot meristem functions continues until the emergence of the whip. The guidance of this altered pattern is potentially primarily related to auxin mobilization in addition to the involvement of other hormonal imbalances. The consequences associated with whip emission are the modulation of typical meristematic functions toward reproductive organ differentiation, requiring strong changes in carbon partitioning and energy production. These changes include the overexpression of genes coding for invertases and trehalose-6P synthase, as well as other enzymes from key metabolic pathways, such as from lignin biosynthesis. This is the first report describing changes in the transcriptional profiles following whip development, providing a hypothetical model and candidate genes to further study sugarcane smut disease progression.
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Affiliation(s)
- Patricia D. C. Schaker
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
| | - Alessandra C. Palhares
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
| | - Lucas M. Taniguti
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
| | - Leila P. Peters
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
| | - Silvana Creste
- Instituto Agronômico de Campinas, Centro de Cana, Ribeirão Preto, São Paulo, Brazil
| | - Karen S. Aitken
- CSIRO Agriculture, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Maria L. C. Vieira
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
| | - Claudia B. Monteiro-Vitorello
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
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Abley K, Locke JCW, Leyser HMO. Developmental mechanisms underlying variable, invariant and plastic phenotypes. ANNALS OF BOTANY 2016; 117:733-48. [PMID: 27072645 PMCID: PMC4845803 DOI: 10.1093/aob/mcw016] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/18/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND Discussions of phenotypic robustness often consider scenarios where invariant phenotypes are optimal and assume that developmental mechanisms have evolved to buffer the phenotypes of specific traits against stochastic and environmental perturbations. However, plastic plant phenotypes that vary between environments or variable phenotypes that vary stochastically within an environment may also be advantageous in some scenarios. SCOPE Here the conditions under which invariant, plastic and variable phenotypes of specific traits may confer a selective advantage in plants are examined. Drawing on work from microbes and multicellular organisms, the mechanisms that may give rise to each type of phenotype are discussed. CONCLUSION In contrast to the view of robustness as being the ability of a genotype to produce a single, invariant phenotype, changes in a phenotype in response to the environment, or phenotypic variability within an environment, may also be delivered consistently (i.e. robustly). Thus, for some plant traits, mechanisms have probably evolved to produce plasticity or variability in a reliable manner.
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Affiliation(s)
- Katie Abley
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - James C W Locke
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - H M Ottoline Leyser
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
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Xu M, Hu T, Smith MR, Poethig RS. Epigenetic Regulation of Vegetative Phase Change in Arabidopsis. THE PLANT CELL 2016; 28:28-41. [PMID: 26704382 PMCID: PMC4746683 DOI: 10.1105/tpc.15.00854] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 12/09/2015] [Accepted: 12/18/2015] [Indexed: 05/18/2023]
Abstract
Vegetative phase change in flowering plants is regulated by a decrease in the level of miR156. The molecular mechanism of this temporally regulated decrease in miR156 expression is still unknown. Most of the miR156 in Arabidopsis thaliana shoots is produced by MIR156A and MIR156C. We found that the downregulation of these genes during vegetative phase change is associated with an increase in their level of histone H3 lysine 27 trimethylation (H3K27me3) and requires this chromatin modification. The increase in H3K27me3 at MIR156A/MIR156C is associated with an increase in the binding of PRC2 to these genes and is mediated redundantly by the E(z) homologs SWINGER and CURLY LEAF. The CHD3 chromatin remodeler PICKLE (PKL) promotes the addition of H3K27me3 to MIR156A/MIR156C but is not responsible for the temporal increase in this chromatin mark. PKL is bound to the promoters of MIR156A/MIR156C, where it promotes low levels of H3K27ac early in shoot development and stabilizes the nucleosome at the +1 position. These results suggest a molecular mechanism for the initiation and maintenance of vegetative phase change in plants.
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Affiliation(s)
- Mingli Xu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Tieqiang Hu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Michael R Smith
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - R Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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Picó S, Ortiz-Marchena MI, Merini W, Calonje M. Deciphering the Role of POLYCOMB REPRESSIVE COMPLEX1 Variants in Regulating the Acquisition of Flowering Competence in Arabidopsis. PLANT PHYSIOLOGY 2015; 168:1286-97. [PMID: 25897002 PMCID: PMC4528732 DOI: 10.1104/pp.15.00073] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/16/2015] [Indexed: 05/18/2023]
Abstract
Polycomb group (PcG) proteins play important roles in regulating developmental phase transitions in plants; however, little is known about the role of the PcG machinery in regulating the transition from juvenile to adult phase. Here, we show that Arabidopsis (Arabidopsis thaliana) B lymphoma Moloney murine leukemia virus insertion region1 homolog (BMI1) POLYCOMB REPRESSIVE COMPLEX1 (PRC1) components participate in the repression of microRNA156 (miR156). Loss of AtBMI1 function leads to the up-regulation of the primary transcript of MIR156A and MIR156C at the time the levels of miR156 should decline, resulting in an extended juvenile phase and delayed flowering. Conversely, the PRC1 component EMBRYONIC FLOWER (EMF1) participates in the regulation of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE and MIR172 genes. Accordingly, plants impaired in EMF1 function displayed misexpression of these genes early in development, which contributes to a CONSTANS-independent up-regulation of FLOWERING LOCUS T (FT) leading to the earliest flowering phenotype described in Arabidopsis. Our findings show how the different regulatory roles of two functional PRC1 variants coordinate the acquisition of flowering competence and help to reach the threshold of FT necessary to flower. Furthermore, we show how two central regulatory mechanisms, such as PcG and microRNA, assemble to achieve a developmental outcome.
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Affiliation(s)
- Sara Picó
- Institute of Plant Biochemistry and Photosynthesis, Instituto de Bioquímica Vegetal y Fotosíntesis-Consejo Superior de Investigaciones Científicas-University of Seville, Isla de La Cartuja, 41092 Seville, Spain
| | - M Isabel Ortiz-Marchena
- Institute of Plant Biochemistry and Photosynthesis, Instituto de Bioquímica Vegetal y Fotosíntesis-Consejo Superior de Investigaciones Científicas-University of Seville, Isla de La Cartuja, 41092 Seville, Spain
| | - Wiam Merini
- Institute of Plant Biochemistry and Photosynthesis, Instituto de Bioquímica Vegetal y Fotosíntesis-Consejo Superior de Investigaciones Científicas-University of Seville, Isla de La Cartuja, 41092 Seville, Spain
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis, Instituto de Bioquímica Vegetal y Fotosíntesis-Consejo Superior de Investigaciones Científicas-University of Seville, Isla de La Cartuja, 41092 Seville, Spain
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41
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Luo M, Tai R, Yu CW, Yang S, Chen CY, Lin WD, Schmidt W, Wu K. Regulation of flowering time by the histone deacetylase HDA5 in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:925-936. [PMID: 25922987 DOI: 10.1111/tpj.12868] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 03/30/2015] [Accepted: 04/15/2015] [Indexed: 05/20/2023]
Abstract
The acetylation level of histones on lysine residues regulated by histone acetyltransferases and histone deacetylases plays an important but under-studied role in the control of gene expression in plants. With the aim of characterizing the Arabidopsis RPD3/HDA1 family histone deacetylase HDA5, we present evidence showing that HDA5 displays deacetylase activity. Mutants defective in the expression of HDA5 displayed a late-flowering phenotype. Expression of the flowering repressor genes FLC and MAF1 was up-regulated in hda5 mutants. Furthermore, the gene activation markers, histone H3 acetylation and H3K4 trimethylation on FLC and MAF1 chromatin were increased in hda5-1 mutants. Chromatin immunoprecipitation analysis showed that HDA5 binds to the chromatin of FLC and MAF1. Bimolecular fluorescence complementation assays and co-immunoprecipitation assays showed that HDA5 interacts with FVE, FLD and HDA6, indicating that these proteins are present in a protein complex involved in the regulation of flowering time. Comparing gene expression profiles of hda5 and hda6 mutants by RNA-seq revealed that HDA5 and HDA6 co-regulate gene expression in multiple development processes and pathways.
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Affiliation(s)
- Ming Luo
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, No. 723, Xingke Road, 510650, Guangzhou, China
- Institute of Plant Biology, College of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, 10617, Taipei, Taiwan
| | - Ready Tai
- Institute of Plant Biology, College of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, 10617, Taipei, Taiwan
| | - Chun-Wei Yu
- Institute of Plant Biology, College of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, 10617, Taipei, Taiwan
| | - Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, No. 723, Xingke Road, 510650, Guangzhou, China
| | - Chia-Yang Chen
- Institute of Plant Biology, College of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, 10617, Taipei, Taiwan
| | - Wen-Dar Lin
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, 11529, Taipei, Taiwan
| | - Wolfgang Schmidt
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, 11529, Taipei, Taiwan
| | - Keqiang Wu
- Institute of Plant Biology, College of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, 10617, Taipei, Taiwan
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42
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Bouché F, Detry N, Périlleux C. Heat can erase epigenetic marks of vernalization in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2015; 10:e990799. [PMID: 25648822 PMCID: PMC4622702 DOI: 10.4161/15592324.2014.990799] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 06/11/2014] [Accepted: 06/11/2014] [Indexed: 05/19/2023]
Abstract
Vernalization establishes a memory of winter that must be maintained for weeks or months in order to promote flowering the following spring. The stability of the vernalized state varies among plant species and depends on the duration of cold exposure. In Arabidopsis thaliana, winter leads to epigenetic silencing of the floral repressor gene FLOWERING LOCUS C (FLC) and the duration of cold is measured through the dynamics of chromatin modifications during and after cold. The growing conditions encountered post-vernalization are thus critical for the maintenance of the vernalized state. We reported that high temperature leads to devernalization and, consistently, to FLC reactivation in Arabidopsis seedlings. Here we show that the repressive epigenetic mark H3K27me3 decreases at the FLC locus when vernalized seedlings are grown at 30°C, unless they were first exposed to a stabilizing period at 20°C. Ambient temperature thus controls the epigenetic memory of winter.
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Affiliation(s)
- Frédéric Bouché
- University of Liège; Laboratory of Plant Physiology; PhytoSYSTEMS; Liège, Belgium
| | - Nathalie Detry
- University of Liège; Laboratory of Plant Physiology; PhytoSYSTEMS; Liège, Belgium
| | - Claire Périlleux
- University of Liège; Laboratory of Plant Physiology; PhytoSYSTEMS; Liège, Belgium
- Correspondence to: Claire Périlleux;
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Golembeski GS, Imaizumi T. Photoperiodic Regulation of Florigen Function in Arabidopsis thaliana. THE ARABIDOPSIS BOOK 2015; 13:e0178. [PMID: 26157354 PMCID: PMC4489636 DOI: 10.1199/tab.0178] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
One mechanism through which flowering in response to seasonal change is brought about is by sensing the fluctuation in day-length; the photoperiod. Flowering induction occurs through the production of the florigenic protein FLOWERING LOCUS T (FT) and its movement from the phloem companion cells in the leaf vasculature into the shoot apex, where meristematic reprogramming occurs. FT activation in response to photoperiod condition is accomplished largely through the activity of the transcription factor CONSTANS (CO). Regulation of CO expression and protein stability, as well as the timing of other components via the circadian clock, is a critical mechanism by which plants are able to respond to photoperiod to initiate the floral transition. Modulation of FT expression in response to external and internal stimuli via components of the flowering network is crucial to mediate a fluid flowering response to a variety of environmental parameters. In addition, the regulated movement of FT protein from the phloem to the shoot apex, and interactions that determine floral meristem cell fate, constitute novel mechanisms through which photoperiodic information is translated into flowering time.
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Affiliation(s)
- Greg S. Golembeski
- University of Washington, Department of Biology, Seattle, WA, 98195-1800
| | - Takato Imaizumi
- University of Washington, Department of Biology, Seattle, WA, 98195-1800
- Address correspondence to
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Capovilla G, Schmid M, Posé D. Control of flowering by ambient temperature. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:59-69. [PMID: 25326628 DOI: 10.1093/jxb/eru416] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The timing of flowering is a crucial decision in the life cycle of plants since favourable conditions are needed to maximize reproductive success and, hence, the survival of the species. It is therefore not surprising that plants constantly monitor endogenous and environmental signals, such as day length (photoperiod) and temperature, to adjust the timing of the floral transition. Temperature in particular has been shown to have a tremendous effect on the timing of flowering: the effect of prolonged periods of cold, called the vernalization response, has been extensively studied and the underlying epigenetic mechanisms are reasonably well understood in Arabidopsis thaliana. In contrast, the effect of moderate changes in ambient growth temperature on the progression of flowering, the thermosensory pathway, is only starting to be understood on the molecular level. Several genes and molecular mechanisms underlying the thermosensory pathway have already been identified and characterized in detail. At a time when global temperature is rising due to climate change, this knowledge will be pivotal to ensure crop production in the future.
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Affiliation(s)
- Giovanna Capovilla
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstr. 35, D-72076 Tübingen, Germany
| | - Markus Schmid
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstr. 35, D-72076 Tübingen, Germany
| | - David Posé
- Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
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45
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Ding B, Wang GL. Chromatin versus pathogens: the function of epigenetics in plant immunity. FRONTIERS IN PLANT SCIENCE 2015; 6:675. [PMID: 26388882 PMCID: PMC4557108 DOI: 10.3389/fpls.2015.00675] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/15/2015] [Indexed: 05/17/2023]
Abstract
To defend against pathogens, plants have developed a sophisticated innate immunity that includes effector recognition, signal transduction, and rapid defense responses. Recent evidence has demonstrated that plants utilize the epigenetic control of gene expression to fine-tune their defense when challenged by pathogens. In this review, we highlight the current understanding of the molecular mechanisms of histone modifications (i.e., methylation, acetylation, and ubiquitination) and chromatin remodeling that contribute to plant immunity against pathogens. Functions of key histone-modifying and chromatin remodeling enzymes are discussed.
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Affiliation(s)
- Bo Ding
- State Key Laboratory of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Guo-Liang Wang
- State Key Laboratory of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
- Department of Plant Pathology, The Ohio State University, ColumbusOH, USA
- *Correspondence: Guo-Liang Wang, Department of Plant Pathology, The Ohio State University, 2021 Coffey Road, Columbus, OH 43210, USA,
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Hu Q, Jin Y, Shi H, Yang W. GmFLD, a soybean homolog of the autonomous pathway gene FLOWERING LOCUS D, promotes flowering in Arabidopsis thaliana. BMC PLANT BIOLOGY 2014; 14:263. [PMID: 25287450 PMCID: PMC4190295 DOI: 10.1186/s12870-014-0263-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 09/25/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Flowering at an appropriate time is crucial for seed maturity and reproductive success in all flowering plants. Soybean (Glycine max) is a typical short day plant, and both photoperiod and autonomous pathway genes exist in soybean genome. However, little is known about the functions of soybean autonomous pathway genes. In this article, we examined the functions of a soybean homolog of the autonomous pathway gene FLOWERING LOCUS D (FLD), GmFLD in the flowering transition of A. thaliana. RESULTS In soybean, GmFLD is highly expressed in expanded cotyledons of seedlings, roots, and young pods. However, the expression levels are low in leaves and shoot apexes. Expression of GmFLD in A. thaliana (Col) resulted in early flowering of the transgenic plants, and rescued the late flowering phenotype of the A. thaliana fld mutant. In GmFLD transgenic plants (Col or fld background), the FLC (FLOWERING LOCUS C) transcript levels decreased whereas the floral integrators, FT and SOC1, were up-regulated when compared with the corresponding non-transgenic genotypes. Furthermore, chromatin immuno-precipitation analysis showed that in the transgenic rescued lines (fld background), the levels of both tri-methylation of histone H3 Lys-4 and acetylation of H4 decreased significantly around the transcriptional start site of FLC. This is consistent with the function of GmFLD as a histone demethylase. CONCLUSIONS Our results suggest that GmFLD is a functional ortholog of the Arabidopsis FLD and may play an important role in the regulation of chromatin state in soybean. The present data provides the first evidence for the evolutionary conservation of the components in the autonomous pathway in soybean.
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Affiliation(s)
- Qin Hu
- />Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079 People’s Republic of China
| | - Ye Jin
- />Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079 People’s Republic of China
| | - Huazhong Shi
- />Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079 People’s Republic of China
- />Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409 USA
| | - Wannian Yang
- />Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079 People’s Republic of China
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