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Maple R, Zhu P, Hepworth J, Wang JW, Dean C. Flowering time: From physiology, through genetics to mechanism. PLANT PHYSIOLOGY 2024; 195:190-212. [PMID: 38417841 PMCID: PMC11060688 DOI: 10.1093/plphys/kiae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/12/2024] [Accepted: 02/12/2024] [Indexed: 03/01/2024]
Abstract
Plant species have evolved different requirements for environmental/endogenous cues to induce flowering. Originally, these varying requirements were thought to reflect the action of different molecular mechanisms. Thinking changed when genetic and molecular analysis in Arabidopsis thaliana revealed that a network of environmental and endogenous signaling input pathways converge to regulate a common set of "floral pathway integrators." Variation in the predominance of the different input pathways within a network can generate the diversity of requirements observed in different species. Many genes identified by flowering time mutants were found to encode general developmental and gene regulators, with their targets having a specific flowering function. Studies of natural variation in flowering were more successful at identifying genes acting as nodes in the network central to adaptation and domestication. Attention has now turned to mechanistic dissection of flowering time gene function and how that has changed during adaptation. This will inform breeding strategies for climate-proof crops and help define which genes act as critical flowering nodes in many other species.
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Affiliation(s)
- Robert Maple
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Pan Zhu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jo Hepworth
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- New Cornerstone Science Laboratory, Shanghai 200032, China
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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2
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Suhaimi AH, Kobayashi MJ, Satake A, Ng CC, Lee SL, Muhammad N, Numata S, Otani T, Kondo T, Tani N, Yeoh SH. An ecological transcriptome approach to capture the molecular and physiological mechanisms of mass flowering in Shorea curtisii. PeerJ 2023; 11:e16368. [PMID: 38047035 PMCID: PMC10693236 DOI: 10.7717/peerj.16368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/08/2023] [Indexed: 12/05/2023] Open
Abstract
Climatic factors have commonly been attributed as the trigger of general flowering, a unique community-level mass flowering phenomenon involving most dipterocarp species that forms the foundation of Southeast Asian tropical rainforests. This intriguing flowering event is often succeeded by mast fruiting, which provides a temporary yet substantial burst of food resources for animals, particularly frugivores. However, the physiological mechanism that triggers general flowering, particularly in dipterocarp species, is not well understood largely due to its irregular and unpredictable occurrences in the tall and dense forests. To shed light on this mechanism, we employed ecological transcriptomic analyses on an RNA-seq dataset of a general flowering species, Shorea curtisii (Dipterocarpaceae), sequenced from leaves and buds collected at multiple vegetative and flowering phenological stages. We assembled 64,219 unigenes from the transcriptome of which 1,730 and 3,559 were differentially expressed in the leaf and the bud, respectively. Differentially expressed unigene clusters were found to be enriched with homologs of Arabidopsis thaliana genes associated with response to biotic and abiotic stresses, nutrient level, and hormonal treatments. When combined with rainfall data, our transcriptome data reveals that the trees were responding to a brief period of drought prior to the elevated expression of key floral promoters and followed by differential expression of unigenes that indicates physiological changes associated with the transition from vegetative to reproductive stages. Our study is timely for a representative general flowering dipterocarp species that occurs in forests that are under the constant threat of deforestation and climate change as it pinpoints important climate sensitive and flowering-related homologs and offers a glimpse into the cascade of gene expression before and after the onset of floral initiation.
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Affiliation(s)
- Ahmad Husaini Suhaimi
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Masaki J. Kobayashi
- Forestry Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
| | - Akiko Satake
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Ching Ching Ng
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Soon Leong Lee
- Forestry Biotechnology Division, Forest Research Institute Malaysia, Selangor, Malaysia
| | - Norwati Muhammad
- Forestry Biotechnology Division, Forest Research Institute Malaysia, Selangor, Malaysia
| | - Shinya Numata
- Department of Tourism Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Tatsuya Otani
- Shikoku Research Center, Forestry Research and Management Organization, Kochi, Japan
| | - Toshiaki Kondo
- Bio-Resources and Utilization Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
| | - Naoki Tani
- Forestry Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Suat Hui Yeoh
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
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3
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Xiao F, Zhao Y, Wang X, Mao Y, Jian X. Comparative transcriptome analysis of dioecious floral development in Trachycarpus fortunei using Illumina and PacBio SMRT sequencing. BMC PLANT BIOLOGY 2023; 23:536. [PMID: 37919651 PMCID: PMC10623883 DOI: 10.1186/s12870-023-04551-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 10/22/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Trachycarpus fortunei is a plant with significant economic and ornamental value. Both male and female flowers of T. fortunei originate as bisexual flowers, and selective abortion occurs during floral development. However, the regulatory mechanisms underlying this process remain unclear in T. fortunei. In this study, transcriptome sequencing with Illumina and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) platforms were used to investigate gene expression differences between male and female T. fortunei plants. RESULTS A total of 833,137 full-length non-chimeric (FLNC) reads were obtained, and 726,846 high-quality full-length transcripts were identified. A total of 159 genes were differentially expressed between male and female flowers at all development stages. Some of the differentially expressed genes (DEGs) showed male bias, including serine/threonine-protein kinase (STPK), THUMP1 homolog and other genes. Through single-nucleotide polymorphisms(SNPs) identification, 28 genes were considered as potential sex-associated SNPs. Time-Ordered Gene Co-expression Network (TO-GCN) analysis revealed that MADS2 and MADS26 may play important roles in the development of female and male flowers T. fortune plants, respectively. CONCLUSIONS These findings provide a genetic basis for flower development and differentiation in T. fortunei, and improve our understanding of the mechanisms underlying sexual differentiation in T. fortunei.
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Affiliation(s)
- Feng Xiao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yang Zhao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Xiurong Wang
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yuexiong Mao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xueyan Jian
- School of Continuing Education, Yanbian University, Yanji, 133002, Jilin, China
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4
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Satake A, Ohta K, Takeda-Kamiya N, Toyooka K, Kusumi J. Seasonal gene expression signatures of delayed fertilization in Fagaceae. Mol Ecol 2023; 32:4801-4813. [PMID: 37464469 DOI: 10.1111/mec.17079] [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: 10/07/2022] [Revised: 06/10/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023]
Abstract
In the family Fagaceae, fertilization is delayed by several weeks to 1 year after pollination, leading to 1- or 2-year fruiting species depending on whether fruiting occurs in the same or the next year after flowering. To investigate physiological responses underlying the regulation of delayed fertilization, we monitored seasonal changes in genome-wide gene expression in tissues including leaves and buds over 2 years under natural conditions in one- (Quercus glauca) and 2-year fruiting species (Lithocarpus edulis). Genes associated with metabolic changes in response to winter cold, photosynthesis and cell proliferation, which are essential for survival and growth, showed highly conserved seasonal expression profiles between species. However, seasonal expression profiles diverged between species in genes associated with pollination, an important process contributing to the origin and maintenance of the reproductive barrier between plant species. By comparing seasonal progression of ovule development and gene expression in pistillate flowers, we revealed that ovules started developing after winter in the 2-year fruiting species, which could be linked to the activation of genes involved in fertilization and female gametophyte development after winter. These findings suggest that the 2-year fruiting species may have evolved a requirement of winter cold to prevent fertilization before winter and facilitate fertilization and embryo development in the following spring when temperature rises. This study offers new possibilities to explore the evolution of reproductive strategies in Fagaceae.
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Affiliation(s)
- Akiko Satake
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Kayoko Ohta
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Noriko Takeda-Kamiya
- Technology Platform Division, Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Kiminori Toyooka
- Technology Platform Division, Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Junko Kusumi
- Department of Environmental Changes, Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
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Lim H, Kobayashi MJ, Marsoem SN, Irawati D, Kosugi A, Kondo T, Tani N. Transcriptomic responses of oil palm ( Elaeis guineensis) stem to waterlogging at plantation in relation to precipitation seasonality. FRONTIERS IN PLANT SCIENCE 2023; 14:1213496. [PMID: 37636106 PMCID: PMC10448820 DOI: 10.3389/fpls.2023.1213496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023]
Abstract
Global warming-induced climate change causes significant agricultural problems by increasing the incidence of drought and flooding events. Waterlogging is an inevitable consequence of these changes but its effects on oil palms have received little attention and are poorly understood. Recent waterlogging studies have focused on oil palm seedlings, with particular emphasis on phenology. However, the transcriptomic waterlogging response of mature oil palms remains elusive in real environments. We therefore investigated transcriptomic changes over time in adult oil palms at plantations over a two-year period with pronounced seasonal variation in precipitation. A significant transcriptional waterlogging response was observed in the oil palm stem core but not in leaf samples when gene expression was correlated with cumulative precipitation over two-day periods. Pathways and processes upregulated or enriched in the stem core response included hypoxia, ethylene signaling, and carbon metabolism. Post-waterlogging recovery in oil palms was found to be associated with responses to heat stress and carotenoid biosynthesis. Nineteen transcription factors (TFs) potentially involved in the waterlogging response of mature oil palms were also identified. These data provide new insights into the transcriptomic responses of planted oil palms to waterlogging and offer valuable guidance on the sensitivity of oil palm plantations to future climate changes.
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Affiliation(s)
- Hui Lim
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masaki J. Kobayashi
- Forestry Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
| | | | - Denny Irawati
- Faculty of Forestry, Universitas Gadjah Mada (UGM), Yogyakarta, Indonesia
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Toshiaki Kondo
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
| | - Naoki Tani
- Forestry Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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6
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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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7
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Miura T, Tokumoto Y, Shin N, Shimizu KK, Pungga RAS, Ichie T. Utility of commercial high‐resolution satellite imagery for monitoring general flowering in Sarawak, Borneo. Ecol Res 2023. [DOI: 10.1111/1440-1703.12382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Tomoaki Miura
- Department of Natural Resources and Environmental Management University of Hawai'i at Mānoa Honolulu Hawaii USA
- Research Institute for Global Change Japan Agency for Marine‐Earth Science and Technology Kanazawa‐ku, Yokohama Japan
| | - Yuji Tokumoto
- Tenure Track Promotion Office University of Miyazaki Miyazaki Japan
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- University Research Priority Program, Global Change and Biodiversity University of Zurich Zurich Switzerland
- Kihara Institute for Biological Research Yokohama City University Yokohama Japan
| | - Nagai Shin
- Research Institute for Global Change Japan Agency for Marine‐Earth Science and Technology Kanazawa‐ku, Yokohama Japan
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- University Research Priority Program, Global Change and Biodiversity University of Zurich Zurich Switzerland
- Kihara Institute for Biological Research Yokohama City University Yokohama Japan
| | - Runi Anak Sylvester Pungga
- Research and Development Division, International Affairs Division Forest Department Sarawak Kuching Sarawak Malaysia
| | - Tomoaki Ichie
- Faculty of Agriculture and Marine Science Kochi University Nankoku Japan
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8
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Tsujii Y, Sakai S, Ushio M, Aiba S, Kitayama K. Variations in the reproductive cycle of Bornean montane tree species along elevational gradients on ultrabasic and non‐ultrabasic soils. Biotropica 2022. [DOI: 10.1111/btp.13177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Yuki Tsujii
- Center for Ecological Research Kyoto University Otsu Japan
- Faculty of Science Kyushu University Fukuoka Japan
- School of Natural Sciences Macquarie University Sydney New South Wales Australia
- Hawkesbury Institute for the Environment Western Sydney University Penrith New South Wales Australia
| | - Shoko Sakai
- Center for Ecological Research Kyoto University Otsu Japan
| | - Masayuki Ushio
- Center for Ecological Research Kyoto University Otsu Japan
- Hakubi Center Kyoto University Kyoto Japan
- Department of Ocean Science The Hong Kong University of Science and Technology Kowloon Hong Kong SAR
| | - Shin‐ichiro Aiba
- Faculty of Environmental Earth Science Hokkaido University Sapporo Japan
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9
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Tokunaga H, Quynh DTN, Anh NH, Nhan PT, Matsui A, Takahashi S, Tanaka M, Anh NM, Van Dong N, Ham LH, Higo A, Hoa TM, Ishitani M, Minh NBN, Hy NH, Srean P, Thu VA, Tung NB, Vu NA, Yamaguchi K, Tsuji H, Utsumi Y, Seki M. Field transcriptome analysis reveals a molecular mechanism for cassava-flowering in a mountainous environment in Southeast Asia. PLANT MOLECULAR BIOLOGY 2022; 109:233-248. [PMID: 32902791 DOI: 10.1007/s11103-020-01057-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 08/17/2020] [Indexed: 05/12/2023]
Abstract
The field survey in this article showed in 'KU50', a popular variety and late-branching type of cassava in Southeast Asia, that flowering rarely occurs in normal-field conditions in Southeast Asia but is strongly induced in the dry season in the mountainous region. Flowering time is correlated with the expression patterns of MeFT1 and homologs of Arabidopsis GI, PHYA, and NF-Ys. Cassava (Manihot esculenta Crantz) is a tropical crop that is propagated vegetatively rather than sexually by seed. Flowering rarely occurs in the erect-type variety grown in Southeast Asia, but it is known that cassava produces flowers every year in mountainous regions. Data pertaining to the effect of environmental factors on flowering time and gene expression in cassava, however, is limited. The aim of the present study was to determine the kinds of environmental conditions that regulate flowering time in cassava and the underlying molecular mechanisms. The flowering status of KU50, a popular variety in Southeast Asia and late-branching type of cassava, was monitored in six fields in Vietnam and Cambodia. At non-flowering and flowering field locations in North Vietnam, the two FLOWERING LOCUS T (FT)-like genes, MeFT1 and MeFT2, were characterized by qPCR, and the pattern of expression of flowering-related genes and genes responsive to environmental signals were analyzed by using RNA sequencing data from time-series samples. Results indicate that cassava flowering was induced in the dry season in the mountain region, and that flowering time was correlated with the expression of MeFT1, and homologs of Arabidopsis GI, PHYA, and NF-Ys. Based upon these data, we hypothesize that floral induction in cassava is triggered by some conditions present in the mountain regions during the dry season.
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Affiliation(s)
- Hiroki Tokunaga
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan.
- International Laboratory for Cassava Molecular Breeding (ILCMB), AGI, Hanoi, Vietnam.
| | - Do Thi Nhu Quynh
- International Laboratory for Cassava Molecular Breeding (ILCMB), AGI, Hanoi, Vietnam
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | - Nguyen Hai Anh
- International Laboratory for Cassava Molecular Breeding (ILCMB), AGI, Hanoi, Vietnam
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | - Pham Thi Nhan
- Hung Loc Agricultural Research Center (HLARC), Dong Nai, Vietnam
| | - Akihiro Matsui
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | | | - Maho Tanaka
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Ngo Minh Anh
- International Laboratory for Cassava Molecular Breeding (ILCMB), AGI, Hanoi, Vietnam
- JICA Vietnam Office, Hanoi, Vietnam
| | - Nguyen Van Dong
- International Laboratory for Cassava Molecular Breeding (ILCMB), AGI, Hanoi, Vietnam
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | - Le Huy Ham
- International Laboratory for Cassava Molecular Breeding (ILCMB), AGI, Hanoi, Vietnam
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | - Asuka Higo
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
| | - Truong Minh Hoa
- Hung Loc Agricultural Research Center (HLARC), Dong Nai, Vietnam
| | - Manabu Ishitani
- International Laboratory for Cassava Molecular Breeding (ILCMB), AGI, Hanoi, Vietnam
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Nguyen Huu Hy
- Hung Loc Agricultural Research Center (HLARC), Dong Nai, Vietnam
| | - Pao Srean
- University of Battambang (UBB), Battambang, Cambodia
| | - Vu Anh Thu
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
- International Laboratory for Cassava Molecular Breeding (ILCMB), AGI, Hanoi, Vietnam
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | - Nguyen Ba Tung
- Hung Loc Agricultural Research Center (HLARC), Dong Nai, Vietnam
| | - Nguyen Anh Vu
- International Laboratory for Cassava Molecular Breeding (ILCMB), AGI, Hanoi, Vietnam
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | - Kaho Yamaguchi
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
| | - Hiroyuki Tsuji
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
| | - Yoshinori Utsumi
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
- International Laboratory for Cassava Molecular Breeding (ILCMB), AGI, Hanoi, Vietnam
| | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan.
- International Laboratory for Cassava Molecular Breeding (ILCMB), AGI, Hanoi, Vietnam.
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan.
- Cluster for Pioneering Research, RIKEN, Saitama, Japan.
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10
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Satake A, Nagahama A, Sasaki E. A cross-scale approach to unravel the molecular basis of plant phenology in temperate and tropical climates. THE NEW PHYTOLOGIST 2022; 233:2340-2353. [PMID: 34862973 DOI: 10.1111/nph.17897] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
Plants have evolved to time their leafing, flowering and fruiting in appropriate seasons for growth, reproduction and resting. As a consequence of their adaptation to geographically different environments, there is a rich diversity in plant phenology from temperate and tropical climates. Recent progress in genetic and molecular studies will provide numerous opportunities to study the genetic basis of phenological traits and the history of adaptation of phenological traits to seasonal and aseasonal environments. Integrating molecular data with long-term phenology and climate data into predictive models will be a powerful tool to forecast future phenological changes in the face of global environmental change. Here, we review the cross-scale approach from genes to plant communities from three aspects: the latitudinal gradient of plant phenology at the community level, the environmental and genetic factors underlying the diversity of plant phenology, and an integrated approach to forecast future plant phenology based on genetically informed knowledge. Synthesizing the latest knowledge about plant phenology from molecular, ecological and mathematical perspectives will help us understand how natural selection can lead to the further evolution of the gene regulatory mechanisms in phenological traits in future forest ecosystems.
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Affiliation(s)
- Akiko Satake
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, 819-0395, Japan
| | - Ai Nagahama
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, 819-0395, Japan
| | - Eriko Sasaki
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, 819-0395, Japan
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11
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Satake A, Kelly D. Studying the genetic basis of masting. Philos Trans R Soc Lond B Biol Sci 2021; 376:20210116. [PMID: 34657458 PMCID: PMC8520782 DOI: 10.1098/rstb.2021.0116] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2021] [Indexed: 11/12/2022] Open
Abstract
The mechanisms underlying mast seeding have traditionally been studied by collecting long-term observational data on seed crops and correlating seedfall with environmental variables. Significant progress in ecological genomics will improve our understanding of the evolution of masting by clarifying the genetic basis of masting traits and the role of natural selection in shaping those traits. Here, we summarize three important aspects in studying the evolution of masting at the genetic level: which traits govern masting, whether those traits are genetically regulated, and which taxa show wide variation in these traits. We then introduce recent studies on the molecular mechanisms of masting. Those studies measure seasonal changes in gene expression in natural conditions to quantify how multiple environmental factors combine to regulate floral initiation, which in many masting plant species is the single largest contributor to among-year variation in seed crops. We show that Fagaceae offers exceptional opportunities for evolutionary investigations because of its diversity at both the phenotypic and genetic levels and existing documented genome sequences. This article is part of the theme issue 'The ecology and evolution of synchronized seed production in plants'.
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Affiliation(s)
- Akiko Satake
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Dave Kelly
- Department of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
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12
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Samarth, Lee R, Kelly D, Turnbull MH, Macknight R, Poole AM, Jameson PE. A novel TFL1 gene induces flowering in the mast seeding alpine snow tussock, Chionochloa pallens (Poaceae). Mol Ecol 2021; 31:822-838. [PMID: 34779078 DOI: 10.1111/mec.16273] [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: 12/23/2020] [Revised: 10/07/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
Masting, the synchronous, highly variable flowering across years by a population of perennial plants, has been reported to be precipitated by various factors including nitrogen levels, drought conditions, and spring and summer temperatures. However, the molecular mechanism leading to the initiation of flowering in masting plants in particular years remains largely unknown, despite the potential impact of climate change on masting phenology. We studied genes controlling flowering in the alpine snow tussock Chionochloa pallens (Poaceae), a strongly masting perennial grass. We used a range of in situ and manipulated plants to obtain leaf samples from tillers (shoots) which subsequently remained vegetative or flowered. Here, we show that a novel orthologue of TERMINAL FLOWER 1 (TFL1; normally a repressor of flowering in other species) promotes the induction of flowering in C. pallens (hence Anti-TFL1), a conclusion supported by structural, functional and expression analyses. Global transcriptomic analysis indicated differential expression of CpTPS1, CpGA20ox1, CpREF6 and CpHDA6, emphasizing the role of endogenous cues and epigenetic regulation in terms of responsiveness of plants to initiate flowering. Our molecular-based study provides insights into the cellular mechanism of flowering in masting plants and will supplement ecological and statistical models to predict how masting will respond to global climate change.
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Affiliation(s)
- Samarth
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Robyn Lee
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Dave Kelly
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Matthew H Turnbull
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Richard Macknight
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Anthony M Poole
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Bioinformatics Institute, University of Auckland, Auckland, New Zealand
| | - Paula E Jameson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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13
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Ng KKS, Kobayashi MJ, Fawcett JA, Hatakeyama M, Paape T, Ng CH, Ang CC, Tnah LH, Lee CT, Nishiyama T, Sese J, O'Brien MJ, Copetti D, Isa MNM, Ong RC, Putra M, Siregar IZ, Indrioko S, Kosugi Y, Izuno A, Isagi Y, Lee SL, Shimizu KK. The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests. Commun Biol 2021; 4:1166. [PMID: 34620991 PMCID: PMC8497594 DOI: 10.1038/s42003-021-02682-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/17/2021] [Indexed: 02/08/2023] Open
Abstract
Hyperdiverse tropical rainforests, such as the aseasonal forests in Southeast Asia, are supported by high annual rainfall. Its canopy is dominated by the species-rich tree family of Dipterocarpaceae (Asian dipterocarps), which has both ecological (e.g., supports flora and fauna) and economical (e.g., timber production) importance. Recent ecological studies suggested that rare irregular drought events may be an environmental stress and signal for the tropical trees. We assembled the genome of a widespread but near threatened dipterocarp, Shorea leprosula, and analyzed the transcriptome sequences of ten dipterocarp species representing seven genera. Comparative genomic and molecular dating analyses suggested a whole-genome duplication close to the Cretaceous-Paleogene extinction event followed by the diversification of major dipterocarp lineages (i.e. Dipterocarpoideae). Interestingly, the retained duplicated genes were enriched for genes upregulated by no-irrigation treatment. These findings provide molecular support for the relevance of drought for tropical trees despite the lack of an annual dry season.
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Affiliation(s)
- Kevin Kit Siong Ng
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia.
| | - Masaki J Kobayashi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
- Forestry Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Jeffrey A Fawcett
- Department of Evolutionary Studies of Biosystems, SOKENDAI, The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
- RIKEN iTHEMS, Wako, Saitama, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
- Functional Genomics Center Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Timothy Paape
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
| | - Chin Hong Ng
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Choon Cheng Ang
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
| | - Lee Hong Tnah
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Chai Ting Lee
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Tomoaki Nishiyama
- Division of Integrated Omics research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- AIST-Tokyo Tech RWBC-OIL, Meguro-ku, Tokyo, Japan
- Humanome Lab Inc., Chuo-ku, Tokyo, Japan
| | - Michael J O'Brien
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, c/Tulipán s/n., E-28933, Móstoles, Spain
| | - Dario Copetti
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | | | | | - Mahardika Putra
- Faculty of Forestry, Bogor Agricultural University, Bogor, Indonesia
| | | | - Sapto Indrioko
- Faculty of Forestry, Gadjah Mada University, Yogyakarta, Indonesia
| | - Yoshiko Kosugi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Ayako Izuno
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Forestry and Forest Products Research Institute (FFPRI), Tsukuba, Ibaraki, Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Soon Leong Lee
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia.
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.
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14
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Samarth, Lee R, Kelly D, Turnbull MH, Macknight RC, Poole AM, Jameson PE. Molecular control of the floral transition in the mast seeding plant Celmisia lyallii (Asteraceae). Mol Ecol 2021; 30:1846-1863. [PMID: 33624370 DOI: 10.1111/mec.15859] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 02/06/2021] [Accepted: 02/15/2021] [Indexed: 12/21/2022]
Abstract
Mast flowering (or masting) is synchronous, highly variable flowering among years in populations of perennial plants. Despite having widespread consequences for seed consumers, endangered fauna and human health, masting is hard to predict. While observational studies show links to various weather patterns in different plant species, the mechanism(s) underpinning the regulation of masting is still not fully explained. We studied floral induction in Celmisia lyallii (Asteraceae), a mast flowering herbaceous alpine perennial, comparing gene expression in flowering and nonflowering plants. We performed translocation experiments to induce the floral transition in C. lyallii plants followed by both global and targeted expression analysis of flowering-pathway genes. Differential expression analysis showed elevated expression of ClSOC1 and ClmiR172 (promoters of flowering) in leaves of plants that subsequently flowered, in contrast to elevated expression of ClAFT and ClTOE1 (repressors of flowering) in leaves of plants that did not flower. The warm summer conditions that promoted flowering led to differential regulation of age and hormonal pathway genes, including ClmiR172 and ClGA20ox2, known to repress the expression of floral repressors and permit flowering. Upregulated expression of epigenetic modifiers of floral promoters also suggests that plants may maintain a novel "summer memory" across years to induce flowering. These results provide a basic mechanistic understanding of floral induction in masting plants and evidence of their ability to imprint various environmental cues to synchronize flowering, allowing us to better predict masting events under climate change.
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Affiliation(s)
- Samarth
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Robyn Lee
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Dave Kelly
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Matthew H Turnbull
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Anthony M Poole
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Bioinformatics Institute, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Paula E Jameson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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15
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Satake A, Leong Yao T, Kosugi Y, Chen Y. Testing the environmental prediction hypothesis for community‐wide mass flowering in South‐East Asia. Biotropica 2021. [DOI: 10.1111/btp.12903] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Akiko Satake
- Department of Biology Faculty of Science Kyushu University Fukuoka Japan
| | | | - Yoshiko Kosugi
- Graduate School of Agriculture Kyoto University Kyoto Japan
| | - Yu‐Yun Chen
- Department of Natural Resources and Environmental Studies National Dong Hwa University Hualien Taiwan
- Center for Interdisciplinary Research on Ecology and Sustainability National Dong Hwa University Hualien Taiwan
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16
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Kelly D, Turnbull MH, Jameson PE. Molecular control of masting: an introduction to an epigenetic summer memory. ANNALS OF BOTANY 2020; 125:851-858. [PMID: 31960889 PMCID: PMC7218805 DOI: 10.1093/aob/mcaa004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 01/09/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND Mast flowering ('masting') is characterized by mass synchronized flowering at irregular intervals in populations of perennial plants over a wide geographical area, resulting in irregular high seed production. While masting is a global phenomenon, it is particularly prevalent in the alpine flora of New Zealand. Increases in global temperature may alter the masting pattern, affecting wider communities with a potential impact on plant-pollinator interactions, seed set and food availability for seed-consuming species. SCOPE This review summarizes an ecological temperature model (ΔT) that is being used to predict the intensity of a masting season. We introduce current molecular studies on flowering and the concept of an 'epigenetic summer memory' as a driver of mast flowering. We propose a hypothetical model based on temperature-associated epigenetic modifications of the floral integrator genes FLOWERING LOCUS T, FLOWERING LOCUS C and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1. CONCLUSIONS Genome-wide transcriptomic and targeted gene expression analyses are needed to establish the developmental and physiological processes associated with masting. Such analyses may identify changes in gene expression that can be used to predict the intensity of a forthcoming masting season, as well as to determine the extent to which climate change will influence the mass synchronized flowering of masting species, with downstream impacts on their associated communities.
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Affiliation(s)
- Dave Kelly
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Matthew H Turnbull
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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17
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Gaudinier A, Blackman BK. Evolutionary processes from the perspective of flowering time diversity. THE NEW PHYTOLOGIST 2020; 225:1883-1898. [PMID: 31536639 DOI: 10.1111/nph.16205] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/30/2019] [Indexed: 05/18/2023]
Abstract
Although it is well appreciated that genetic studies of flowering time regulation have led to fundamental advances in the fields of molecular and developmental biology, the ways in which genetic studies of flowering time diversity have enriched the field of evolutionary biology have received less attention despite often being equally profound. Because flowering time is a complex, environmentally responsive trait that has critical impacts on plant fitness, crop yield, and reproductive isolation, research into the genetic architecture and molecular basis of its evolution continues to yield novel insights into our understanding of domestication, adaptation, and speciation. For instance, recent studies of flowering time variation have reconstructed how, when, and where polygenic evolution of phenotypic plasticity proceeded from standing variation and de novo mutations; shown how antagonistic pleiotropy and temporally varying selection maintain polymorphisms in natural populations; and provided important case studies of how assortative mating can evolve and facilitate speciation with gene flow. In addition, functional studies have built detailed regulatory networks for this trait in diverse taxa, leading to new knowledge about how and why developmental pathways are rewired and elaborated through evolutionary time.
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Affiliation(s)
- Allison Gaudinier
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Benjamin K Blackman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
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18
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Bogdziewicz M, Ascoli D, Hacket‐Pain A, Koenig WD, Pearse I, Pesendorfer M, Satake A, Thomas P, Vacchiano G, Wohlgemuth T, Tanentzap A. From theory to experiments for testing the proximate mechanisms of mast seeding: an agenda for an experimental ecology. Ecol Lett 2020; 23:210-220. [PMID: 31858712 PMCID: PMC6973031 DOI: 10.1111/ele.13442] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/22/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
Abstract
Highly variable and synchronised production of seeds by plant populations, known as masting, is implicated in many important ecological processes, but how it arises remains poorly understood. The lack of experimental studies prevents underlying mechanisms from being explicitly tested, and thereby precludes meaningful predictions on the consequences of changing environments for plant reproductive patterns and global vegetation dynamics. Here we review the most relevant proximate drivers of masting and outline a research agenda that takes the biology of masting from a largely observational field of ecology to one rooted in mechanistic understanding. We divide the experimental framework into three main processes: resource dynamics, pollen limitation and genetic and hormonal regulation, and illustrate how specific predictions about proximate mechanisms can be tested, highlighting the few successful experiments as examples. We envision that the experiments we outline will deliver new insights into how and why masting patterns might respond to a changing environment.
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Affiliation(s)
- Michał Bogdziewicz
- Department of Systematic ZoologyFaculty of BiologyAdam Mickiewicz University in PoznańUmutlowska 8961‐614PoznańPoland
| | - Davide Ascoli
- Department of Agricultural, Forest and Food SciencesUniversity of Turin10095 GrugliascoTorinoItaly
| | - Andrew Hacket‐Pain
- Department of Geography and PlanningSchool of Environmental SciencesUniversity of LiverpoolLiverpoolUK
| | | | - Ian Pearse
- Fort Collins Science Center U.S. Geological SurveyFort CollinsCOUSA
| | - Mario Pesendorfer
- Lab of OrnithologyCornell UniversityIthacaNY14850USA
- Institute of Forest EcologyDepartment of Forest and Soil SciencesUniversity of Natural Resources and Life SciencesViennaAustria
| | - Akiko Satake
- Department of BiologyFaculty of ScienceKyushu University819‐0395FukuokaJapan
| | - Peter Thomas
- School of Life SciencesKeele UniversityStaffordshireST5 5BGUK
| | | | - Thomas Wohlgemuth
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLForest Dynamics, Zürcherstrasse 111CH‐8903BirmensdorfSwitzerland
| | - Andrew Tanentzap
- Department of Plant SciencesUniversity of CambridgeDowning StCambridgeCB2 3EAUK
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19
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Ushio M, Osada Y, Kumagai T, Kume T, Pungga RAS, Nakashizuka T, Itioka T, Sakai S. Dynamic and synergistic influences of air temperature and rainfall on general flowering in a Bornean lowland tropical forest. Ecol Res 2019. [DOI: 10.1111/1440-1703.12057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Masayuki Ushio
- Hakubi Center Kyoto University Kyoto Japan
- Center for Ecological Research Kyoto University Otsu Japan
- PRESTO Japan Science and Technology Agency Kawaguchi Japan
| | - Yutaka Osada
- Graduate School of Life Science Tohoku University Sendai Japan
| | - Tomo'omi Kumagai
- Graduate School of Agricultural and Life Sciences The University of Tokyo Tokyo Japan
| | - Tomonori Kume
- Kasuya Research Forest Kyushu University Fukuoka Japan
| | | | - Tohru Nakashizuka
- Research Department Research Institute for Humanity and Nature Kyoto Japan
| | - Takao Itioka
- Graduate School of Human and Environmental Studies Kyoto University Kyoto Japan
| | - Shoko Sakai
- Center for Ecological Research Kyoto University Otsu Japan
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20
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Todesco M, Cronk Q. The genetic dimension of pest pressure in the tropical rainforest. Mol Ecol 2019; 26:2407-2409. [PMID: 28449375 DOI: 10.1111/mec.14078] [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: 02/07/2017] [Revised: 02/15/2017] [Accepted: 02/21/2017] [Indexed: 10/19/2022]
Abstract
Wet tropical forests are among the most diverse ecosystems on Earth and can host several hundreds of tree species per hectare. To maintain such diversity, the community must contain large numbers of relatively rare species rather than be dominated by a few very common trees, as is often the case in temperate forests. Explaining the mechanisms preventing dominance by common species has been a major task of tropical forest ecology. One of the most promising mechanisms is negative density dependence (NDD) of tree abundance driven by pests, including fungal diseases ('pest pressure'). NDD entails that the chance of survival of a sapling increases with the distance from a mature tree of the same species, thus preventing species from becoming locally dominant. Curiously, the strength of NDD is negatively correlated with abundance, meaning that tree species that are more common generally show weaker NDD (Comita et al. ). Interactions between plants and soil pathogens have been shown to play an important role in NDD (Klironomos ), and rare species are apparently more strongly affected (Mangan et al. ). However, the genetic mechanisms underlying this phenomenon have remained obscure. In this issue of Molecular Ecology, Marden et al. () suggest that reduced diversity of the genes involved in pathogen recognition (Resistance genes or R genes) could explain why NDD is stronger in locally rare species.
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Affiliation(s)
- Marco Todesco
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - Quentin Cronk
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
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21
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Field transcriptome revealed a novel relationship between nitrate transport and flowering in Japanese beech. Sci Rep 2019; 9:4325. [PMID: 30867453 PMCID: PMC6416253 DOI: 10.1038/s41598-019-39608-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/29/2019] [Indexed: 11/09/2022] Open
Abstract
Recent advances in molecular and genetic studies about flowering time control have been increasingly available to elucidate the physiological mechanism underlying masting, the intermittent and synchronized production of a large amount of flowers and seeds in plant populations. To identify unexplored developmental and physiological processes associated with masting, genome-wide transcriptome analysis is a promising tool, but such analyses have yet to be performed. We established a field transcriptome using a typical masting species, Japanese beech (Fagus crenata Blume), over two years, and analyzed the data using a nonlinear time-series analysis called convergent cross mapping. Our field transcriptome was found to undergo numerous changes depending on the status of floral induction and season. An integrated approach of high-throughput transcriptomics and causal inference was successful at detecting novel causal regulatory relationships between nitrate transport and florigen synthesis/transport in a forest tree species. The synergistic activation of nitrate transport and floral transition could be adaptive to simultaneously satisfy floral transition at the appropriate timing and the nitrogen demand needed for flower formation.
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22
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Affiliation(s)
- Shoko Sakai
- Center for Ecological Research Kyoto University Otsu Japan
| | - Kaoru Kitajima
- Graduate School of Agriculture Kyoto University Kyoto Japan
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23
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Satake A, Chen Y, Fletcher C, Kosugi Y. Drought and cool temperature cue general flowering synergistically in the aseasonal tropical forests of Southeast Asia. Ecol Res 2019. [DOI: 10.1111/1440-1703.1012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Akiko Satake
- Department of Biology Faculty of Science, Kyushu University Fukuoka Japan
| | - Yu‐Yun Chen
- Department of Natural Resources and Environmental Studies National Dong Hwa University Hualien Taiwan
| | | | - Yoshiko Kosugi
- Division of Environmental Science and Technology, Laboratory of Forest Hydrology, Graduate School of Agriculture Kyoto University Kyoto Japan
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24
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Zaidem ML, Groen SC, Purugganan MD. Evolutionary and ecological functional genomics, from lab to the wild. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:40-55. [PMID: 30444573 DOI: 10.1111/tpj.14167] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/10/2018] [Accepted: 11/13/2018] [Indexed: 05/12/2023]
Abstract
Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve. In particular, by bringing these studies from the laboratory to the field, EEFG studies allow us to gain greater knowledge of how plants function in their natural contexts.
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Affiliation(s)
- Maricris L Zaidem
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
| | - Simon C Groen
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
- Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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25
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Satake A, Kawatsu K, Chiba Y, Kitamura K, Han Q. Synchronized expression of FLOWERING LOCUS T
between branches underlies mass flowering in Fagus crenata. POPUL ECOL 2018. [DOI: 10.1002/1438-390x.1010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Akiko Satake
- Department of Biology; Faculty of Science, Kyushu University; Fukuoka Japan
| | - Kazutaka Kawatsu
- Graduate School of Life Sciences; Tohoku University; Sendai Japan
| | - Yukako Chiba
- Graduate School of Life Science; Hokkaido University; Sapporo Japan
| | - Keiko Kitamura
- Hokkaido Research Center; Forestry and Forest Products Research Institute; Sapporo Japan
| | - Qingmin Han
- Department of Plant Ecology; Forestry and Forest Products Research Institute; Tsukuba Japan
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26
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Nagahama A, Kubota Y, Satake A. Climate warming shortens flowering duration: a comprehensive assessment of plant phenological responses based on gene expression analyses and mathematical modeling. Ecol Res 2018. [DOI: 10.1007/s11284-018-1625-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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27
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Richards CL, Alonso C, Becker C, Bossdorf O, Bucher E, Colomé-Tatché M, Durka W, Engelhardt J, Gaspar B, Gogol-Döring A, Grosse I, van Gurp TP, Heer K, Kronholm I, Lampei C, Latzel V, Mirouze M, Opgenoorth L, Paun O, Prohaska SJ, Rensing SA, Stadler PF, Trucchi E, Ullrich K, Verhoeven KJF. Ecological plant epigenetics: Evidence from model and non-model species, and the way forward. Ecol Lett 2017; 20:1576-1590. [PMID: 29027325 DOI: 10.1111/ele.12858] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/15/2017] [Accepted: 09/04/2017] [Indexed: 12/15/2022]
Abstract
Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which contribute to a more mechanistic understanding but have limited ecological realism. Understanding the significance of epigenetics for plant ecology requires increased transfer of knowledge and methods from model species research to genomes of evolutionarily divergent species, and examination of responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non-model species, which is challenging given the large and often polyploid genomes of plants. Collaboration among molecular geneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.
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Affiliation(s)
- Christina L Richards
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | | | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology, 1030, Vienna, Austrian Academy of Sciences, Vienna Biocenter (VBC), Austria
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, University of Tübingen, 72076, Tübingen, Germany
| | - Etienne Bucher
- Institut de Recherche en Horticulture et Semences, 49071, Beaucouzé Cedex, France
| | - Maria Colomé-Tatché
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, 9713, Groningen, The Netherlands.,Institute of Computational Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Walter Durka
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, 06120, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Jan Engelhardt
- Institut für Informatik, University of Leipzig, 04107, Leipzig, Germany
| | - Bence Gaspar
- Plant Evolutionary Ecology, University of Tübingen, 72076, Tübingen, Germany
| | - Andreas Gogol-Döring
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany.,Institute of Computer Science, University of Halle, 06120, Halle, Germany
| | - Ivo Grosse
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany.,Institute of Computer Science, University of Halle, 06120, Halle, Germany
| | - Thomas P van Gurp
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Katrin Heer
- Conservation Biology, Philipps-University of Marburg, 35037, Marburg, Germany
| | - Ilkka Kronholm
- Department of Biological and Environmental Sciences, Center of Excellence in Biological Interactions, University of Jyväskylä, 40014, Jyväskylän yliopisto, Finland
| | - Christian Lampei
- Institute of Plant Breeding, Seed Science and Population Genetics, 70599, Stuttgart, Germany
| | - Vít Latzel
- Institute of Botany, The Czech Academy of Sciences, 25243, Průhonice, Czech Republic
| | - Marie Mirouze
- Institut de Recherche pour le Développement, Laboratoire Génome et Développement des Plantes, 66860, Perpignan, France
| | - Lars Opgenoorth
- Department of Ecology, Philipps-University Marburg, 35037, Marburg, Germany
| | - Ovidiu Paun
- Plant Ecological Genomics, University of Vienna, 1030, Vienna, Austria
| | - Sonja J Prohaska
- Institut für Informatik, University of Leipzig, 04107, Leipzig, Germany.,The Santa Fe Institute, Santa Fe NM, 87501, USA
| | - Stefan A Rensing
- Plant Cell Biology, Philipps-University Marburg, 35037, Marburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79098, Freiburg, Germany
| | - Peter F Stadler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany.,Institut für Informatik, University of Leipzig, 04107, Leipzig, Germany.,The Santa Fe Institute, Santa Fe NM, 87501, USA.,Max Planck Institute for Mathematics in the Sciences, 04103, Leipzig, Germany
| | - Emiliano Trucchi
- Plant Ecological Genomics, University of Vienna, 1030, Vienna, Austria
| | - Kristian Ullrich
- Plant Cell Biology, Philipps-University Marburg, 35037, Marburg, Germany
| | - Koen J F Verhoeven
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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28
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Yeoh SH, Satake A, Numata S, Ichie T, Lee SL, Basherudin N, Muhammad N, Kondo T, Otani T, Hashim M, Tani N. Unravelling proximate cues of mass flowering in the tropical forests of South-East Asia from gene expression analyses. Mol Ecol 2017; 26:5074-5085. [PMID: 28749031 DOI: 10.1111/mec.14257] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 07/05/2017] [Accepted: 07/12/2017] [Indexed: 12/30/2022]
Abstract
Elucidating the physiological mechanisms of the irregular yet concerted flowering rhythm of mass flowering tree species in the tropics requires long-term monitoring of flowering phenology, exogenous and endogenous environmental factors, as well as identifying interactions and dependencies among these factors. To investigate the proximate factors for floral initiation of mast seeding trees in the tropics, we monitored the expression dynamics of two key flowering genes, meteorological conditions and endogenous resources over two flowering events of Shorea curtisii and Shorea leprosula in the Malay Peninsula. Comparisons of expression dynamics of genes studied indicated functional conservation of FLOWERING LOCUS T (FT) and LEAFY (LFY) in Shorea. The genes were highly expressed at least 1 month before anthesis for both species. A mathematical model considering the synergistic effect of cool temperature and drought on activation of the flowering gene was successful in predicting the observed gene expression patterns. Requirement of both cool temperature and drought for floral transition suggested by the model implies that flowering phenologies of these species are sensitive to climate change. Our molecular phenology approach in the tropics sheds light on the conserved role of flowering genes in plants inhabiting different climate zones and can be widely applied to dissect the flowering processes in other plant species.
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Affiliation(s)
- Suat Hui Yeoh
- Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Akiko Satake
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan.,Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Shinya Numata
- Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Hachiouji, Tokyo, Japan
| | - Tomoaki Ichie
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Soon Leong Lee
- Forestry Biotechnology Division, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Norlia Basherudin
- Forestry Biotechnology Division, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Norwati Muhammad
- Forestry Biotechnology Division, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Toshiaki Kondo
- Graduate School for International Development and Cooperation, Hiroshima University, Higashihiroshima, Hiroshima, Japan
| | - Tatsuya Otani
- Shikoku Research Center, Forestry and Forest Products Research Institute (FFPRI), Kochi, Japan
| | - Mazlan Hashim
- Geosciences & Digital Earth Centre (INSTeG), Research Institute of Sustainable Environment (RISE), Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Naoki Tani
- Forestry Biotechnology Division, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia.,Forestry Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
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29
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Miyazaki Y, Satake A. Relationship between seasonal progression of floral meristem development and FLOWERING LOCUS T expression in the deciduous tree Fagus crenata. Ecol Res 2017. [DOI: 10.1007/s11284-017-1462-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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30
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Roberts WR, Roalson EH. Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae). BMC Genomics 2017; 18:240. [PMID: 28320315 PMCID: PMC5359931 DOI: 10.1186/s12864-017-3623-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 03/11/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Flowers have an amazingly diverse display of colors and shapes, and these characteristics often vary significantly among closely related species. The evolution of diverse floral form can be thought of as an adaptive response to pollination and reproduction, but it can also be seen through the lens of morphological and developmental constraints. To explore these interactions, we use RNA-seq across species and development to investigate gene expression and sequence evolution as they relate to the evolution of the diverse flowers in a group of Neotropical plants native to Mexico-magic flowers (Achimenes, Gesneriaceae). RESULTS The assembled transcriptomes contain between 29,000 and 42,000 genes expressed during development. We combine sequence orthology and coexpression clustering with analyses of protein evolution to identify candidate genes for roles in floral form evolution. Over 25% of transcripts captured were distinctive to Achimenes and overrepresented by genes involved in transcription factor activity. Using a model-based clustering approach we find dynamic, temporal patterns of gene expression among species. Selection tests provide evidence of positive selection in several genes with roles in pigment production, flowering time, and morphology. Combining these approaches to explore genes related to flower color and flower shape, we find distinct patterns that correspond to transitions of floral form among Achimenes species. CONCLUSIONS The floral transcriptomes developed from four species of Achimenes provide insight into the mechanisms involved in the evolution of diverse floral form among closely related species with different pollinators. We identified several candidate genes that will serve as an important and useful resource for future research. High conservation of sequence structure, patterns of gene coexpression, and detection of positive selection acting on few genes suggests that large phenotypic differences in floral form may be caused by genetic differences in a small set of genes. Our characterized floral transcriptomes provided here should facilitate further analyses into the genomics of flower development and the mechanisms underlying the evolution of diverse flowers in Achimenes and other Neotropical Gesneriaceae.
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Affiliation(s)
- Wade R. Roberts
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164-1030 USA
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236 USA
| | - Eric H. Roalson
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164-1030 USA
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236 USA
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31
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Izuno A, Kitayama K, Onoda Y, Tsujii Y, Hatakeyama M, Nagano AJ, Honjo MN, Shimizu-Inatsugi R, Kudoh H, Shimizu KK, Isagi Y. The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha
(Myrtaceae). Mol Ecol 2017; 26:1515-1532. [DOI: 10.1111/mec.14016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/13/2016] [Accepted: 12/28/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Ayako Izuno
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Kanehiro Kitayama
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
| | - Yusuke Onoda
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
| | - Yuki Tsujii
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
- Functional Genomics Center Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Atsushi J. Nagano
- Faculty of Agriculture; Ryukoku University; 1-5 Yokatani, Seta Ohe-cho Otsu Shiga 520-2194 Japan
- PRESTO, Japan Science and Technology Agency; 4-1-8 Honcho Kawaguchi, Saitama 332-0012 Japan
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
| | - Mie N. Honjo
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Hiroshi Kudoh
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
- Kihara Institute for Biological Research; Yokohama City University; 641-12 Maioka, Totsuka-ward Yokohama Kanagawa 244-0813 Japan
| | - Yuji Isagi
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
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32
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Blackman BK. Changing Responses to Changing Seasons: Natural Variation in the Plasticity of Flowering Time. PLANT PHYSIOLOGY 2017; 173:16-26. [PMID: 27872243 PMCID: PMC5210766 DOI: 10.1104/pp.16.01683] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 11/20/2016] [Indexed: 05/19/2023]
Abstract
The mechanisms by which the environment regulates flowering time have evolved as crops and wild populations have adapted to diverse climates, and the specific variants involved are increasingly known.
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Affiliation(s)
- Benjamin K Blackman
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
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33
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Groen SC, Purugganan MD. Systems genetics of plant adaptation to environmental stresses. AMERICAN JOURNAL OF BOTANY 2016; 103:2019-2021. [PMID: 27864265 DOI: 10.3732/ajb.1600340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 10/19/2016] [Indexed: 05/22/2023]
Affiliation(s)
- Simon C Groen
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 10003 USA
| | - Michael D Purugganan
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 10003 USA
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34
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Affiliation(s)
- Angela M Hancock
- Department of Plant Developmental Biology, Max Planck Institute of Plant Breeding Research, Cologne, Germany.
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35
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Galbiati F, Chiozzotto R, Locatelli F, Spada A, Genga A, Fornara F. Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice. PLANT, CELL & ENVIRONMENT 2016; 39:1982-93. [PMID: 27111837 DOI: 10.1111/pce.12760] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/10/2016] [Indexed: 05/20/2023]
Abstract
Plants show a high degree of developmental plasticity in response to external cues, including day length and environmental stress. Water scarcity in particular can interfere with photoperiodic flowering, resulting in the acceleration of the switch to reproductive growth in several species, a process called drought escape. However, other strategies are possible and drought stress can also delay flowering, albeit the underlying mechanisms have never been addressed at the molecular level. We investigated these interactions in rice, a short day species in which drought stress delays flowering. A protocol that allows the synchronization of drought with the floral transition was set up to profile the transcriptome of leaves subjected to stress under distinct photoperiods. We identified clusters of genes that responded to drought differently depending on day length. Exposure to drought stress under floral-inductive photoperiods strongly reduced transcription of EARLY HEADING DATE 1 (Ehd1), HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1), primary integrators of day length signals, providing a molecular connection between stress and the photoperiodic pathway. However, phenotypic and transcriptional analyses suggested that OsGIGANTEA (OsGI) does not integrate drought and photoperiodic signals as in Arabidopsis, highlighting molecular differences between long and short day model species.
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Affiliation(s)
- Francesca Galbiati
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
- Department of Agricultural and Environmental Sciences - Production, Territory, Agroenergy, University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - Remo Chiozzotto
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133, Milan, Italy
| | - Franca Locatelli
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133, Milan, Italy
| | - Alberto Spada
- Department of Agricultural and Environmental Sciences - Production, Territory, Agroenergy, University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - Annamaria Genga
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133, Milan, Italy
| | - Fabio Fornara
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
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36
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Shimizu‐Inatsugi R, Terada A, Hirose K, Kudoh H, Sese J, Shimizu KK. Plant adaptive radiation mediated by polyploid plasticity in transcriptomes. Mol Ecol 2016; 26:193-207. [DOI: 10.1111/mec.13738] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 05/27/2016] [Accepted: 06/01/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Rie Shimizu‐Inatsugi
- Department of Evolutionary Biology and Environmental Studies and Department of Plant and Microbial Biology University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Aika Terada
- PRESTO Japan Science and Technology Agency 4‐1‐8 Honcho Kawaguchi Saitama 332‐0012 Japan
- Department of Computational Biology and Medical Science Graduate School of Frontier Sciences The University of Tokyo 5‐1‐5 Kashiwanoha Kashiwa Chiba 277‐8561 Japan
- Biotechnology Research Institute for Drug Discovery National Institute of Advanced Industrial Science and Technology (AIST) 2‐4‐7 Aomi Koto‐ku Tokyo 135‐0064 Japan
| | - Kyosuke Hirose
- Center for Ecological Research Kyoto University Hirano 2‐509‐3 Otsu 520‐2113 Japan
| | - Hiroshi Kudoh
- Center for Ecological Research Kyoto University Hirano 2‐509‐3 Otsu 520‐2113 Japan
| | - Jun Sese
- Biotechnology Research Institute for Drug Discovery National Institute of Advanced Industrial Science and Technology (AIST) 2‐4‐7 Aomi Koto‐ku Tokyo 135‐0064 Japan
- Artificial Intelligence Research Center AIST 2‐4‐7 Aomi Koto‐ku Tokyo 135‐0064 Japan
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies and Department of Plant and Microbial Biology University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
- Biotechnology Research Institute for Drug Discovery National Institute of Advanced Industrial Science and Technology (AIST) 2‐4‐7 Aomi Koto‐ku Tokyo 135‐0064 Japan
- Center for Ecological Research Kyoto University Hirano 2‐509‐3 Otsu 520‐2113 Japan
- Kihara Institute for Biological Research Yokohama City University 641‐12 Maioka, Totsuka‐ward Yokohama Kanagawa 244‐0813 Japan
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37
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Abe T, Tachiki Y, Kon H, Nagasaka A, Onodera K, Minamino K, Han Q, Satake A. Parameterisation and validation of a resource budget model for masting using spatiotemporal flowering data of individual trees. Ecol Lett 2016; 19:1129-39. [PMID: 27449602 DOI: 10.1111/ele.12651] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 06/05/2016] [Accepted: 06/17/2016] [Indexed: 11/26/2022]
Abstract
Synchronised and fluctuating reproduction by plant populations, called masting, is widespread in diverse taxonomic groups. Here, we propose a new method to explore the proximate mechanism of masting by combining spatiotemporal flowering data, biochemical analysis of resource allocation and mathematical modelling. Flowering data of 170 trees over 13 years showed the emergence of clustering with trees in a given cluster mutually synchronised in reproduction, which was successfully explained by resource budget models. Analysis of resources invested in the development of reproductive organs showed that parametric values used in the model are significantly different between nitrogen and carbon. Using a fully parameterised model, we showed that the observed flowering pattern is explained only when the interplay between nitrogen dynamics and climatic cues was considered. This result indicates that our approach successfully identified resource type-specific roles on masting and that the method is suitable for a wide range of plant species.
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Affiliation(s)
- Tomoyuki Abe
- Hokkaido Research Organization, Forestry Research Institute, Higashiyama, Koshunai, Bibai, 079-0198, Japan
| | - Yuuya Tachiki
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, 819-0395, Japan
| | - Hirokazu Kon
- Hokkaido Research Organization, Forestry Research Institute, Higashiyama, Koshunai, Bibai, 079-0198, Japan
| | - Akiko Nagasaka
- Hokkaido Research Organization, Forestry Research Institute, Higashiyama, Koshunai, Bibai, 079-0198, Japan
| | - Kensuke Onodera
- Hokkaido Research Organization, Forestry Research Institute, Higashiyama, Koshunai, Bibai, 079-0198, Japan
| | - Kazuhiro Minamino
- Hokkaido Research Organization, Forestry Research Institute, Higashiyama, Koshunai, Bibai, 079-0198, Japan
| | - Qingmin Han
- Hokkaido Research Center, Forestry and Forest Products Research Institute, Sapporo, 062-8516, Japan
| | - Akiko Satake
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, 819-0395, Japan
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38
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Satake A, Seki M, Iima M, Teramoto T, Nishiura Y. Florigen distribution determined by a source-sink balance explains the diversity of inflorescence structures in Arabidopsis. J Theor Biol 2016; 395:227-237. [PMID: 26845309 DOI: 10.1016/j.jtbi.2016.01.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 01/17/2016] [Accepted: 01/19/2016] [Indexed: 11/29/2022]
Abstract
The ability to continue flowering after loss of inductive environmental cues that trigger flowering is termed floral commitment. Reversible transition involving a switch from floral development back to vegetative development has been found in Arabidopsis mutants and many plant species. Although the molecular basis for floral commitment remains unclear, recent studies suggest that the persistent activity of FLOWERING LOCUS T (FT) at inflorescences is required for floral commitment in Arabidopsis thaliana. Because FT encodes a mobile signal, florigen, which is generally transported from leaves to meristems through the phloem, understanding the transportation dynamics of FT is required to explore the role of FT on floral commitment. Here we developed a transportation model of leaf- and inflorescence-derived florigen and sucrose based on pressure-flow hypothesis. Depending on the demanded level of florigen supply for floral commitment of each floral meristem, the model predicted the change in inflorescence pattern from stable commitment to flower, transient flowering, and complete reversion. FT activity in inflorescence partly suppressed floral reversion, but complete suppression was achieved only when inflorescence became a source of sucrose. This finding highlights the importance of monitoring the spatio-temporal sucrose distribution and floral stimulus to understand inflorescence development mechanism.
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Affiliation(s)
- Akiko Satake
- Departmnet of Biology, Faculty of Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Motohide Seki
- Departmnet of Informatics, Faculty of Information Science and Electrical Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Makoto Iima
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8521, Japan
| | - Takashi Teramoto
- School of Medicine, Asahikawa Medical University, 2-1-1-1, Midorigaoka-higashi, Asahikawa 078-8510, Japan
| | - Yasumasa Nishiura
- WPI Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
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39
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Kudoh H. Molecular phenology in plants: in natura systems biology for the comprehensive understanding of seasonal responses under natural environments. THE NEW PHYTOLOGIST 2016; 210:399-412. [PMID: 26523957 DOI: 10.1111/nph.13733] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/27/2015] [Indexed: 06/05/2023]
Abstract
Phenology refers to the study of seasonal schedules of organisms. Molecular phenology is defined here as the study of the seasonal patterns of organisms captured by molecular biology techniques. The history of molecular phenology is reviewed briefly in relation to advances in the quantification technology of gene expression. High-resolution molecular phenology (HMP) data have enabled us to study phenology with an approach of in natura systems biology. I review recent analyses of FLOWERING LOCUS C (FLC), a temperature-responsive repressor of flowering, along the six steps in the typical flow of in natura systems biology. The extensive studies of the regulation of FLC have made this example a successful case in which a comprehensive understanding of gene functions has been progressing. The FLC-mediated long-term memory of past temperatures creates time lags with other seasonal signals, such as photoperiod and short-term temperature. Major signals that control flowering time have a phase lag between them under natural conditions, and hypothetical phase lag calendars are proposed as mechanisms of season detection in plants. Transcriptomic HMP brings a novel strategy to the study of molecular phenology, because it provides a comprehensive representation of plant functions. I discuss future perspectives of molecular phenology from the standpoints of molecular biology, evolutionary biology and ecology.
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Affiliation(s)
- Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan
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40
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Nagai S, Ichie T, Yoneyama A, Kobayashi H, Inoue T, Ishii R, Suzuki R, Itioka T. Usability of time-lapse digital camera images to detect characteristics of tree phenology in a tropical rainforest. ECOL INFORM 2016. [DOI: 10.1016/j.ecoinf.2016.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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41
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Molecular and Functional Characterization of FLOWERING LOCUS T Homologs in Allium cepa. Molecules 2016; 21:molecules21020217. [PMID: 26891287 PMCID: PMC6274202 DOI: 10.3390/molecules21020217] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/04/2016] [Accepted: 02/09/2016] [Indexed: 01/20/2023] Open
Abstract
Onion bulbing is an important agricultural trait affecting economic value and is regulated by flowering-related genes. FLOWERING LOCUS T (FT)-like gene function is crucial for the initiation of flowering in various plant species and also in asexual reproduction in tuber plants. By employing various computational analysis using RNA-Seq data, we identified eight FT-like genes (AcFT) encoding PEBP (phosphatidylethanolamine-binding protein) domains in Allium cepa. Sequence and phylogenetic analyses of FT-like proteins revealed six proteins that were identical to previously reported AcFT1-6 proteins, as well as one (AcFT7) with a highly conserved region shared with AcFT6 and another (comp106231) with low similarity to MFT protein, but containing a PEBP domain. Homology modelling of AcFT7 proteins showed similar structures and conservation of amino acids crucial for function in AtFT (Arabidopsis) and Hd3a (rice), with variation in the C-terminal region. Further, we analyzed AcFT expression patterns in different transitional stages, as well as under SD (short-day), LD (long-day), and drought treatment in two contrasting genotypic lines EM (early maturation, 36101) and LM (late maturation, 36122). The FT transcript levels were greatly affected by various environmental factors such as photoperiod, temperature and drought. Our results suggest that AcFT7 is a member of the FT-like genes in Allium cepa and may be involved in regulation of onion bulbing, similar to other FT genes. In addition, AcFT4 and AcFT7 could be involved in establishing the difference in timing of bulb maturity between the two contrasting onion lines.
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Kooyers NJ. The evolution of drought escape and avoidance in natural herbaceous populations. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 234:155-62. [PMID: 25804818 DOI: 10.1016/j.plantsci.2015.02.012] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/04/2015] [Accepted: 02/19/2015] [Indexed: 05/03/2023]
Abstract
While the functional genetics and physiological mechanisms controlling drought resistance in crop plants have been intensely studied, less research has examined the genetic basis of adaptation to drought stress in natural populations. Drought resistance adaptations in nature reflect natural rather than human-mediated selection and may identify novel mechanisms for stress tolerance. Adaptations conferring drought resistance have historically been divided into alternative strategies including drought escape (rapid development to complete a life cycle before drought) and drought avoidance (reducing water loss to prevent dehydration). Recent studies in genetic model systems such as Arabidopsis, Mimulus, and Panicum have begun to elucidate the genes, expression profiles, and physiological changes responsible for ecologically important variation in drought resistance. Similar to most crop plants, variation in drought escape and avoidance is complex, underlain by many QTL of small effect, and pervasive gene by environment interactions. Recently identified major-effect alleles point to a significant role for genetic constraints in limiting the concurrent evolution of both drought escape and avoidance strategies, although these constraints are not universally found. This progress suggests that understanding the mechanistic basic and fitness consequences of gene by environment interactions will be critical for crop improvement and forecasting population persistence in unpredictable environments.
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Affiliation(s)
- Nicholas J Kooyers
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA.
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Alvarez M, Schrey AW, Richards CL. Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution? Mol Ecol 2015; 24:710-25. [PMID: 25604587 DOI: 10.1111/mec.13055] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 12/16/2014] [Accepted: 12/18/2014] [Indexed: 12/13/2022]
Abstract
Molecular ecology has moved beyond the use of a relatively small number of markers, often noncoding, and it is now possible to use whole-genome measures of gene expression with microarrays and RNAseq (i.e. transcriptomics) to capture molecular response to environmental challenges. While transcriptome studies are shedding light on the mechanistic basis of traits as complex as personality or physiological response to catastrophic events, these approaches are still challenging because of the required technical expertise, difficulties with analysis and cost. Still, we found that in the last 10 years, 575 studies used microarrays or RNAseq in ecology. These studies broadly address three questions that reflect the progression of the field: (i) How much variation in gene expression is there and how is it structured? (ii) How do environmental stimuli affect gene expression? (iii) How does gene expression affect phenotype? We discuss technical aspects of RNAseq and microarray technology, and a framework that leverages the advantages of both. Further, we highlight future directions of research, particularly related to moving beyond correlation and the development of additional annotation resources. Measuring gene expression across an array of taxa in ecological settings promises to enrich our understanding of ecology and genome function.
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Affiliation(s)
- Mariano Alvarez
- Department of Integrative Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL, 33620, USA
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Zhao X, Yu H, Kong L, Liu S, Li Q. Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions. PLoS One 2014; 9:e111915. [PMID: 25369077 PMCID: PMC4219811 DOI: 10.1371/journal.pone.0111915] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/01/2014] [Indexed: 12/29/2022] Open
Abstract
Environmental salinity creates a key barrier to limit the distribution of most aquatic organisms. Adaptation to osmotic fluctuation is believed to be a factor facilitating species diversification. Adaptive evolution often involves beneficial mutations at more than one locus. Bivalves hold great interest, with numerous species living in waters, as osmoconformers, who maintain the osmotic pressure balance mostly by free amino acids. In this study, 107,076,589 reads from two groups of Crassostrea hongkongensis were produced and the assembled into 130,629 contigs. Transcripts putatively involved in stress-response, innate immunity and cell processes were identified according to Gene ontology and KEGG pathway analyses. Comparing with the transcriptome of C. gigas to characterize the diversity of transcripts between species with osmotic divergence, we identified 182,806 high-quality single nucleotide polymorphisms (SNPs) for C. hongkongensis, and 196,779 SNPs for C. gigas. Comparison of 11,602 pairs of putative orthologs allowed for identification of 14 protein-coding genes that experienced strong positive selection (Ka/Ks>1). In addition, 45 genes that may show signs of moderate positive selection (1 ≥ Ka/Ks>0.5) were also identified. Based on Ks ratios and divergence time between the two species published previously, we estimated a neutral transcriptome-wide substitution mutation rate of 1.39 × 10(-9) per site per year. Several genes were differentially expressed across the control and treated groups of each species. This is the first time to sequence the transcriptome of C. hongkongensis and provide the most comprehensive transcriptomic resource available for it. The increasing amount of transcriptome data on Crassostrea provides an excellent resource for phylogenetic analysis. A large number of SNPs identified in this work are expected to provide valuable resources for future marker and genotyping assay development. The analysis of natural selection provides an innovative view on the adaptation within species and sets the basis for future genetic and evolutionary studies.
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Affiliation(s)
- Xuelin Zhao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- * E-mail:
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Miyazaki Y, Maruyama Y, Chiba Y, Kobayashi MJ, Joseph B, Shimizu KK, Mochida K, Hiura T, Kon H, Satake A. Nitrogen as a key regulator of flowering in
Fagus crenata
: understanding the physiological mechanism of masting by gene expression analysis. Ecol Lett 2014; 17:1299-309. [DOI: 10.1111/ele.12338] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/14/2014] [Accepted: 07/10/2014] [Indexed: 10/24/2022]
Affiliation(s)
- Yuko Miyazaki
- Graduate School of Environmental Sciences Hokkaido University Sapporo 060‐0810 Japan
- Graduate School of Environmental and Life Science Okayama University Okayama 700‐8530 Japan
| | - Yosuke Maruyama
- Graduate School of Life Science Hokkaido University Sapporo 060‐0810 Japan
| | - Yukako Chiba
- Graduate School of Life Science Hokkaido University Sapporo 060‐0810 Japan
- Faculty of Science Hokkaido University Sapporo 060‐0810 Japan
| | - Masaki J. Kobayashi
- Institute of Evolutionary Biology and Environmental Studies Institute of Plant Biology University of Zurich CH‐8057 Zurich Switzerland
| | - Benesh Joseph
- Institute of Evolutionary Biology and Environmental Studies Institute of Plant Biology University of Zurich CH‐8057 Zurich Switzerland
| | - Kentaro K. Shimizu
- Institute of Evolutionary Biology and Environmental Studies Institute of Plant Biology University of Zurich CH‐8057 Zurich Switzerland
| | - Keiichi Mochida
- Biomass Research Platform Team Biomass Engineering Program Cooperation Division RIKEN Center for Sustainable Resource Science Yokohama 230‐0045 Japan
| | - Tsutom Hiura
- Tomakomai Experimental Forest Field Science Center of Hokkaido University Tomakomai 053‐0035 Japan
| | - Hirokazu Kon
- Hokkaido Research Organization Forestry Research Institute Higashiyama Koshunai Bibai 079‐0198 Japan
| | - Akiko Satake
- Graduate School of Environmental Sciences Hokkaido University Sapporo 060‐0810 Japan
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Weston DJ, Wullschleger SD, Tuskan GA. Extending the Arabidopsis flowering paradigm to a mass flowering phenomenon in the tropics. Mol Ecol 2014; 22:4603-5. [PMID: 24167825 DOI: 10.1111/mec.12473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Flowering time is a critical life history trait, one that is shaped by evolution to maximize fecundity, reproductive success and fitness (Amasino 2010). This is especially true of annual plants where the cycle of floral initiation, pollination and seed production occur at regular intervals to ensure the survival of the species. In long-lived perennials, however, flowering can be an intermittent phenomenon and thus a challenge to understand. In this issue of Molecular Ecology, Kobayashi et al. (2013) tackle this particular challenge by applying modern-day molecular techniques to the ‘spectacular and mysterious’ mass flowering that takes places in mixed dipterocarp forests of South-East Asia. Here, amidst an almost unimaginable diversity of forbs, shrubs and trees, these authors used next-generation sequencing technology to characterize what they refer to as the ‘ecological transcriptome’ in an attempt to glimpse into the functional genomic reprogramming of Shorea beccariana at pre- and postflowering developmental transitions. They encountered many of the challenges that are often underappreciated yet typical for tropical ecological research including sample collection within a ~40-m high tree canopy, unpredictable flowering intervals and determining the most appropriate preflowering state for sampling. Despite these challenges, the authors were able to integrate gene ontology relationships with gene-clustering algorithms and environmental data to support the hypothesis that drought is a key trigger for flowering in S. beccariana. The cloning and transgenic expression of selected S. beccariana genes to corroborate presumed protein function is a key feature of their work and seldom applied within an ecological framework. As illustrated by Kobayashi et al. (2013), the inclusion of molecular biology, genomics and bioinformatics has the potential to shed light on long-standing questions of ecological concern.
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Armengaud J, Trapp J, Pible O, Geffard O, Chaumot A, Hartmann EM. Non-model organisms, a species endangered by proteogenomics. J Proteomics 2014; 105:5-18. [PMID: 24440519 DOI: 10.1016/j.jprot.2014.01.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 12/24/2013] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
UNLABELLED Previously, large-scale proteomics was possible only for organisms whose genomes were sequenced, meaning the most common model organisms. The use of next-generation sequencers is now changing the deal. With "proteogenomics", the use of experimental proteomics data to refine genome annotations, a higher integration of omics data is gaining ground. By extension, combining genomic and proteomic data is becoming routine in many research projects. "Proteogenomic"-flavored approaches are currently expanding, enabling the molecular studies of non-model organisms at an unprecedented depth. Today draft genomes can be obtained using next-generation sequencers in a rather straightforward way and at a reasonable cost for any organism. Unfinished genome sequences can be used to interpret tandem mass spectrometry proteomics data without the need for time-consuming genome annotation, and the use of RNA-seq to establish nucleotide sequences that are directly translated into protein sequences appears promising. There are, however, certain drawbacks that deserve further attention for RNA-seq to become more efficient. Here, we discuss the opportunities of working with non-model organisms, the proteomic methods that have been used until now, and the dramatic improvements proffered by proteogenomics. These put the distinction between model and non-model organisms in great danger, at least in terms of proteomics! BIOLOGICAL SIGNIFICANCE Model organisms have been crucial for in-depth analysis of cellular and molecular processes of life. Focusing the efforts of thousands of researchers on the Escherichia coli bacterium, Saccharomyces cerevisiae yeast, Arabidopsis thaliana plant, Danio rerio fish and other models for which genetic manipulation was possible was certainly worthwhile in terms of fundamental and invaluable biological insights. Until recently, proteomics of non-model organisms was limited to tedious, homology-based techniques, but today draft genomes or RNA-seq data can be straightforwardly obtained using next-generation sequencers, allowing the establishment of a draft protein database for any organism. Thus, proteogenomics opens new perspectives for molecular studies of non-model organisms, although they are still difficult experimental organisms. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France.
| | - Judith Trapp
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France; Irstea, UR MALY, F-69626 Villeurbanne, France
| | - Olivier Pible
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France
| | | | | | - Erica M Hartmann
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France
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Rieseberg L, Vines T, Gow J, Kane N. Molecular Ecology continues to perform well according to the major publication metrics. Introduction. Mol Ecol 2014; 23:1-15. [PMID: 24372750 DOI: 10.1111/mec.12586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 11/06/2013] [Indexed: 11/28/2022]
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Riboni M, Robustelli Test A, Galbiati M, Tonelli C, Conti L. Environmental stress and flowering time: the photoperiodic connection. PLANT SIGNALING & BEHAVIOR 2014; 9:e29036. [PMID: 25763486 PMCID: PMC4091191 DOI: 10.4161/psb.29036] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 04/27/2014] [Accepted: 04/28/2014] [Indexed: 05/19/2023]
Abstract
Plants maximize their chances to survive adversities by reprogramming their development according to environmental conditions. Adaptive variations in the timing to flowering reflect the need for plants to set seeds under the most favorable conditions. A complex network of genetic pathways allows plants to detect and integrate external (e.g., photoperiod and temperature) and/or internal (e.g., age) information to initiate the floral transition. Furthermore different types of environmental stresses play an important role in the floral transition. The emerging picture is that stress conditions often affect flowering through modulation of the photoperiodic pathway. In this review we will discuss different modes of cross talk between stress signaling and photoperiodic flowering, highlighting the central role of the florigen genes in this process.
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Affiliation(s)
- Matteo Riboni
- Department of Biosciences; Università degli Studi di Milano; Milan, Italy
| | | | - Massimo Galbiati
- Department of Biosciences; Università degli Studi di Milano; Milan, Italy
- Fondazione Filarete; Milan, Italy
| | - Chiara Tonelli
- Department of Biosciences; Università degli Studi di Milano; Milan, Italy
| | - Lucio Conti
- Department of Biosciences; Università degli Studi di Milano; Milan, Italy
- Correspondence to: Lucio Conti,
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