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Wang H, Li X, Meng B, Fan Y, Khan SU, Qian M, Zhang M, Yang H, Lu K. Exploring silique number in Brassica napus L.: Genetic and molecular advances for improving yield. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1897-1912. [PMID: 38386569 PMCID: PMC11182599 DOI: 10.1111/pbi.14309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024]
Abstract
Silique number is a crucial yield-related trait for the genetic enhancement of rapeseed (Brassica napus L.). The intricate molecular process governing the regulation of silique number involves various factors. Despite advancements in understanding the mechanisms regulating silique number in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the molecular processes involved in controlling silique number in rapeseed remain largely unexplored. In this review, we identify candidate genes and review the roles of genes and environmental factors in regulating rapeseed silique number. We use genetic regulatory networks for silique number in Arabidopsis and grain number in rice to uncover possible regulatory pathways and molecular mechanisms involved in regulating genes associated with rapeseed silique number. A better understanding of the genetic network regulating silique number in rapeseed will provide a theoretical basis for the genetic improvement of this trait and genetic resources for the molecular breeding of high-yielding rapeseed.
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Affiliation(s)
- Hui Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Xiaodong Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Boyu Meng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Yonghai Fan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Shahid Ullah Khan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Mingchao Qian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Minghao Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Haikun Yang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Kun Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
- Engineering Research Center of South Upland Agriculture, Ministry of EducationChongqingP.R. China
- Academy of Agricultural SciencesSouthwest UniversityBeibeiChongqingP.R. China
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Mehta D, Scandola S, Kennedy C, Lummer C, Gallo MCR, Grubb LE, Tan M, Scarpella E, Uhrig RG. Twilight length alters growth and flowering time in Arabidopsis via LHY/ CCA1. SCIENCE ADVANCES 2024; 10:eadl3199. [PMID: 38941453 PMCID: PMC11212724 DOI: 10.1126/sciadv.adl3199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 05/28/2024] [Indexed: 06/30/2024]
Abstract
Decades of research have uncovered how plants respond to two environmental variables that change across latitudes and over seasons: photoperiod and temperature. However, a third such variable, twilight length, has so far gone unstudied. Here, using controlled growth setups, we show that the duration of twilight affects growth and flowering time via the LHY/CCA1 clock genes in the model plant Arabidopsis. Using a series of progressively truncated no-twilight photoperiods, we also found that plants are more sensitive to twilight length compared to equivalent changes in solely photoperiods. Transcriptome and proteome analyses showed that twilight length affects reactive oxygen species metabolism, photosynthesis, and carbon metabolism. Genetic analyses suggested a twilight sensing pathway from the photoreceptors PHY E, PHY B, PHY D, and CRY2 through LHY/CCA1 to flowering modulation through the GI-FT pathway. Overall, our findings call for more nuanced models of day-length perception in plants and posit that twilight is an important determinant of plant growth and development.
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Affiliation(s)
- Devang Mehta
- Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
- Leuven Plant Institute, KU Leuven, B-3001 Leuven, Belgium
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Sabine Scandola
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Curtis Kennedy
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Christina Lummer
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | | | - Lauren E. Grubb
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Maryalle Tan
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Enrico Scarpella
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - R. Glen Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2E9, Canada
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Madrigal Y, Alzate JF, Pabón-Mora N. Evolution of major flowering pathway integrators in Orchidaceae. PLANT REPRODUCTION 2024; 37:85-109. [PMID: 37823912 PMCID: PMC11180029 DOI: 10.1007/s00497-023-00482-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/10/2023] [Indexed: 10/13/2023]
Abstract
The Orchidaceae is a mega-diverse plant family with ca. 29,000 species with a large variety of life forms that can colonize transitory habitats. Despite this diversity, little is known about their flowering integrators in response to specific environmental factors. During the reproductive transition in flowering plants a vegetative apical meristem (SAM) transforms into an inflorescence meristem (IM) that forms bracts and flowers. In model grasses, like rice, a flowering genetic regulatory network (FGRN) controlling reproductive transitions has been identified, but little is known in the Orchidaceae. In order to analyze the players of the FRGN in orchids, we performed comprehensive phylogenetic analyses of CONSTANS-like/CONSTANS-like 4 (COL/COL4), FLOWERING LOCUS D (FD), FLOWERING LOCUS C/FRUITFULL (FLC/FUL) and SUPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) gene lineages. In addition to PEBP and AGL24/SVP genes previously analyzed, here we identify an increase of orchid homologs belonging to COL4, and FUL gene lineages in comparison with other monocots, including grasses, due to orchid-specific gene lineage duplications. Contrariwise, local duplications in Orchidaceae are less frequent in the COL, FD and SOC1 gene lineages, which points to a retention of key functions under strong purifying selection in essential signaling factors. We also identified changes in the protein sequences after such duplications, variation in the evolutionary rates of resulting paralogous clades and targeted expression of isolated homologs in different orchids. Interestingly, vernalization-response genes like VERNALIZATION1 (VRN1) and FLOWERING LOCUS C (FLC) are completely lacking in orchids, or alternatively are reduced in number, as is the case of VERNALIZATION2/GHD7 (VRN2). Our findings point to non-canonical factors sensing temperature changes in orchids during reproductive transition. Expression data of key factors gathered from Elleanthus auratiacus, a terrestrial orchid in high Andean mountains allow us to characterize which copies are actually active during flowering. Altogether, our data lays down a comprehensive framework to assess gene function of a restricted number of homologs identified more likely playing key roles during the flowering transition, and the changes of the FGRN in neotropical orchids in comparison with temperate grasses.
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Affiliation(s)
- Yesenia Madrigal
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F Alzate
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
| | - Natalia Pabón-Mora
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia.
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Pechar GS, Sánchez-Pina MA, Coronado-Parra T, Bretó P, García-Almodóvar RC, Liu L, Aranda MA, Donaire L. Developmental stages and episode-specific regulatory genes in andromonoecious melon flower development. ANNALS OF BOTANY 2024; 133:305-320. [PMID: 38041589 PMCID: PMC11005788 DOI: 10.1093/aob/mcad186] [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: 09/07/2023] [Accepted: 12/01/2023] [Indexed: 12/03/2023]
Abstract
BACKGROUND AND AIMS Given the lack of specific studies on floral development in melon (Cucumis melo L.), we carried out an extensive study involving morphological and transcriptomic analyses to characterize floral development in this species. METHODS Using an andromonoecious line, we analysed the development of floral buds in male and hermaphrodite flowers with both light microscopy and scanning electron microscopy. Based on flower lengths, we established a correlation between the developmental stages and four main episodes of floral development and conducted an extensive RNA sequencing analysis of these episodes. KEY RESULTS We identified 12 stages of floral development, from the appearance of the floral meristems to anthesis. The main structural differences between male and hermaphrodite flowers appeared between stages 6 and 7; later stages of development leading to the formation of organs and structures in both types of flowers were also described. We analysed the gene expression patterns of the four episodes in flower development to find the genes that were specific to each given episode. Among others, we identified genes that defined the passage from one episode to the next according to the ABCDE model of floral development. CONCLUSIONS This work combines a detailed morphological analysis and a comprehensive transcriptomic study to enable characterization of the structural and molecular mechanisms that determine the floral development of an andromonoecious genotype in melon. Taken together, our results provide a first insight into gene regulation networks in melon floral development that are crucial for flowering and pollen formation, highlighting potential targets for genetic manipulation to improve crop yield of melon in the future.
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Affiliation(s)
- Giuliano S Pechar
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Department of Stress Biology and Plant Pathology, PO Box 164, 30100 Espinardo, Murcia, Spain
| | - M Amelia Sánchez-Pina
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Department of Stress Biology and Plant Pathology, PO Box 164, 30100 Espinardo, Murcia, Spain
| | - Teresa Coronado-Parra
- Microscopy Core Facility, Área Científica y Técnica de Investigación, Universidad de Murcia, PO Box 164, 30100 Espinardo, Murcia, Spain
| | - Pau Bretó
- Abiopep S.L., R&D Department, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2º, 30100 Espinardo, Murcia, Spain
| | - Roque Carlos García-Almodóvar
- Abiopep S.L., R&D Department, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2º, 30100 Espinardo, Murcia, Spain
| | - Lifeng Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou 450009, Henan, China
| | - Miguel A Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Department of Stress Biology and Plant Pathology, PO Box 164, 30100 Espinardo, Murcia, Spain
| | - Livia Donaire
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Department of Stress Biology and Plant Pathology, PO Box 164, 30100 Espinardo, Murcia, Spain
- Abiopep S.L., R&D Department, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2º, 30100 Espinardo, Murcia, Spain
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He H, Chen X, Wang T, Zhang X, Liu Z, Qu S, Gu Z, Huang M, Huang H. Flower development and a functional analysis of related genes in Impatiens uliginosa. FRONTIERS IN PLANT SCIENCE 2024; 15:1370949. [PMID: 38590746 PMCID: PMC10999631 DOI: 10.3389/fpls.2024.1370949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/26/2024] [Indexed: 04/10/2024]
Abstract
Impatiens uliginosa is a plant of the Impatiens, with peculiar flowers. In this study, we combined morphogenesis and molecular biology to explore its development of flowers. An analysis of basic observational data and paraffin sectioning showed that it took approximately 13 d for the floral organs to differentiate. An analysis of the development of inflorescences and floral organs by scanning electron microscopy showed that the inflorescence of I. uliginosa is a spiral raceme. The floral organs differentiated in the following order: lateral sepals (Ls), posterior sepal (Ps), anterior sepals (As), anterior petal (Ap), lateral petals (Lp), stamens (St) and gynoecium (Gy). I. uliginosa was found to have four sepals, and the connate stamens are caused by the fusion and growth of filament appendages. The results of fluorescence quantification and virus-induced gene silencing showed that I. uliginosa had its own unique model for flower development, and there was functional diversity of IuAP1 and IuDEF. Among them, IuAP1 controls the formation of bract s (Br), regulates the morphogenesis of posterior sepal, controls the anthocyanin precipitation of the anterior petals and the formation of lateral petals. IuDEF regulates the morphogenesis of lateral sepals, the length of development of the spur, and controls the size of yellow flower color plaques of the lateral petals. In this study, the process of flower development and the function of flower development genes of I. uliginosa were preliminarily verified. This study provides basic guidance and new concepts that can be used to study the development of Impatiens flowers.
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Affiliation(s)
- Haihao He
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, China
| | - Xinyi Chen
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, China
| | - Tianye Wang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, China
| | - Xiaoli Zhang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, China
| | - Zedong Liu
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, China
| | - Suping Qu
- Flower Research Institute, Yunnan Academy of Agricultural Sciences China, Kunming, China
| | - Zhijia Gu
- Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Meijuan Huang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, China
| | - Haiquan Huang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, China
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Shi Y, Zhang S, Gui Q, Qing H, Li M, Yi C, Guo H, Chen H, Xu J, Ding F. The SOC1 gene plays an important role in regulating litchi flowering time. Genomics 2024; 116:110804. [PMID: 38307485 DOI: 10.1016/j.ygeno.2024.110804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/16/2024] [Accepted: 01/29/2024] [Indexed: 02/04/2024]
Abstract
Litchi (Litchi chinensis Sonn.) is a valuable subtropical fruit tree with high-quality fruit. However, its economic benefits and sustainable development are restrained by a number of challenges. One major challenge is the lack of extremely early and late maturing high-quality varieties due to limited availability of varieties suitable for commercial cultivation and outdated breeding methods, resulting in an imbalanced supply and low price of litchi. Flowering time is a crucial genetic factor influencing the maturation period of litchi. Our previous research has highlighted the pivotal role of the LcFT1 gene in regulating the flowering time of litchi and identified a gene associated with LcFT1 (named as LcSOC1) based on RNA-Seq and weight gene co-expression network (WGCNA) analysis. This study further investigated the function of LcSOC1. Subcellular localization analysis revealed that LcSOC1 is primarily localized in the nucleus, where it acts as a transcription factor. LcSOC1 overexpression in Nicotiana tabacum and Arabidopsis thaliana resulted in significant early flowering. Furthermore, LcSOC1 was found to be expressed in various tissues, with the highest expression in mature leaves. Analysis of spatial and temporal expression patterns of LcSOC1 in litchi varieties with different flowering time under low temperature treatment and across an annual cycle demonstrated that LcSOC1 is responsive to low temperature induction. Interestingly, early maturing varieties exhibited higher sensitivity to low temperature, with significantly premature induction of LcSOC1 expression relative to late maturing varieties. Activation of LcSOC1 triggered the transition of litchi into the flowering phase. These findings demonstrate that LcSOC1 plays a pivotal role in regulating the flowering process and determining the flowering time in litchi. Overall, this study provides theoretical guidance and important target genes for molecular breeding to regulate litchi production period.
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Affiliation(s)
- Yuyu Shi
- College of Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Agricultural and Animal Husbandry Industry Development Research Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Shuwei Zhang
- Guangxi Key Laboratory of Genetic Improvement of Crops, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China.
| | - Qiulin Gui
- College of Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Agricultural and Animal Husbandry Industry Development Research Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Haowei Qing
- College of Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Agricultural and Animal Husbandry Industry Development Research Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Ming Li
- Guangxi Key Laboratory of Genetic Improvement of Crops, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Chenxin Yi
- Guangxi Key Laboratory of Genetic Improvement of Crops, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Huiqin Guo
- Guangxi Key Laboratory of Genetic Improvement of Crops, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Houbin Chen
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
| | - Jiongzhi Xu
- College of Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Agricultural and Animal Husbandry Industry Development Research Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Feng Ding
- Guangxi Key Laboratory of Genetic Improvement of Crops, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China.
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Poulet A, Zhao M, Peng Y, Tham F, Jaudal M, Zhang L, van Wolfswinkel JC, Putterill J. Gene-edited Mtsoc1 triple mutant Medicago plants do not flower. FRONTIERS IN PLANT SCIENCE 2024; 15:1357924. [PMID: 38469328 PMCID: PMC10926907 DOI: 10.3389/fpls.2024.1357924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/02/2024] [Indexed: 03/13/2024]
Abstract
Optimized flowering time is an important trait that ensures successful plant adaptation and crop productivity. SOC1-like genes encode MADS transcription factors, which are known to play important roles in flowering control in many plants. This includes the best-characterized eudicot model Arabidopsis thaliana (Arabidopsis), where SOC1 promotes flowering and functions as a floral integrator gene integrating signals from different flowering-time regulatory pathways. Medicago truncatula (Medicago) is a temperate reference legume with strong genomic and genetic resources used to study flowering pathways in legumes. Interestingly, despite responding to similar floral-inductive cues of extended cold (vernalization) followed by warm long days (VLD), such as in winter annual Arabidopsis, Medicago lacks FLC and CO which are key regulators of flowering in Arabidopsis. Unlike Arabidopsis with one SOC1 gene, multiple gene duplication events have given rise to three MtSOC1 paralogs within the Medicago genus in legumes: one Fabaceae group A SOC1 gene, MtSOC1a, and two tandemly repeated Fabaceae group B SOC1 genes, MtSOC1b and MtSOC1c. Previously, we showed that MtSOC1a has unique functions in floral promotion in Medicago. The Mtsoc1a Tnt1 retroelement insertion single mutant showed moderately delayed flowering in long- and short-day photoperiods, with and without prior vernalization, compared to the wild-type. In contrast, Mtsoc1b Tnt1 single mutants did not have altered flowering time or flower development, indicating that it was redundant in an otherwise wild-type background. Here, we describe the generation of Mtsoc1a Mtsoc1b Mtsoc1c triple mutant lines using CRISPR-Cas9 gene editing. We studied two independent triple mutant lines that segregated plants that did not flower and were bushy under floral inductive VLD. Genotyping indicated that these non-flowering plants were homozygous for the predicted strong mutant alleles of the three MtSOC1 genes. Gene expression analyses using RNA-seq and RT-qPCR indicated that these plants remained vegetative. Overall, the non-flowering triple mutants were dramatically different from the single Mtsoc1a mutant and the Arabidopsis soc1 mutant; implicating multiple MtSOC1 genes in critical overlapping roles in the transition to flowering in Medicago.
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Affiliation(s)
- Axel Poulet
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, United States
| | - Min Zhao
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Yongyan Peng
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Mt Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - FangFei Tham
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Mauren Jaudal
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Mt Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Lulu Zhang
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Josien C. van Wolfswinkel
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, United States
| | - Joanna Putterill
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
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Huang X, Lyu T, Li Z, Lyu Y. Hydrangea arborescens 'Annabelle' Flower Formation and Flowering in the Current Year. PLANTS (BASEL, SWITZERLAND) 2023; 12:4103. [PMID: 38140430 PMCID: PMC10748224 DOI: 10.3390/plants12244103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/24/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023]
Abstract
The perennial woody plant Hydrangea arborescens 'Annabelle' is of great research value due to its unique mechanism of flower development that occurs in the current year, resulting in decorative flowers that can be enjoyed for a relatively long period of time. However, the mechanisms underlying the regulation of current-year flower development in H. arborescens 'Annabelle' are still not fully understood. In this study, we conducted an associated analysis to explore the core regulating network in H. arborescens 'Annabelle' by combining phenological observations, physiological assays, and transcriptome comparisons across seven flower developmental stages. Through this analysis, we constructed a gene co-expression network (GCN) based on the highest reciprocal rank (HRR), using 509 differentially expressed genes (DEGs) identified from seven flowering-related pathways, as well as the biosynthesis of eight flowering-related phytohormones and signal transduction in the transcriptomic analysis. According to the analysis of the GCN, we identified 14 key genes with the highest functional connectivity that played critical roles in specific development stages. We confirmed that 135 transcription factors (AP2/ERF, bHLH, CO-like, GRAS, MIKC, SBP, WRKY) were highly co-expressed with the 14 key genes, indicating their close associations with the development of current-year flowers. We further proposed a hypothetical model of a gene regulatory network for the development of the whole flower. This model suggested that the photoperiod, aging, and gibberellin pathways, along with the phytohormones abscisic acid (ABA), gibberellin (GA), brassinosteroid (BR), and jasmonic acid (JA), work synergistically to promote the floral transition. Additionally, auxin, GA, JA, ABA, and salicylic acid (SA) regulated the blooming process by involving the circadian clock. Cytokinin (CTK), ethylene (ETH), and SA were key regulators that affected flower senescence. Additionally, several floral integrators (HaLFY, HaSOC1-2, HaAP1, HaFULL, HaAGL24, HaFLC, etc.) were dominant contributors to the development of H. arborescens flowers. Overall, this research provides a comprehensive understanding of the dynamic mechanism underlying the entire process of current-year flower development, thereby offering valuable insights for further studies on the flower development of H. arborescens 'Annabelle'.
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Affiliation(s)
- Xiaoxu Huang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, China National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Tong Lyu
- Beijing Flower Engineering Technology Research Center, Plant Institute, China National Botanical Garden North Garden, Beijing 100093, China
| | - Zheng Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, China National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Yingmin Lyu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, China National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
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Cerise M, da Silveira Falavigna V, Rodríguez-Maroto G, Signol A, Severing E, Gao H, van Driel A, Vincent C, Wilkens S, Iacobini FR, Formosa-Jordan P, Pajoro A, Coupland G. Two modes of gene regulation by TFL1 mediate its dual function in flowering time and shoot determinacy of Arabidopsis. Development 2023; 150:dev202089. [PMID: 37971083 PMCID: PMC10730086 DOI: 10.1242/dev.202089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/04/2023] [Indexed: 11/19/2023]
Abstract
Plant organ primordia develop successively at the shoot apical meristem (SAM). In Arabidopsis, primordia formed early in development differentiate into vegetative leaves, whereas those formed later generate inflorescence branches and flowers. TERMINAL FLOWER 1 (TFL1), a negative regulator of transcription, acts in the SAM to delay flowering and to maintain inflorescence meristem indeterminacy. We used confocal microscopy, time-resolved transcript profiling and reverse genetics to elucidate this dual role of TFL1. We found that TFL1 accumulates dynamically in the SAM reflecting its dual function. Moreover, TFL1 represses two major sets of genes. One set includes genes that promote flowering, expression of which increases earlier in tfl1 mutants. The other set is spatially misexpressed in tfl1 inflorescence meristems. The misexpression of these two gene sets in tfl1 mutants depends upon FD transcription factor, with which TFL1 interacts. Furthermore, the MADS-box gene SEPALLATA 4, which is upregulated in tfl1, contributes both to the floral transition and shoot determinacy defects of tfl1 mutants. Thus, we delineate the dual function of TFL1 in shoot development in terms of its dynamic spatial distribution and different modes of gene repression.
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Affiliation(s)
- Martina Cerise
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Vítor da Silveira Falavigna
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Gabriel Rodríguez-Maroto
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Antoine Signol
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Edouard Severing
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - He Gao
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Annabel van Driel
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Coral Vincent
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Sandra Wilkens
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Francesca Romana Iacobini
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Pau Formosa-Jordan
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Alice Pajoro
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Institute of Molecular Biology and Pathology, National Research Council, c/o Department Biology and Biotechnology ‘C. Darwin’ Sapienza University, Rome 00185, Italy
| | - George Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
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10
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Rodríguez-Bolaños M, Martínez T, Juárez S, Quiroz S, Domínguez A, Garay-Arroyo A, Sanchez MDLP, Álvarez-Buylla ER, García-Ponce B. XAANTAL1 Reveals an Additional Level of Flowering Regulation in the Shoot Apical Meristem in Response to Light and Increased Temperature in Arabidopsis. Int J Mol Sci 2023; 24:12773. [PMID: 37628953 PMCID: PMC10454237 DOI: 10.3390/ijms241612773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Light and photoperiod are environmental signals that regulate flowering transition. In plants like Arabidopsis thaliana, this regulation relies on CONSTANS, a transcription factor that is negatively posttranslational regulated by phytochrome B during the morning, while it is stabilized by PHYA and cryptochromes 1/2 at the end of daylight hours. CO induces the expression of FT, whose protein travels from the leaves to the apical meristem, where it binds to FD to regulate some flowering genes. Although PHYB delays flowering, we show that light and PHYB positively regulate XAANTAL1 and other flowering genes in the shoot apices. Also, the genetic data indicate that XAL1 and FD participate in the same signaling pathway in flowering promotion when plants are grown under a long-day photoperiod at 22 °C. By contrast, XAL1 functions independently of FD or PIF4 to induce flowering at higher temperatures (27 °C), even under long days. Furthermore, XAL1 directly binds to FD, SOC1, LFY, and AP1 promoters. Our findings lead us to propose that light and temperature influence the floral network at the meristem level in a partially independent way of the signaling generated from the leaves.
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Affiliation(s)
- Mónica Rodríguez-Bolaños
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Tania Martínez
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Saray Juárez
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Stella Quiroz
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
- Laboratory of Pathogens and Host Immunity, University of Montpellier, 34 090 Montpellier, France
| | - Andrea Domínguez
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Adriana Garay-Arroyo
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - María de la Paz Sanchez
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Elena R. Álvarez-Buylla
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Berenice García-Ponce
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
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11
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Zhang J, Chen L, Cai Y, Su Q, Chen Y, Li M, Hou W. A novel MORN-motif type gene GmMRF2 controls flowering time and plant height of soybean. Int J Biol Macromol 2023; 245:125464. [PMID: 37348581 DOI: 10.1016/j.ijbiomac.2023.125464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023]
Abstract
The flowering time of soybean is a highly important agronomic characteristic, which affects the adaptability and yield. AtMRF1, a MORN-repeat motif gene, acts as a floral promoter in Arabidopsis, its functions in soybean are not yet understood. Here, we employed qRT-PCR to analyze the tissue expression patten of MRF1 homologs in soybean and determined that the GmMRF2 gene, containing a MORN-motif, highly expressed in the shoot and responded to photoperiod. GmMRF2 overexpression soybean lines exhibited earlier flowering time under long-day (LD) conditions, and increased plant height under both LD and short-day (SD) conditions compared to wild-type (WT) plants. The expression levels of gibberellic acid (GA) pathway genes that positively regulate plant height genes and flowering-promoting genes were up-regulated in the GmMRF2 overexpression lines, were up-regulated in the GmMRF2 overexpression lines. Further study revealed that GmMRF2 interacted with GmTCP15 to co-induce the expression of GmSOC1b. Together, our results preliminarily reveal the functions and mechanisms of GmMRF2 in regulating flowering time and plant height, provide a new promising gene for soybean crop improvement.
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Affiliation(s)
- Jialing Zhang
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Chen
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yupeng Cai
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiang Su
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingying Chen
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Min Li
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wensheng Hou
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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12
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Steel L, Welling M, Ristevski N, Johnson K, Gendall A. Comparative genomics of flowering behavior in Cannabis sativa. FRONTIERS IN PLANT SCIENCE 2023; 14:1227898. [PMID: 37575928 PMCID: PMC10421669 DOI: 10.3389/fpls.2023.1227898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/03/2023] [Indexed: 08/15/2023]
Abstract
Cannabis sativa L. is a phenotypically diverse and multi-use plant used in the production of fiber, seed, oils, and a class of specialized metabolites known as phytocannabinoids. The last decade has seen a rapid increase in the licit cultivation and processing of C. sativa for medical end-use. Medical morphotypes produce highly branched compact inflorescences which support a high density of glandular trichomes, specialized epidermal hair-like structures that are the site of phytocannabinoid biosynthesis and accumulation. While there is a focus on the regulation of phytocannabinoid pathways, the genetic determinants that govern flowering time and inflorescence structure in C. sativa are less well-defined but equally important. Understanding the molecular mechanisms that underly flowering behavior is key to maximizing phytocannabinoid production. The genetic basis of flowering regulation in C. sativa has been examined using genome-wide association studies, quantitative trait loci mapping and selection analysis, although the lack of a consistent reference genome has confounded attempts to directly compare candidate loci. Here we review the existing knowledge of flowering time control in C. sativa, and, using a common reference genome, we generate an integrated map. The co-location of known and putative flowering time loci within this resource will be essential to improve the understanding of C. sativa phenology.
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Affiliation(s)
| | | | | | | | - Anthony Gendall
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe Institute for Sustainable Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia
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13
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Zahn IE, Roelofsen C, Angenent GC, Bemer M. TM3 and STM3 Promote Flowering Together with FUL2 and MBP20, but Act Antagonistically in Inflorescence Branching in Tomato. PLANTS (BASEL, SWITZERLAND) 2023; 12:2754. [PMID: 37570908 PMCID: PMC10420972 DOI: 10.3390/plants12152754] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023]
Abstract
The moment at which a plant transitions to reproductive development is paramount to its life cycle and is strictly controlled by many genes. The transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) plays a central role in this process in Arabidopsis. However, the role of SOC1 in tomato (Solanum lycopersicum) has been sparsely studied. Here, we investigated the function of four tomato SOC1 homologs in the floral transition and inflorescence development. We thoroughly characterized the SOC1-like clade throughout the Solanaceae and selected four tomato homologs that are dynamically expressed upon the floral transition. We show that of these homologs, TOMATO MADS 3 (TM3) and SISTER OF TM3 (STM3) promote the primary and sympodial transition to flowering, while MADS-BOX PROTEIN 23 (MBP23) and MBP18 hardly contribute to flowering initiation in the indeterminate cultivar Moneyberg. Protein-protein interaction assays and whole-transcriptome analysis during reproductive meristem development revealed that TM3 and STM3 interact and share many targets with FRUITFULL (FUL) homologs, including cytokinin regulators. Furthermore, we observed that mutating TM3/STM3 affects inflorescence development, but counteracts the inflorescence-branching phenotype of ful2 mbp20. Collectively, this indicates that TM3/STM3 promote the floral transition together with FUL2/MBP20, while these transcription factors have opposite functions in inflorescence development.
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Affiliation(s)
- Iris E. Zahn
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (I.E.Z.); (G.C.A.)
| | - Chris Roelofsen
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (I.E.Z.); (G.C.A.)
| | - Gerco C. Angenent
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (I.E.Z.); (G.C.A.)
- Business Unit Bioscience, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Marian Bemer
- Business Unit Bioscience, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
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14
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Wu J, Yang Y, Wang J, Wang Y, Yin L, An Z, Du K, Zhu Y, Qi J, Shen WH, Dong A. Histone chaperones AtChz1A and AtChz1B are required for H2A.Z deposition and interact with the SWR1 chromatin-remodeling complex in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2023; 239:189-207. [PMID: 37129076 DOI: 10.1111/nph.18940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/28/2023] [Indexed: 05/03/2023]
Abstract
The histone variant H2A.Z plays key functions in transcription and genome stability in all eukaryotes ranging from yeast to human, but the molecular mechanisms by which H2A.Z is incorporated into chromatin remain largely obscure. Here, we characterized the two homologs of yeast Chaperone for H2A.Z-H2B (Chz1) in Arabidopsis thaliana, AtChz1A and AtChz1B. AtChz1A/AtChz1B were verified to bind to H2A.Z-H2B and facilitate nucleosome assembly in vitro. Simultaneous knockdown of AtChz1A and AtChz1B, which exhibit redundant functions, led to a genome-wide reduction in H2A.Z and phenotypes similar to those of the H2A.Z-deficient mutant hta9-1hta11-2, including early flowering and abnormal flower morphologies. Interestingly, AtChz1A was found to physically interact with ACTIN-RELATED PROTEIN 6 (ARP6), an evolutionarily conserved subunit of the SWR1 chromatin-remodeling complex. Genetic interaction analyses showed that atchz1a-1atchz1b-1 was hypostatic to arp6-1. Consistently, genome-wide profiling analyses revealed partially overlapping genes and fewer misregulated genes and H2A.Z-reduced chromatin regions in atchz1a-1atchz1b-1 compared with arp6-1. Together, our results demonstrate that AtChz1A and AtChz1B act as histone chaperones to assist the deposition of H2A.Z into chromatin via interacting with SWR1, thereby playing critical roles in the transcription of genes involved in flowering and many other processes.
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Affiliation(s)
- Jiabing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yue Yang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jiachen Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Youchao Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Liufan Yin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Zengxuan An
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Kangxi Du
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yan Zhu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cédex, France
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
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15
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Wang X, Liu Z, Bai J, Sun S, Song J, Li R, Cui X. Antagonistic regulation of target genes by the SISTER OF TM3-JOINTLESS2 complex in tomato inflorescence branching. THE PLANT CELL 2023; 35:2062-2078. [PMID: 36881857 PMCID: PMC10226558 DOI: 10.1093/plcell/koad065] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 05/30/2023]
Abstract
Inflorescence branch number is a yield-related trait controlled by cell fate determination in meristems. Two MADS-box transcription factors (TFs)-SISTER OF TM3 (STM3) and JOINTLESS 2 (J2)-have opposing regulatory roles in inflorescence branching. However, the mechanisms underlying their regulatory functions in inflorescence determinacy remain unclear. Here, we characterized the functions of these TFs in tomato (Solanum lycopersicum) floral meristem and inflorescence meristem (IM) through chromatin immunoprecipitation and sequencing analysis of their genome-wide occupancy. STM3 and J2 activate or repress the transcription of a set of common putative target genes, respectively, through recognition and binding to CArG box motifs. FRUITFULL1 (FUL1) is a shared putative target of STM3 and J2 and these TFs antagonistically regulate FUL1 in inflorescence branching. Moreover, STM3 physically interacts with J2 to mediate its cytosolic redistribution and restricts J2 repressor activity by reducing its binding to target genes. Conversely, J2 limits STM3 regulation of target genes by transcriptional repression of the STM3 promoter and reducing STM3-binding activity. Our study thus reveals an antagonistic regulatory relationship in which STM3 and J2 control tomato IM determinacy and branch number.
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Affiliation(s)
- Xiaotian Wang
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zhiqiang Liu
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingwei Bai
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Sun
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jia Song
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ren Li
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xia Cui
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
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16
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Käppel S, Rümpler F, Theißen G. Cracking the Floral Quartet Code: How Do Multimers of MIKC C-Type MADS-Domain Transcription Factors Recognize Their Target Genes? Int J Mol Sci 2023; 24:ijms24098253. [PMID: 37175955 PMCID: PMC10178880 DOI: 10.3390/ijms24098253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
MADS-domain transcription factors (MTFs) are involved in the control of many important processes in eukaryotes. They are defined by the presence of a unique and highly conserved DNA-binding domain, the MADS domain. MTFs bind to double-stranded DNA as dimers and recognize specific sequences termed CArG boxes (such as 5'-CC(A/T)6GG-3') and similar sequences that occur hundreds of thousands of times in a typical flowering plant genome. The number of MTF-encoding genes increased by around two orders of magnitude during land plant evolution, resulting in roughly 100 genes in flowering plant genomes. This raises the question as to how dozens of different but highly similar MTFs accurately recognize the cis-regulatory elements of diverse target genes when the core binding sequence (CArG box) occurs at such a high frequency. Besides the usual processes, such as the base and shape readout of individual DNA sequences by dimers of MTFs, an important sublineage of MTFs in plants, termed MIKCC-type MTFs (MC-MTFs), has evolved an additional mechanism to increase the accurate recognition of target genes: the formation of heterotetramers of closely related proteins that bind to two CArG boxes on the same DNA strand involving DNA looping. MC-MTFs control important developmental processes in flowering plants, ranging from root and shoot to flower, fruit and seed development. The way in which MC-MTFs bind to DNA and select their target genes is hence not only of high biological interest, but also of great agronomic and economic importance. In this article, we review the interplay of the different mechanisms of target gene recognition, from the ordinary (base readout) via the extravagant (shape readout) to the idiosyncratic (recognition of the distance and orientation of two CArG boxes by heterotetramers of MC-MTFs). A special focus of our review is on the structural prerequisites of MC-MTFs that enable the specific recognition of target genes.
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Affiliation(s)
- Sandra Käppel
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Florian Rümpler
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Günter Theißen
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
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17
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Dong X, Zhang LP, Tang YH, Yu D, Cheng F, Dong YX, Jiang XD, Qian FM, Guo ZH, Hu JY. Arabidopsis AGAMOUS-LIKE16 and SUPPRESSOR OF CONSTANS1 regulate the genome-wide expression and flowering time. PLANT PHYSIOLOGY 2023; 192:154-169. [PMID: 36721922 PMCID: PMC10152661 DOI: 10.1093/plphys/kiad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/12/2022] [Accepted: 12/26/2022] [Indexed: 05/03/2023]
Abstract
Flowering transition is tightly coordinated by complex gene regulatory networks, in which AGAMOUS-LIKE 16 (AGL16) plays important roles. Here, we identified the molecular function and binding properties of AGL16 and demonstrated its partial dependency on the SUPPRESSOR OF CONSTANS 1 (SOC1) function in regulating flowering. AGL16 bound to promoters of more than 2,000 genes via CArG-box motifs with high similarity to that of SOC1 in Arabidopsis (Arabidopsis thaliana). Approximately 70 flowering genes involved in multiple pathways were potential targets of AGL16. AGL16 formed a protein complex with SOC1 and shared a common set of targets. Intriguingly, only a limited number of genes were differentially expressed in the agl16-1 loss-of-function mutant. However, in the soc1-2 knockout background, AGL16 repressed and activated the expression of 375 and 182 genes, respectively, with more than a quarter bound by AGL16. Corroborating these findings, AGL16 repressed the flowering time more strongly in soc1-2 than in the Col-0 background. These data identify a partial inter-dependency between AGL16 and SOC1 in regulating genome-wide gene expression and flowering time, while AGL16 provides a feedback regulation on SOC1 expression. Our study sheds light on the complex background dependency of AGL16 in flowering regulation, thus providing additional insights into the molecular coordination of development and environmental adaptation.
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Affiliation(s)
- Xue Dong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan Province, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Li-Ping Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan Province, China
| | - Yin-Hua Tang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan Province, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming 650201, Yunnan Province, China
| | - Dongmei Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan Province, China
| | - Fang Cheng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan Province, China
| | - Yin-Xin Dong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan Province, China
| | - Xiao-Dong Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan Province, China
| | - Fu-Ming Qian
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan Province, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan Province, China
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18
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Laanen P, Cuypers A, Saenen E, Horemans N. Flowering under enhanced ionising radiation conditions and its regulation through epigenetic mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:246-259. [PMID: 36731286 DOI: 10.1016/j.plaphy.2023.01.049] [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: 06/27/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
As sessile organisms, plants have to deal with unfavourable conditions by acclimating or adapting in order to survive. Regulation of flower induction is one such mechanism to ensure reproduction and species survival. Flowering is a tightly regulated process under the control of a network of genes, which can be affected by environmental cues and stress. The effects of ionising radiation (IR) on flowering, however, have been poorly studied. Understanding the effects of ionising radiation on flowering, including the timing, gene pathways, and epigenetics involved, is crucial in the continuing effort of environmental radiation protection. The review shows that plants alter their flowering pattern in response to IR, with various flowering related genes (eg. FLOWERING LOCUS C (FLC), FLOWERING LOCUS T (FT), CONSTANS (CO), GIGANTEA (GI), APETALA1 (AP1), LEAFY (LFY)) and epigenetic processes (DNA methylation, and miRNA expression eg. miRNA169, miR156, miR172) being affected. Thereby, showing a hypothetical IR-induced flowering mechanism. Further research on the interaction between IR and flowering in plants is, however, needed to elucidate the mechanisms behind the stress-induced flowering response.
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Affiliation(s)
- Pol Laanen
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
| | - Ann Cuypers
- Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
| | - Eline Saenen
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium.
| | - Nele Horemans
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
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19
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Johnson SE, Tittes S, Franks SJ. Rapid, nonparallel genomic evolution of Brassica rapa (field mustard) under experimental drought. J Evol Biol 2023; 36:550-562. [PMID: 36721268 DOI: 10.1111/jeb.14152] [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: 04/20/2022] [Revised: 09/22/2022] [Accepted: 12/08/2022] [Indexed: 02/02/2023]
Abstract
While we know that climate change can potentially cause rapid phenotypic evolution, our understanding of the genetic basis and degree of genetic parallelism of rapid evolutionary responses to climate change is limited. In this study, we combined the resurrection approach with an evolve-and-resequence design to examine genome-wide evolutionary changes following drought. We exposed genetically similar replicate populations of the annual plant Brassica rapa derived from a field population in southern California to four generations of experimental drought or watered conditions in a greenhouse. Genome-wide sequencing of ancestral and descendant population pools identified hundreds of SNPs that showed evidence of rapidly evolving in response to drought. Several of these were in stress response genes, and two were identified in a prior study of drought response in this species. However, almost all genetic changes were unique among experimental populations, indicating that the evolutionary changes were largely nonparallel, despite the fact that genetically similar replicates of the same founder population had experienced controlled and consistent selection regimes. This nonparallelism of evolution at the genetic level is potentially because of polygenetic adaptation allowing for multiple different genetic routes to similar phenotypic outcomes. Our findings help to elucidate the relationship between rapid phenotypic and genomic evolution and shed light on the degree of parallelism and predictability of genomic evolution to environmental change.
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Affiliation(s)
- Stephen E Johnson
- Department of Biological Sciences and Louis Calder Center, Fordham University, Bronx, New York, USA
| | - Silas Tittes
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Steven J Franks
- Department of Biological Sciences and Louis Calder Center, Fordham University, Bronx, New York, USA
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20
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John M, Grimm D, Korte A. Predicting Gene Regulatory Interactions Using Natural Genetic Variation. Methods Mol Biol 2023; 2698:301-322. [PMID: 37682482 DOI: 10.1007/978-1-0716-3354-0_18] [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: 09/09/2023]
Abstract
Genome-wide association studies (GWAS) are a powerful tool to elucidate the genotype-phenotype map. Although GWAS are usually used to assess simple univariate associations between genetic markers and traits of interest, it is also possible to infer the underlying genetic architecture and to predict gene regulatory interactions. In this chapter, we describe the latest methods and tools to perform GWAS by calculating permutation-based significance thresholds. For this purpose, we first provide guidelines on univariate GWAS analyses that are extended in the second part of this chapter to more complex models that enable the inference of gene regulatory networks and how these networks vary.
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Affiliation(s)
- Maura John
- Technical University of Munich & Weihenstephan-Triesdorf University of Applied Sciences, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany
| | - Dominik Grimm
- Technical University of Munich & Weihenstephan-Triesdorf University of Applied Sciences, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany
| | - Arthur Korte
- Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany.
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21
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Spitzer-Rimon B, Shafran-Tomer H, Gottlieb GH, Doron-Faigenboim A, Zemach H, Kamenetsky-Goldstein R, Flaishman M. Non-photoperiodic transition of female cannabis seedlings from juvenile to adult reproductive stage. PLANT REPRODUCTION 2022; 35:265-277. [PMID: 36063227 DOI: 10.1007/s00497-022-00449-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Vegetative-to-reproductive phase transition in female cannabis seedlings occurs autonomously with the de novo development of single flowers. To ensure successful sexual reproduction, many plant species originating from seedlings undergo juvenile-to-adult transition. This phase transition precedes and enables the vegetative-to-reproductive shift in plants, upon perception of internal and/or external signals such as temperature, photoperiod, metabolite levels, and phytohormones. This study demonstrates that the juvenile seedlings of cannabis gradually shift to the adult vegetative stage, as confirmed by the formation of lobed leaves, and upregulation of the phase-transition genes. In the tested cultivar, the switch to the reproductive stage occurs with the development of a pair of single flowers in the 7th node. Histological analysis indicated that transition to the reproductive stage is accomplished by the de novo establishment of new flower meristems which are not present in a vegetative stage, or as dormant meristems at nodes 4 and 6. Moreover, there were dramatic changes in the transcriptomic profile of flowering-related genes among nodes 4, 6, and 7. Downregulation of flowering repressors and an intense increase in the transcription of phase transition-related genes occur in parallel with an increase in the transcription of flowering integrators and meristem identity genes. These results support and provide molecular evidence for previous findings that cannabis possesses an autonomous flowering mechanism and the transition to reproductive phase is controlled in this plant mainly by internal signals.
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Affiliation(s)
- Ben Spitzer-Rimon
- Institute of Plant Sciences, Agricultural Research Organization-Volcani, HaMaccabbim Road 68, 7505101, Rishon LeZion, Israel.
| | - Hadas Shafran-Tomer
- Institute of Plant Sciences, Agricultural Research Organization-Volcani, HaMaccabbim Road 68, 7505101, Rishon LeZion, Israel
| | - Gilad H Gottlieb
- Institute of Plant Sciences, Agricultural Research Organization-Volcani, HaMaccabbim Road 68, 7505101, Rishon LeZion, Israel
| | - Adi Doron-Faigenboim
- Institute of Plant Sciences, Agricultural Research Organization-Volcani, HaMaccabbim Road 68, 7505101, Rishon LeZion, Israel
| | - Hanita Zemach
- Institute of Plant Sciences, Agricultural Research Organization-Volcani, HaMaccabbim Road 68, 7505101, Rishon LeZion, Israel
| | - Rina Kamenetsky-Goldstein
- Institute of Plant Sciences, Agricultural Research Organization-Volcani, HaMaccabbim Road 68, 7505101, Rishon LeZion, Israel
| | - Moshe Flaishman
- Institute of Plant Sciences, Agricultural Research Organization-Volcani, HaMaccabbim Road 68, 7505101, Rishon LeZion, Israel
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22
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Li X, Liao J, Bai H, Bei J, Li K, Luo M, Shen W, Yang C, Gao C. Arabidopsis flowering integrator SOC1 transcriptionally regulates autophagy in response to long-term carbon starvation. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6589-6599. [PMID: 35852462 DOI: 10.1093/jxb/erac298] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/02/2022] [Indexed: 06/15/2023]
Abstract
Autophagy is a highly conserved, self-digestion process that is essential for plant adaptations to various environmental stresses. Although the core components of autophagy in plants have been well established, the molecular basis for its transcriptional regulation remains to be fully characterized. In this study, we demonstrate that SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), a MADS-box family transcription factor that determines flowering transition in Arabidopsis, functions as a transcriptional repressor of autophagy. EMSAs, ChIP-qPCR assays, and dual-luciferase receptor assays showed that SOC1 can bind to the promoters of ATG4b, ATG7, and ATG18c via the conserved CArG box. qRT-PCR analysis showed that the three ATG genes ATG4b, ATG7, and ATG18c were up-regulated in the soc1-2 mutant. In line with this, the mutant also displayed enhanced autophagy activity, as revealed by increased autophagosome formation and elevated autophagic flux compared with the wild type. More importantly, SOC1 negatively affected the tolerance of plants to long-term carbon starvation, and this process requires a functional autophagy pathway. Finally, we found that SOC1 was repressed upon carbon starvation at both the transcriptional and protein levels. Overall, our study not only uncovers an important transcriptional mechanism that contributes to the regulation of plant autophagy in response to nutrient starvation, but also highlights novel cellular functions of the flowering integrator SOC1.
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Affiliation(s)
- Xibao Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jun Liao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Haiyan Bai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jieying Bei
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Kailin Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Ming Luo
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Wenjin Shen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Chao Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
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23
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Zhang S, Deng L, Zhao L, Wu C. Genome-wide binding analysis of transcription factor Rice Indeterminate 1 reveals a complex network controlling rice floral transition. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1690-1705. [PMID: 35789063 DOI: 10.1111/jipb.13325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
RICE INDETERMINATE 1 (RID1) plays a critical role in controlling floral transition in rice (Oryza sativa). However, the molecular basis for this effect, particularly the target genes and regulatory specificity, remains largely unclear. Here, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) in young leaves at the pre-floral-transition stage to identify the target genes of RID1, identifying 2,680 genes associated with RID1 binding sites genome-wide. RID1 binding peaks were highly enriched for TTTGTC, the direct binding motif of the INDETERMINATE DOMAIN protein family that includes RID1. Interestingly, CACGTG and GTGGGCCC, two previously uncharacterized indirect binding motifs, were enriched through the interactions of RID1 with the novel flowering-promoting proteins OsPIL12 and OsTCP11, respectively. Moreover, the ChIP-seq data demonstrated that RID1 bound to numerous rice heading-date genes, such as HEADING DATE 1 (HD1) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (OsFKF1). Notably, transcriptome sequencing (RNA-seq) analysis revealed roles of RID1 in diverse developmental pathways. Genetic analysis combined with genome-wide ChIP-seq and RNA-seq results showed that RID1 directly binds to the promoter of OsERF#136 (a repressor of rice flowering) and negatively regulates its expression. Overall, our findings provide new insights into the molecular and genetic mechanisms underlying rice floral transition and characterize OsERF#136 as a previously unrecognized direct target of RID1.
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Affiliation(s)
- Shuo Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Deng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
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24
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Cui F, Ye X, Li X, Yang Y, Hu Z, Overmyer K, Brosché M, Yu H, Salojärvi J. Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis. PLANT COMMUNICATIONS 2022; 3:100307. [PMID: 35605198 PMCID: PMC9284290 DOI: 10.1016/j.xplc.2022.100307] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/09/2022] [Accepted: 02/24/2022] [Indexed: 05/25/2023]
Abstract
Vaccinium darrowii is a subtropical wild blueberry species that has been used to breed economically important southern highbush cultivars. The adaptive traits of V. darrowii to subtropical climates can provide valuable information for breeding blueberry and perhaps other plants, especially against the background of global warming. Here, we assembled the V. darrowii genome into 12 pseudochromosomes using Oxford Nanopore long reads complemented with Hi-C scaffolding technologies, and we predicted 41 815 genes using RNA-sequencing evidence. Syntenic analysis across three Vaccinium species revealed a highly conserved genome structure, with the highest collinearity between V. darrowii and Vaccinium corymbosum. This conserved genome structure may explain the high fertility observed during crossbreeding of V. darrowii with other blueberry cultivars. Analysis of gene expansion and tandem duplication indicated possible roles for defense- and flowering-associated genes in the adaptation of V. darrowii to the subtropics. Putative SOC1 genes in V. darrowii were identified based on phylogeny and expression analysis. Blueberries are covered in a thick cuticle layer and contain anthocyanins, which confer their powdery blue color. Using RNA sequencing, we delineated the cuticle biosynthesis pathways of Vaccinium species in V. darrowii. This result can serve as a reference for breeding berries whose colors are appealing to customers. The V. darrowii reference genome, together with the unique traits of this species, including its diploid genome, short vegetative phase, and high compatibility in hybridization with other blueberries, make V. darrowii a potential research model for blueberry species.
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Affiliation(s)
- Fuqiang Cui
- College of Forestry and Biotechnology, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China.
| | - Xiaoxue Ye
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xiaoxiao Li
- College of Forestry and Biotechnology, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Yifan Yang
- College of Forestry and Biotechnology, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Zhubing Hu
- State Key Laboratory of Cotton Biology, Department of Biology, Institute of Plant Stress Biology, Henan University, Kaifeng, China
| | - Kirk Overmyer
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and the Viikki Plant Science Centre, University of Helsinki, PO Box 65 (Viikinkaari 1), 00014 Helsinki, Finland
| | - Mikael Brosché
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and the Viikki Plant Science Centre, University of Helsinki, PO Box 65 (Viikinkaari 1), 00014 Helsinki, Finland
| | - Hong Yu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and the Viikki Plant Science Centre, University of Helsinki, PO Box 65 (Viikinkaari 1), 00014 Helsinki, Finland.
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25
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Zhang C, Zhou Q, Liu W, Wu X, Li Z, Xu Y, Li Y, Imaizumi T, Hou X, Liu T. BrABF3 promotes flowering through the direct activation of CONSTANS transcription in pak choi. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:134-148. [PMID: 35442527 DOI: 10.1111/tpj.15783] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
Drought stress triggers the accumulation of the phytohormone abscisic acid (ABA), which in turn activates the expression of the floral integrator gene CONSTANS (CO), accelerating flowering. However, the molecular mechanism of ABA-induced CO activation remains elusive. Here, we conducted a yeast one-hybrid assay using the CO promoter from Brassica campestris (syn. Brassica rapa) ssp. chinensis (pak choi) to screen the ABA-induced pak choi library and identified the transcription activator ABF3 (BrABF3). BrABF3, the expression of which was induced by ABA in pak choi, directly bound to the CO promoter from both pak choi and Arabidopsis. The BrABF3 promoter is specifically active in the Arabidopsis leaf vascular tissue, where CO is mainly expressed. Impaired BrABF3 expression in pak choi decreased BrCO expression levels and delayed flowering, whereas ectopic expression of BrABF3 in Arabidopsis increased CO expression and induced earlier flowering under the long-day conditions. Electrophoretic mobility shift assay analysis showed that BrABF3 was enriched at the canonical ABA-responsive element-ABRE binding factor (ABRE-ABF) binding motifs of the BrCO promoter. The direct binding of BrABF3 to the ABRE elements of CO was further confirmed by chromatin immunoprecipitation quantitative PCR. In addition, the induction of BrCO transcription by BrABF3 could be repressed by BrCDF1 in the morning. Thus, our results suggest that ABA could accelerate the floral transition by directly activating BrCO transcription through BrABF3 in pak choi.
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Affiliation(s)
- Changwei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qian Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, 27607, USA
| | - Xiaoting Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhubo Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanyuan Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, Washington, 98195-1800, USA
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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26
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Cuerda-Gil D, Hung YH, Panda K, Slotkin RK. A plant tethering system for the functional study of protein-RNA interactions in vivo. PLANT METHODS 2022; 18:75. [PMID: 35658900 PMCID: PMC9166424 DOI: 10.1186/s13007-022-00907-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
The sorting of RNA transcripts dictates their ultimate post-transcriptional fates, such as translation, decay or degradation by RNA interference (RNAi). This sorting of RNAs into distinct fates is mediated by their interaction with RNA-binding proteins. While hundreds of RNA binding proteins have been identified, which act to sort RNAs into different pathways is largely unknown. Particularly in plants, this is due to the lack of reliable protein-RNA artificial tethering tools necessary to determine the mechanism of protein action on an RNA in vivo. Here we generated a protein-RNA tethering system which functions on an endogenous Arabidopsis RNA that is tracked by the quantitative flowering time phenotype. Unlike other protein-RNA tethering systems that have been attempted in plants, our system circumvents the inadvertent triggering of RNAi. We successfully in vivo tethered a protein epitope, deadenylase protein and translation factor to the target RNA, which function to tag, decay and boost protein production, respectively. We demonstrated that our tethering system (1) is sufficient to engineer the downstream fate of an RNA, (2) enables the determination of any protein's function upon recruitment to an RNA, and (3) can be used to discover new interactions with RNA-binding proteins.
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Affiliation(s)
- Diego Cuerda-Gil
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Yu-Hung Hung
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Kaushik Panda
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
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27
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Márquez Gutiérrez R, Cherubino Ribeiro TH, de Oliveira RR, Benedito VA, Chalfun-Junior A. Genome-Wide Analyses of MADS-Box Genes in Humulus lupulus L. Reveal Potential Participation in Plant Development, Floral Architecture, and Lupulin Gland Metabolism. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11091237. [PMID: 35567239 PMCID: PMC9100628 DOI: 10.3390/plants11091237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 05/14/2023]
Abstract
MADS-box transcription factors (TFs) are involved in multiple plant development processes and are most known during the reproductive transition and floral organ development. Very few genes have been characterized in the genome of Humulus lupulus L. (Cannabaceae), an important crop for the pharmaceutical and beverage industries. The MADS-box family has not been studied in this species yet. We identified 65 MADS-box genes in the hop genome, of which 29 encode type-II TFs (27 of subgroup MIKCC and 2 MIKC*) and 36 type-I proteins (26 α, 9 β, and 1 γ). Type-II MADS-box genes evolved more complex architectures than type-I genes. Interestingly, we did not find FLOWERING LOCUS C (FLC) homologs, a transcription factor that acts as a floral repressor and is negatively regulated by cold. This result provides a molecular explanation for a previous work showing that vernalization is not a requirement for hop flowering, which has implications for its cultivation in the tropics. Analysis of gene ontology and expression profiling revealed genes potentially involved in the development of male and female floral structures based on the differential expression of ABC homeotic genes in each whorl of the flower. We identified a gene exclusively expressed in lupulin glands, suggesting a role in specialized metabolism in these structures. In toto, this work contributes to understanding the evolutionary history of MADS-box genes in hop, and provides perspectives on functional genetic studies, biotechnology, and crop breeding.
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Affiliation(s)
- Robert Márquez Gutiérrez
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-900, MG, Brazil; (R.M.G.); (T.H.C.R.); (R.R.d.O.)
| | - Thales Henrique Cherubino Ribeiro
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-900, MG, Brazil; (R.M.G.); (T.H.C.R.); (R.R.d.O.)
| | - Raphael Ricon de Oliveira
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-900, MG, Brazil; (R.M.G.); (T.H.C.R.); (R.R.d.O.)
| | - Vagner Augusto Benedito
- Laboratory of Plant Functional Genetics, Plant and Soil Sciences Division, 3425 Agricultural Sciences Building, West Virginia University, Morgantown, WV 26506-6108, USA
- Correspondence: (V.A.B.); (A.C.-J.)
| | - Antonio Chalfun-Junior
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-900, MG, Brazil; (R.M.G.); (T.H.C.R.); (R.R.d.O.)
- Correspondence: (V.A.B.); (A.C.-J.)
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Harel-Beja R, Ophir R, Sherman A, Eshed R, Rozen A, Trainin T, Doron-Faigenboim A, Tal O, Bar-Yaakov I, Holland D. The Pomegranate Deciduous Trait Is Genetically Controlled by a PgPolyQ- MADS Gene. FRONTIERS IN PLANT SCIENCE 2022; 13:870207. [PMID: 35574086 PMCID: PMC9100744 DOI: 10.3389/fpls.2022.870207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/17/2022] [Indexed: 06/15/2023]
Abstract
The pomegranate (Punica granatum L.) is a deciduous fruit tree that grows worldwide. However, there are variants, which stay green in mild winter conditions and are determined evergreen. The evergreen trait is of commercial and scientific importance as it extends the period of fruit production and provides opportunity to identify genetic functions that are involved in sensing environmental cues. Several different evergreen pomegranate accessions from different genetic sources grow in the Israeli pomegranate collection. The leaves of deciduous pomegranates begin to lose chlorophyll during mid of September, while evergreen accessions continue to generate new buds. When winter temperature decreases 10°C, evergreen variants cease growing, but as soon as temperatures arise budding starts, weeks before the response of the deciduous varieties. In order to understand the genetic components that control the evergreen/deciduous phenotype, several segregating populations were constructed, and high-resolution genetic maps were assembled. Analysis of three segregating populations showed that the evergreen/deciduous trait in pomegranate is controlled by one major gene that mapped to linkage group 3. Fine mapping with advanced F3 and F4 populations and data from the pomegranate genome sequences revealed that a gene encoding for a putative and unique MADS transcription factor (PgPolyQ-MADS) is responsible for the evergreen trait. Ectopic expression of PgPolyQ-MADS in Arabidopsis generated small plants and early flowering. The deduced protein of PgPolyQ-MADS includes eight glutamines (polyQ) at the N-terminus. Three-dimensional protein model suggests that the polyQ domain structure might be involved in DNA binding of PgMADS. Interestingly, all the evergreen pomegranate varieties contain a mutation within the polyQ that cause a stop codon at the N terminal. The polyQ domain of PgPolyQ-MADS resembles that of the ELF3 prion-like domain recently reported to act as a thermo-sensor in Arabidopsis, suggesting that similar function could be attributed to PgPolyQ-MADS protein in control of dormancy. The study of the evergreen trait broadens our understanding of the molecular mechanism related to response to environmental cues. This enables the development of new cultivars that are better adapted to a wide range of climatic conditions.
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Affiliation(s)
- Rotem Harel-Beja
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization - The Volcani Center, Newe Ya’ar Research Center, Ramat Yishai, Israel
| | - Ron Ophir
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization - The Volcani Center, Rishon LeZion, Israel
| | - Amir Sherman
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization - The Volcani Center, Rishon LeZion, Israel
| | - Ravit Eshed
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization - The Volcani Center, Rishon LeZion, Israel
| | - Ada Rozen
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization - The Volcani Center, Rishon LeZion, Israel
| | - Taly Trainin
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization - The Volcani Center, Newe Ya’ar Research Center, Ramat Yishai, Israel
| | - Adi Doron-Faigenboim
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Agricultural Research Organization - The Volcani Center, Rishon LeZion, Israel
| | - Ofir Tal
- Institute of Plant Sciences, Newe Ya’ar Research Center, The Agricultural Research Organization - The Volcani Center, Ramat Yishai, Israel
| | - Irit Bar-Yaakov
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization - The Volcani Center, Newe Ya’ar Research Center, Ramat Yishai, Israel
| | - Doron Holland
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization - The Volcani Center, Newe Ya’ar Research Center, Ramat Yishai, Israel
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Ma L, Yan Y. GhSOC1s Evolve to Respond Differently to the Environmental Cues and Promote Flowering in Partially Independent Ways. FRONTIERS IN PLANT SCIENCE 2022; 13:882946. [PMID: 35519808 PMCID: PMC9067242 DOI: 10.3389/fpls.2022.882946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Gossypium hirsutum is most broadly cultivated in the world due to its broader adaptation to the environment and successful breeding of early maturity varieties. However, how cotton responds to environmental cues to adjust flowering time to achieve reproductive success is largely unknown. SOC1 functions as an essential integrator for the endogenous and exogenous signals to maximize reproduction. Thus we identified six SOC1-like genes in Gossypium that clustered into two groups. GhSOC1-1 contained a large intron and clustered with monocot SOC1s, while GhSOC1-2/3 were close to dicot SOC1s. GhSOC1s expression gradually increased during seedling development suggesting their conserved function in promoting flowering, which was supported by the early flowering phenotype of 35S:GhSOC1-1 Arabidopsis lines and the delayed flowering of cotton silencing lines. Furthermore, GhSOC1-1 responded to short-day and high temperature conditions, while GhSOC1-2 responded to long-day conditions. GhSOC1-3 might function to promote flowering in response to low temperature and cold. Taken together, our results demonstrate that GhSOC1s respond differently to light and temperature and act cooperatively to activate GhLFY expression to promote floral transition and enlighten us in cotton adaptation to environment that is helpful in improvement of cotton maturity.
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BcSOC1 Promotes Bolting and Stem Elongation in Flowering Chinese Cabbage. Int J Mol Sci 2022; 23:ijms23073459. [PMID: 35408819 PMCID: PMC8998877 DOI: 10.3390/ijms23073459] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/20/2022] [Accepted: 03/20/2022] [Indexed: 02/05/2023] Open
Abstract
Flowering Chinese cabbage is one of the most economically important stalk vegetables. However, the molecular mechanisms underlying bolting, which is directly related to stalk quality and yield, in this species remain unknown. Previously, we examined five key stem development stages in flowering Chinese cabbage. Here, we identified a gene, BcSOC1 (SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1), in flowering Chinese cabbage using transcriptome analysis, whose expression was positively correlated with bolting. Exogenous gibberellin (GA3) and low-temperature treatments significantly upregulated BcSOC1 and promoted early bolting and flowering. Additionally, BcSOC1 overexpression accelerated early flowering and stem elongation in both Arabidopsis and flowering Chinese cabbage, whereas its knockdown dramatically delayed bolting and flowering and inhibited stem elongation in the latter; the inhibition of stem elongation was more notable than delayed flowering. BcSOC1 overexpression also induced cell expansion by upregulating genes encoding cell wall structural proteins, such as BcEXPA11 (cell wall structural proteins and enzymes) and BcXTH3 (xyloglucan endotransglycosidase/hydrolase), upon exogenous GA3 and low-temperature treatments. Moreover, the length of pith cells was correlated with stem height, and BcSOC1 interacted with BcAGL6 (AGAMOUS-LIKE 6) and BcAGL24 (AGAMOUS-LIKE 24). Thus, BcSOC1 plays a vital role in bolting and stem elongation of flowering Chinese cabbage and may play a novel role in regulating stalk development, apart from the conserved function of Arabidopsis SOC1 in flowering alone.
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Identification and regulatory network analysis of SPL family transcription factors in Populus euphratica Oliv. heteromorphic leaves. Sci Rep 2022; 12:2856. [PMID: 35190606 PMCID: PMC8861001 DOI: 10.1038/s41598-022-06942-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 02/09/2022] [Indexed: 11/08/2022] Open
Abstract
The SQUAMOSA promoter-binding protein-like (SPL) family play a key role in guiding the switch of plant growth from juvenile to adult phases. Populus euphratica Oliv. exhibit typical heterophylly, and is therefore an ideal model for studying leaf shape development. To investigate the role and regulated networks of SPLs in the morphogenesis of P. euphratica heteromorphic leaves. In this study, 33 P. euphratica SPL (PeuSPL) genes were identified from P. euphratica genome and transcriptome data. Phylogenetic analysis depicted the classification of these SPL genes into two subgroups. The expression profiles and regulatory networks of P. euphratica SPL genes analysis displayed that major P. euphratica SPL family members gradually increases from linear to broad-ovate leaves, and they were involved in the morphogenesis regulation, stress response, transition from vegetative to reproductive growth, photoperiod, and photosynthesis etc. 14 circRNAs, and 33 lncRNAs can promote the expression of 12 of the P. euphratica SPLs by co-decoying miR156 in heteromorphic leaf morphogenesis. However, it was found that the effect of PeuSPL2-4 and PeuSPL9 in leaf shape development was contrasting to their homologous genes of Arabidopsis. Therefore, it was suggested that the SPL family were evolutionarily conserved for regulation growth, but were varies in different plant for regulation of the organ development.
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Wang B, Hu W, Fang Y, Feng X, Fang J, Zou T, Zheng S, Ming R, Zhang J. Comparative Analysis of the MADS-Box Genes Revealed Their Potential Functions for Flower and Fruit Development in Longan ( Dimocarpus longan). FRONTIERS IN PLANT SCIENCE 2022; 12:813798. [PMID: 35154209 PMCID: PMC8829350 DOI: 10.3389/fpls.2021.813798] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/16/2021] [Indexed: 06/01/2023]
Abstract
Longan (Dimocarpus longan Lour.) is an important economic crop widely planted in tropical and subtropical regions, and flower and fruit development play decisive effects on the longan yield and fruit quality formation. MCM1, AGAMOUS, DEFICIENS, Serum Response Factor (MADS)-box transcription factor family plays important roles for the flowering time, floral organ identity, and fruit development in plants. However, there is no systematic information of MADS-box family in longan. In this study, 114 MADS-box genes were identified from the longan genome, phylogenetic analysis divided them into type I (Mα, Mβ, Mγ) and type II (MIKC*, MIKC C ) groups, and MIKC C genes were further clustered into 12 subfamilies. Comparative genomic analysis of 12 representative plant species revealed the conservation of type II in Sapindaceae and analysis of cis-elements revealed that Dof transcription factors might directly regulate the MIKC C genes. An ABCDE model was proposed for longan based on the phylogenetic analysis and expression patterns of MADS-box genes. Transcriptome analysis revealed that MIKC C genes showed wide expression spectrums, particularly in reproductive organs. From 35 days after KClO3 treatment, 11 MIKC genes were up-regulated, suggesting a crucial role in off-season flower induction, while DlFLC, DlSOC1, DlSVP, and DlSVP-LIKE may act as the inhibitors. The gene expression patterns of longan fruit development indicated that DlSTK, DlSEP1/2, and DlMADS53 could be involved in fruit growth and ripening. This paper carried out the whole genome identification and analysis of the longan MADS-box family for the first time, which provides new insights for further understanding its function in flowers and fruit.
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Affiliation(s)
- Baiyu Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenshun Hu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Breeding Engineering Technology Research Center for Longan & Loquat, Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yaxue Fang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoxi Feng
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jingping Fang
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Tengyue Zou
- College of Mechanical and Electrical Engineering, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shaoquan Zheng
- Fujian Breeding Engineering Technology Research Center for Longan & Loquat, Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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Chávez-Hernández EC, Quiroz S, García-Ponce B, Álvarez-Buylla ER. The flowering transition pathways converge into a complex gene regulatory network that underlies the phase changes of the shoot apical meristem in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:852047. [PMID: 36017258 PMCID: PMC9396034 DOI: 10.3389/fpls.2022.852047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/04/2022] [Indexed: 05/08/2023]
Abstract
Post-embryonic plant development is characterized by a period of vegetative growth during which a combination of intrinsic and extrinsic signals triggers the transition to the reproductive phase. To understand how different flowering inducing and repressing signals are associated with phase transitions of the Shoot Apical Meristem (SAM), we incorporated available data into a dynamic gene regulatory network model for Arabidopsis thaliana. This Flowering Transition Gene Regulatory Network (FT-GRN) formally constitutes a dynamic system-level mechanism based on more than three decades of experimental data on flowering. We provide novel experimental data on the regulatory interactions of one of its twenty-three components: a MADS-box transcription factor XAANTAL2 (XAL2). These data complement the information regarding flowering transition under short days and provides an example of the type of questions that can be addressed by the FT-GRN. The resulting FT-GRN is highly connected and integrates developmental, hormonal, and environmental signals that affect developmental transitions at the SAM. The FT-GRN is a dynamic multi-stable Boolean system, with 223 possible initial states, yet it converges into only 32 attractors. The latter are coherent with the expression profiles of the FT-GRN components that have been experimentally described for the developmental stages of the SAM. Furthermore, the attractors are also highly robust to initial states and to simulated perturbations of the interaction functions. The model recovered the meristem phenotypes of previously described single mutants. We also analyzed the attractors landscape that emerges from the postulated FT-GRN, uncovering which set of signals or components are critical for reproductive competence and the time-order transitions observed in the SAM. Finally, in the context of such GRN, the role of XAL2 under short-day conditions could be understood. Therefore, this model constitutes a robust biological module and the first multi-stable, dynamical systems biology mechanism that integrates the genetic flowering pathways to explain SAM phase transitions.
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Affiliation(s)
- Elva C. Chávez-Hernández
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Stella Quiroz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Berenice García-Ponce,
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Elena R. Álvarez-Buylla,
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Wang X, Liu Z, Sun S, Wu J, Li R, Wang H, Cui X. SISTER OF TM3 activates FRUITFULL1 to regulate inflorescence branching in tomato. HORTICULTURE RESEARCH 2021; 8:251. [PMID: 34848688 PMCID: PMC8633288 DOI: 10.1038/s41438-021-00677-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 07/19/2021] [Accepted: 08/02/2021] [Indexed: 05/19/2023]
Abstract
Selection for favorable inflorescence architecture to improve yield is one of the crucial targets in crop breeding. Different tomato varieties require distinct inflorescence-branching structures to enhance productivity. While a few important genes for tomato inflorescence-branching development have been identified, the regulatory mechanism underlying inflorescence branching is still unclear. Here, we confirmed that SISTER OF TM3 (STM3), a homolog of Arabidopsis SOC1, is a major positive regulatory factor of tomato inflorescence architecture by map-based cloning. High expression levels of STM3 underlie the highly inflorescence-branching phenotype in ST024. STM3 is expressed in both vegetative and reproductive meristematic tissues and in leaf primordia and leaves, indicative of its function in flowering time and inflorescence-branching development. Transcriptome analysis shows that several floral development-related genes are affected by STM3 mutation. Among them, FRUITFULL1 (FUL1) is downregulated in stm3cr mutants, and its promoter is bound by STM3 by ChIP-qPCR analysis. EMSA and dual-luciferase reporter assays further confirmed that STM3 could directly bind the promoter region to activate FUL1 expression. Mutation of FUL1 could partially restore inflorescence-branching phenotypes caused by high STM3 expression in ST024. Our findings provide insights into the molecular and genetic mechanisms underlying inflorescence development in tomato.
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Affiliation(s)
- Xiaotian Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiqiang Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shuai Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jianxin Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ren Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haijing Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xia Cui
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Barrero-Gil J, Mouriz A, Piqueras R, Salinas J, Jarillo JA, Piñeiro M. A MRG-operated chromatin switch at SOC1 attenuates abiotic stress responses during the floral transition. PLANT PHYSIOLOGY 2021; 187:462-471. [PMID: 34618146 PMCID: PMC8418395 DOI: 10.1093/plphys/kiab275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
Plants react to environmental challenges by integrating external cues with endogenous signals to optimize survival and reproductive success. However, the mechanisms underlying this integration remain obscure. While stress conditions are known to impact plant development, how developmental transitions influence responses to adverse conditions has not been addressed. Here, we reveal a molecular mechanism of stress response attenuation during the onset of flowering in Arabidopsis (Arabidopsis thaliana). We show that Arabidopsis MORF-RELATED GENE (MRG) proteins, components of the NuA4 histone acetyltransferase complex that bind trimethylated-lysine 36 in histone H3 (H3K36me3), function as a chromatin switch on the floral integrator SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) to coordinate flowering initiation with plant responsiveness to hostile environments. MRG proteins are required to activate SOC1 expression during flowering induction by promoting histone H4 acetylation. In turn, SOC1 represses a broad array of genes that mediate abiotic stress responses. We propose that during the transition from vegetative to reproductive growth, the MRG-SOC1 module constitutes a central hub in a mechanism that tunes down stress responses to enhance the reproductive success and plant fitness at the expense of costly efforts for adaptation to challenging environments.
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Affiliation(s)
- Javier Barrero-Gil
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología Microbiana y de Plantas, Centro Investigaciones Biológicas “Margarita Salas”, CSIC, Madrid, Spain
| | - Alfonso Mouriz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Raquel Piqueras
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Julio Salinas
- Departamento de Biotecnología Microbiana y de Plantas, Centro Investigaciones Biológicas “Margarita Salas”, CSIC, Madrid, Spain
| | - José A. Jarillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
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Azpeitia E, Tichtinsky G, Le Masson M, Serrano-Mislata A, Lucas J, Gregis V, Gimenez C, Prunet N, Farcot E, Kater MM, Bradley D, Madueño F, Godin C, Parcy F. Cauliflower fractal forms arise from perturbations of floral gene networks. Science 2021; 373:192-197. [PMID: 34244409 DOI: 10.1126/science.abg5999] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/03/2021] [Indexed: 11/02/2022]
Abstract
Throughout development, plant meristems regularly produce organs in defined spiral, opposite, or whorl patterns. Cauliflowers present an unusual organ arrangement with a multitude of spirals nested over a wide range of scales. How such a fractal, self-similar organization emerges from developmental mechanisms has remained elusive. Combining experimental analyses in an Arabidopsis thaliana cauliflower-like mutant with modeling, we found that curd self-similarity arises because the meristems fail to form flowers but keep the "memory" of their transient passage in a floral state. Additional mutations affecting meristem growth can induce the production of conical structures reminiscent of the conspicuous fractal Romanesco shape. This study reveals how fractal-like forms may emerge from the combination of key, defined perturbations of floral developmental programs and growth dynamics.
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Affiliation(s)
- Eugenio Azpeitia
- Laboratoire de Reproduction et Développement des Plantes, Univ. Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, F-69364 Lyon, France
| | - Gabrielle Tichtinsky
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, F-38054 Grenoble, France
| | - Marie Le Masson
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, F-38054 Grenoble, France
| | - Antonio Serrano-Mislata
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), 46022 Valencia, Spain
| | - Jérémy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, F-38054 Grenoble, France
| | - Veronica Gregis
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Carlos Gimenez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), 46022 Valencia, Spain
| | - Nathanaël Prunet
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.,Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Etienne Farcot
- School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Martin M Kater
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Desmond Bradley
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Francisco Madueño
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), 46022 Valencia, Spain
| | - Christophe Godin
- Laboratoire de Reproduction et Développement des Plantes, Univ. Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, F-69364 Lyon, France.
| | - Francois Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, F-38054 Grenoble, France.
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Gioppato HA, Dornelas MC. Plant design gets its details: Modulating plant architecture by phase transitions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 163:1-14. [PMID: 33799013 DOI: 10.1016/j.plaphy.2021.03.046] [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: 07/28/2020] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
Plants evolved different strategies to better adapt to the environmental conditions in which they live: the control of their body architecture and the timing of phase change are two important processes that can improve their fitness. As they age, plants undergo two major phase changes (juvenile to adult and adult to reproductive) that are a response to environmental and endogenous signals. These phase transitions are accompanied by alterations in plant morphology and also by changes in physiology and the behavior of gene regulatory networks. Six main pathways involving environmental and endogenous cues that crosstalk with each other have been described as responsible for the control of plant phase transitions: the photoperiod pathway, the autonomous pathway, the vernalization pathway, the temperature pathway, the GA pathway, and the age pathway. However, studies have revealed that sugar is also involved in phase change and the control of branching behavior. In this review, we discuss recent advances in plant biology concerning the genetic and molecular mechanisms that allow plants to regulate phase transitions in response to the environment. We also propose connections between phase transition and plant architecture control.
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Affiliation(s)
- Helena Augusto Gioppato
- University of Campinas (UNICAMP), Biology Institute, Plant Biology Department, Rua Monteiro Lobato, 255 CEP 13, 083-862, Campinas, SP, Brazil
| | - Marcelo Carnier Dornelas
- University of Campinas (UNICAMP), Biology Institute, Plant Biology Department, Rua Monteiro Lobato, 255 CEP 13, 083-862, Campinas, SP, Brazil.
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Hou D, Li L, Ma T, Pei J, Zhao Z, Lu M, Wu A, Lin X. The SOC1-like gene BoMADS50 is associated with the flowering of Bambusa oldhamii. HORTICULTURE RESEARCH 2021; 8:133. [PMID: 34059654 PMCID: PMC8166863 DOI: 10.1038/s41438-021-00557-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 03/16/2021] [Accepted: 03/26/2021] [Indexed: 05/27/2023]
Abstract
Bamboo is known for its edible shoots and beautiful texture and has considerable economic and ornamental value. Unique among traditional flowering plants, many bamboo plants undergo extensive synchronized flowering followed by large-scale death, seriously affecting the productivity and application of bamboo forests. To date, the molecular mechanism of bamboo flowering characteristics has remained unknown. In this study, a SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1)-like gene, BoMADS50, was identified from Bambusa oldhamii. BoMADS50 was highly expressed in mature leaves and the floral primordium formation period during B. oldhamii flowering and overexpression of BoMADS50 caused early flowering in transgenic rice. Moreover, BoMADS50 could interact with APETALA1/FRUITFULL (AP1/FUL)-like proteins (BoMADS14-1/2, BoMADS15-1/2) in vivo, and the expression of BoMADS50 was significantly promoted by BoMADS14-1, further indicating a synergistic effect between BoMADS50 and BoAP1/FUL-like proteins in regulating B. oldhamii flowering. We also identified four additional transcripts of BoMADS50 (BoMADS50-1/2/3/4) with different nucleotide variations. Although the protein-CDS were polymorphic, they had flowering activation functions similar to those of BoMADS50. Yeast one-hybrid and transient expression assays subsequently showed that both BoMADS50 and BoMADS50-1 bind to the promoter fragment of itself and the SHORT VEGETATIVE PHASE (SVP)-like gene BoSVP, but only BoMADS50-1 can positively induce their transcription. Therefore, nucleotide variations likely endow BoMADS50-1 with strong regulatory activity. Thus, BoMADS50 and BoMADS50-1/2/3/4 are probably important positive flowering regulators in B. oldhamii. Moreover, the functional conservatism and specificity of BoMADS50 and BoMADS50-1 might be related to the synchronized and sporadic flowering characteristics of B. oldhamii.
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Affiliation(s)
- Dan Hou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Ling Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Tengfei Ma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Jialong Pei
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Zhongyu Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Mengzhu Lu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Aimin Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, 510642, Guangzhou, China.
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, 510642, Guangzhou, China.
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China.
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Gómez-Soto D, Ramos-Sánchez JM, Alique D, Conde D, Triozzi PM, Perales M, Allona I. Overexpression of a SOC1-Related Gene Promotes Bud Break in Ecodormant Poplars. FRONTIERS IN PLANT SCIENCE 2021; 12:670497. [PMID: 34113369 PMCID: PMC8185274 DOI: 10.3389/fpls.2021.670497] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/06/2021] [Indexed: 05/04/2023]
Abstract
Perennial species in the boreal and temperate regions are subject to extreme annual variations in light and temperature. They precisely adapt to seasonal changes by synchronizing cycles of growth and dormancy with external cues. Annual dormancy-growth transitions and flowering involve factors that integrate environmental and endogenous signals. MADS-box transcription factors have been extensively described in the regulation of Arabidopsis flowering. However, their participation in annual dormancy-growth transitions in trees is minimal. In this study, we investigate the function of MADS12, a Populus tremula × alba SUPPRESSOR OF CONSTANS OVEREXPRESSION 1 (SOC1)-related gene. Our gene expression analysis reveals that MADS12 displays lower mRNA levels during the winter than during early spring and mid-spring. Moreover, MADS12 activation depends on the fulfillment of the chilling requirement. Hybrid poplars overexpressing MADS12 show no differences in growth cessation and bud set, while ecodormant plants display an early bud break, indicating that MADS12 overexpression promotes bud growth reactivation. Comparative expression analysis of available bud break-promoting genes reveals that MADS12 overexpression downregulates the GIBBERELLINS 2 OXIDASE 4 (GA2ox4), a gene involved in gibberellin catabolism. Moreover, the mid-winter to mid-spring RNAseq profiling indicates that MADS12 and GA2ox4 show antagonistic expression during bud dormancy release. Our results support MADS12 participation in the reactivation of shoot meristem growth during ecodormancy and link MADS12 activation and GA2ox4 downregulation within the temporal events that lead to poplar bud break.
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Affiliation(s)
- Daniela Gómez-Soto
- Centro de Biotecnología y Genómica de Plantas, Instituto de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
| | - José M. Ramos-Sánchez
- Centro de Biotecnología y Genómica de Plantas, Instituto de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
| | - Daniel Alique
- Centro de Biotecnología y Genómica de Plantas, Instituto de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
| | - Daniel Conde
- Centro de Biotecnología y Genómica de Plantas, Instituto de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
| | - Paolo M. Triozzi
- Centro de Biotecnología y Genómica de Plantas, Instituto de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Instituto de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Instituto de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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Ye LX, Zhang JX, Hou XJ, Qiu MQ, Wang WF, Zhang JX, Hu CG, Zhang JZ. A MADS-Box Gene CiMADS43 Is Involved in Citrus Flowering and Leaf Development through Interaction with CiAGL9. Int J Mol Sci 2021; 22:ijms22105205. [PMID: 34069068 PMCID: PMC8156179 DOI: 10.3390/ijms22105205] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022] Open
Abstract
MADS-box genes are involved in various developmental processes including vegetative development, flower architecture, flowering, pollen formation, seed and fruit development. However, the function of most MADS-box genes and their regulation mechanism are still unclear in woody plants compared with model plants. In this study, a MADS-box gene (CiMADS43) was identified in citrus. Phylogenetic and sequence analysis showed that CiMADS43 is a GOA-like Bsister MADS-box gene. It was localized in the nucleus and as a transcriptional activator. Overexpression of CiMADS43 promoted early flowering and leaves curling in transgenic Arabidopsis. Besides, overexpression or knockout of CiMADS43 also showed leaf curl phenotype in citrus similar to that of CiMADS43 overexpressed in Arabidopsis. Protein–protein interaction found that a SEPALLATA (SEP)-like protein (CiAGL9) interacted with CiMADS43 protein. Interestingly, CiAGL9 also can bind to the CiMADS43 promoter and promote its transcription. Expression analysis also showed that these two genes were closely related to seasonal flowering and the development of the leaf in citrus. Our findings revealed the multifunctional roles of CiMADS43 in the vegetative and reproductive development of citrus. These results will facilitate our understanding of the evolution and molecular mechanisms of MADS-box genes in citrus.
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Tian H, Li Y, Wang C, Xu X, Zhang Y, Zeb Q, Zicola J, Fu Y, Turck F, Li L, Lu Z, Liu L. Photoperiod-responsive changes in chromatin accessibility in phloem companion and epidermis cells of Arabidopsis leaves. THE PLANT CELL 2021; 33:475-491. [PMID: 33955490 PMCID: PMC8136901 DOI: 10.1093/plcell/koaa043] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/29/2020] [Indexed: 05/04/2023]
Abstract
Photoperiod plays a key role in controlling the phase transition from vegetative to reproductive growth in flowering plants. Leaves are the major organs perceiving day-length signals, but how specific leaf cell types respond to photoperiod remains unknown. We integrated photoperiod-responsive chromatin accessibility and transcriptome data in leaf epidermis and vascular companion cells of Arabidopsis thaliana by combining isolation of nuclei tagged in specific cell/tissue types with assay for transposase-accessible chromatin using sequencing and RNA-sequencing. Despite a large overlap, vasculature and epidermis cells responded differently. Long-day predominantly induced accessible chromatin regions (ACRs); in the vasculature, more ACRs were induced and these were located at more distal gene regions, compared with the epidermis. Vascular ACRs induced by long days were highly enriched in binding sites for flowering-related transcription factors. Among the highly ranked genes (based on chromatin and expression signatures in the vasculature), we identified TREHALOSE-PHOSPHATASE/SYNTHASE 9 (TPS9) as a flowering activator, as shown by the late flowering phenotypes of T-DNA insertion mutants and transgenic lines with phloem-specific knockdown of TPS9. Our cell-type-specific analysis sheds light on how the long-day photoperiod stimulus impacts chromatin accessibility in a tissue-specific manner to regulate plant development.
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Affiliation(s)
| | | | | | | | - Yajie Zhang
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Qudsia Zeb
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Johan Zicola
- Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany
| | - Yongfu Fu
- National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Franziska Turck
- Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany
| | - Legong Li
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Zefu Lu
- Author for correspondence: (L.L) and (Z.L.)
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An Arabidopsis AT-hook motif nuclear protein mediates somatic embryogenesis and coinciding genome duplication. Nat Commun 2021; 12:2508. [PMID: 33947865 PMCID: PMC8096963 DOI: 10.1038/s41467-021-22815-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/30/2021] [Indexed: 02/02/2023] Open
Abstract
Plant somatic cells can be reprogrammed into totipotent embryonic cells that are able to form differentiated embryos in a process called somatic embryogenesis (SE), by hormone treatment or through overexpression of certain transcription factor genes, such as BABY BOOM (BBM). Here we show that overexpression of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED 15 (AHL15) gene induces formation of somatic embryos on Arabidopsis thaliana seedlings in the absence of hormone treatment. During zygotic embryogenesis, AHL15 expression starts early in embryo development, and AH15 and other AHL genes are required for proper embryo patterning and development beyond the globular stage. Moreover, AHL15 and several of its homologs are upregulated and required for SE induction upon hormone treatment, and they are required for efficient BBM-induced SE as downstream targets of BBM. A significant number of plants derived from AHL15 overexpression-induced somatic embryos are polyploid. Polyploidisation occurs by endomitosis specifically during the initiation of SE, and is caused by strong heterochromatin decondensation induced by AHL15 overexpression.
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Sharma K, Gupta S, Sarma S, Rai M, Sreelakshmi Y, Sharma R. Mutations in tomato 1-aminocyclopropane carboxylic acid synthase2 uncover its role in development beside fruit ripening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:95-112. [PMID: 33370496 DOI: 10.1101/2020.05.12.090431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 11/26/2020] [Accepted: 12/03/2020] [Indexed: 05/24/2023]
Abstract
The role of ethylene in plant development is mostly inferred from its exogenous application. The usage of mutants affecting ethylene biosynthesis proffers a better alternative to decipher its role. In tomato (Solanum lycopersicum), 1-aminocyclopropane carboxylic acid synthase2 (ACS2) is a key enzyme regulating ripening-specific ethylene biosynthesis. We characterised two contrasting acs2 mutants; acs2-1 overproduces ethylene, has higher ACS activity, and has increased protein levels, while acs2-2 is an ethylene underproducer, displays lower ACS activity, and has lower protein levels than wild type. Consistent with high/low ethylene emission, the mutants show opposite phenotypes, physiological responses, and metabolomic profiles compared with the wild type. The acs2-1 mutant shows early seed germination, faster leaf senescence, and accelerated fruit ripening. Conversely, acs2-2 has delayed seed germination, slower leaf senescence, and prolonged fruit ripening. The phytohormone profiles of mutants were mostly opposite in the leaves and fruits. The faster/slower senescence of acs2-1/acs2-2 leaves correlated with the endogenous ethylene/zeatin ratio. The genetic analysis showed that the metabolite profiles of respective mutants co-segregated with the homozygous mutant progeny. Our results uncover that besides ripening, ACS2 participates in the vegetative and reproductive development of tomato. The distinct influence of ethylene on phytohormone profiles indicates the intertwining of ethylene action with other phytohormones in regulating plant development.
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Affiliation(s)
- Kapil Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Soni Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Supriya Sarma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Meenakshi Rai
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
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Kaur S, Atri C, Akhatar J, Mittal M, Kaur R, Banga SS. Genetics of days to flowering, maturity and plant height in natural and derived forms of Brassica rapa L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:473-487. [PMID: 33084931 DOI: 10.1007/s00122-020-03707-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/10/2020] [Indexed: 06/11/2023]
Abstract
Genome wide association studies enabled prediction of many candidate genes for flowering, maturity and plant height under differing day-length conditions. Some genes were envisaged only from derived B. rapa. Flowering and plant height are the key life history traits. These are crucial for adaptation and productivity. Current investigations aimed to examine genotypic differences governing days to flowering, maturity and plant height under contrasting day-length conditions; and identify genomic regions governing the observed phenotypic variations. An association panel comprising 195 inbred lines, representing natural (NR) and derived (DR) forms of Brassica rapa (AA; 2n = 20), was evaluated at two sowing dates and two locations, representing different day-length regimes. Derived B. rapa is a unique pre-breeding material extracted from B. juncea (AABB; 2n = 36). Population structure analysis, using DArT genotypes established derived B. rapa as a genetic resource distinct from natural B. rapa. Genome wide association studies facilitated detection of many trait associated SNPs. Chromosomes A03, A05 and A09 harboured majority of these. Functional annotation of the associated SNPs and surrounding genome space(s) helped to predict 43 candidate genes. Many of these were predicted under specific day-length conditions. Important among these were the genes encoding floral meristem identity (SPL3, SPL15, AP3, BAM2), photoperiodic responses (COL2, AGL18, SPT, NF-YC4), gibberellic acid biosynthesis (GA1) and regulation of flowering (EBS). Some of the predicted genes were detected for DR subpanel alone. Genes controlling hormones, auxins and gibberellins appeared important for the regulation of plant height. Many of the significant SNPs were located on chromosomes harbouring previously reported QTLs and candidate genes. The identified loci may be used for marker-assisted selection after due validation.
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Affiliation(s)
- Snehdeep Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Chhaya Atri
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Javed Akhatar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Meenakshi Mittal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Rimaljeet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Surinder S Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India.
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Madrid E, Chandler JW, Coupland G. Gene regulatory networks controlled by FLOWERING LOCUS C that confer variation in seasonal flowering and life history. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4-14. [PMID: 32369593 PMCID: PMC7816851 DOI: 10.1093/jxb/eraa216] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/28/2020] [Indexed: 05/07/2023]
Abstract
Responses to environmental cues synchronize reproduction of higher plants to the changing seasons. The genetic basis of these responses has been intensively studied in the Brassicaceae. The MADS-domain transcription factor FLOWERING LOCUS C (FLC) plays a central role in the regulatory network that controls flowering of Arabidopsis thaliana in response to seasonal cues. FLC blocks flowering until its transcription is stably repressed by extended exposure to low temperatures in autumn or winter and, therefore, FLC activity is assumed to limit flowering to spring. Recent reviews describe the complex epigenetic mechanisms responsible for FLC repression in cold. We focus on the gene regulatory networks controlled by FLC and how they influence floral transition. Genome-wide approaches determined the in vivo target genes of FLC and identified those whose transcription changes during vernalization or in flc mutants. We describe how studying FLC targets such as FLOWERING LOCUS T, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 15, and TARGET OF FLC AND SVP 1 can explain different flowering behaviours in response to vernalization and other environmental cues, and help define mechanisms by which FLC represses gene transcription. Elucidating the gene regulatory networks controlled by FLC provides access to the developmental and physiological mechanisms that regulate floral transition.
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Affiliation(s)
- Eva Madrid
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Germany
| | - John W Chandler
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Germany
| | - George Coupland
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Germany
- Correspondence:
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Kinoshita A, Vayssières A, Richter R, Sang Q, Roggen A, van Driel AD, Smith RS, Coupland G. Regulation of shoot meristem shape by photoperiodic signaling and phytohormones during floral induction of Arabidopsis. eLife 2020; 9:60661. [PMID: 33315012 PMCID: PMC7771970 DOI: 10.7554/elife.60661] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/12/2020] [Indexed: 11/23/2022] Open
Abstract
Floral transition, the onset of plant reproduction, involves changes in shape and identity of the shoot apical meristem (SAM). The change in shape, termed doming, occurs early during floral transition when it is induced by environmental cues such as changes in day-length, but how it is regulated at the cellular level is unknown. We defined the morphological and cellular features of the SAM during floral transition of Arabidopsis thaliana. Both cell number and size increased during doming, and these changes were partially controlled by the gene regulatory network (GRN) that triggers flowering. Furthermore, dynamic modulation of expression of gibberellin (GA) biosynthesis and catabolism enzymes at the SAM contributed to doming. Expression of these enzymes was regulated by two MADS-domain transcription factors implicated in flowering. We provide a temporal and spatial framework for integrating the flowering GRN with cellular changes at the SAM and highlight the role of local regulation of GA.
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Affiliation(s)
- Atsuko Kinoshita
- Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Alice Vayssières
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - René Richter
- Max Planck Institute for Plant Breeding Research, Cologne, Germany.,School of Agriculture and Food, University of Melbourne, Melbourne, Australia
| | - Qing Sang
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Adrian Roggen
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Richard S Smith
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - George Coupland
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
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47
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Lee JE, Goretti D, Neumann M, Schmid M, You Y. A gibberellin methyltransferase modulates the timing of floral transition at the Arabidopsis shoot meristem. PHYSIOLOGIA PLANTARUM 2020; 170:474-487. [PMID: 32483836 DOI: 10.1111/ppl.13146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/26/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
The transition from vegetative to reproductive growth is a key event in the plant life cycle. Plants therefore use a variety of environmental and endogenous signals to determine the optimal time for flowering to ensure reproductive success. These signals are integrated at the shoot apical meristem (SAM), which subsequently undergoes a shift in identity and begins producing flowers rather than leaves, while still maintaining pluripotency and meristematic function. Gibberellic acid (GA), an important hormone associated with cell growth and differentiation, has been shown to promote flowering in many plant species including Arabidopsis thaliana, but the details of how spatial and temporal regulation of GAs in the SAM contribute to floral transition are poorly understood. In this study, we show that the gene GIBBERELLIC ACID METHYLTRANSFERASE 2 (GAMT2), which encodes a GA-inactivating enzyme, is significantly upregulated at the SAM during floral transition and contributes to the regulation of flowering time. Loss of GAMT2 function leads to early flowering, whereas transgenic misexpression of GAMT2 in specific regions around the SAM delays flowering. We also found that GAMT2 expression is independent of the key floral regulator LEAFY but is strongly increased by the application of exogenous GA. Our results indicate that GAMT2 is a repressor of flowering that may act as a buffer of GA levels at the SAM to help prevent premature flowering.
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Affiliation(s)
- Joanne E Lee
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, SE-901 87, Sweden
| | - Daniela Goretti
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, SE-901 87, Sweden
| | - Manuela Neumann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Markus Schmid
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, SE-901 87, Sweden
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Yuan You
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
- Center for Plant Molecular Biology (ZMBP), Department of General Genetics, University Tübingen, Tübingen, 72076, Germany
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Iqbal S, Pan Z, Wu X, Shi T, Ni X, Bai Y, Gao J, Khalil-Ur-Rehman M, Gao Z. Genome-wide analysis of PmTCP4 transcription factor binding sites by ChIP-Seq during pistil abortion in Japanese apricot. THE PLANT GENOME 2020; 13:e20052. [PMID: 33217203 DOI: 10.1002/tpg2.20052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
The TCP4 transcription factor plays an important role in plant growth and development, especially in flower development. PmTCP4 is involved in the process of pistil abortion in Japanese apricot, but its molecular mechanism, particularly the DNA binding sites and co-regulatory genes, are quite unknown. Therefore, to identify the genome-wide binding sites of PmTCP4 transcription factors and their co-regulatory genes, chromatin immunoprecipitation sequencing (ChIP-Seq) was carried out. ChIP-Seq data produced the maximum enriched peaks in two Japanese apricot cultivars 'Daqiandi' (DQD) and 'Longyan' (LY), which showed that the majority of DNA-protein interactions are relevant and have a significant function in binding sites. Moreover, 720 and 251 peak-associated genes regulated by PmTCP4 were identified in DQD and LY, respectively, and most of them were involved in the flower and pistil development process. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that photosynthesis and oxidative phosphorylation were the most enriched pathways in both cultivars and all identified genes related to these pathways were down-regulated. This study will provide a reference for a better understanding of the PmTCP4 regulatory mechanism during pistil abortion in Japanese apricot.
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Affiliation(s)
- Shahid Iqbal
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhenpeng Pan
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xinxin Wu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai An, China
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography Shenzhen University, Shenzhen, China
| | - Ting Shi
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xiaopeng Ni
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yang Bai
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jie Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Khalil-Ur-Rehman
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhihong Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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The Response of COL and FT Homologues to Photoperiodic Regulation in Carrot (Daucus carota L.). Sci Rep 2020; 10:9984. [PMID: 32561786 PMCID: PMC7305175 DOI: 10.1038/s41598-020-66807-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/22/2020] [Indexed: 11/13/2022] Open
Abstract
Carrot (Daucus carota L.) is a biennial plant requiring vernalization to induce flowering, but long days can promote its premature bolting and flowering. The basic genetic network controlling the flowering time has been constructed for carrot, but there is limited information on the molecular mechanisms underlying the photoperiodic flowering response. The published carrot genome could provide an effective tool for systematically retrieving the key integrator genes of GIGANTEA (GI), CONSTANS-LIKE (COL), FLOWERING LOCUS T (FT), and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) homologues in the photoperiod pathway. In this study, the bolting time of wild species “Songzi” (Ws) could be regulated by different photoperiods, but the orange cultivar “Amsterdam forcing” (Af) displayed no bolting phenomenon. According to the carrot genome and previous de novo transcriptome, 1 DcGI, 15 DcCOLs, 2 DcFTs, and 3 DcSOC1s were identified in the photoperiod pathway. The circadian rhythm peaks of DcGI, DcCOL2, DcCOL5a, and DcCOL13b could be delayed under long days (LDs). The peak value of DcCOL2 in Af (12.9) was significantly higher than that in Ws (6.8) under short day (SD) conditions, and was reduced under LD conditions (5.0). The peak values of DcCOL5a in Ws were constantly higher than those in Af under the photoperiod treatments. The expression levels of DcFT1 in Ws (463.0) were significantly upregulated under LD conditions compared with those in Af (1.4). These responses of DcCOL2, DcCOL5a, and DcFT1 might be related to the different bolting responses of Ws and Af. This study could provide valuable insights into understanding the key integrator genes in the carrot photoperiod pathway.
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Chow CN, Lee TY, Hung YC, Li GZ, Tseng KC, Liu YH, Kuo PL, Zheng HQ, Chang WC. PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. Nucleic Acids Res 2020; 47:D1155-D1163. [PMID: 30395277 PMCID: PMC6323957 DOI: 10.1093/nar/gky1081] [Citation(s) in RCA: 245] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/22/2018] [Indexed: 01/01/2023] Open
Abstract
The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN.itps.ncku.edu.tw/) is an effective resource for predicting regulatory elements and reconstructing transcriptional regulatory networks for plant genes. In this release (PlantPAN 3.0), 17 230 TFs were collected from 78 plant species. To explore regulatory landscapes, genomic locations of TFBSs have been captured from 662 public ChIP-seq samples using standard data processing. A total of 1 233 999 regulatory linkages were identified from 99 regulatory factors (TFs, histones and other DNA-binding proteins) and their target genes across seven species. Additionally, this new version added 2449 matrices extracted from ChIP-seq peaks for cis-regulatory element prediction. In addition to integrated ChIP-seq data, four major improvements were provided for more comprehensive information of TF binding events, including (i) 1107 experimentally verified TF matrices from the literature, (ii) gene regulation network comparison between two species, (iii) 3D structures of TFs and TF-DNA complexes and (iv) condition-specific co-expression networks of TFs and their target genes extended to four species. The PlantPAN 3.0 can not only be efficiently used to investigate critical cis- and trans-regulatory elements in plant promoters, but also to reconstruct high-confidence relationships among TF–targets under specific conditions.
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Affiliation(s)
- Chi-Nga Chow
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Taiwan
| | - Tzong-Yi Lee
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, China
| | - Yu-Cheng Hung
- Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Guan-Zhen Li
- Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Kuan-Chieh Tseng
- Department of Life Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Ya-Hsin Liu
- Department of Life Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Po-Li Kuo
- Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Han-Qin Zheng
- Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Wen-Chi Chang
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Taiwan.,Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan.,Department of Life Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
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