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Li Y, Xia HX, Cushman SA, Zhao H, Guo P, Liu YP, Lin N, Shang FD. A new mechanism of flowering regulation by the competition of isoforms in Osmanthus fragrans. ANNALS OF BOTANY 2023; 132:1089-1102. [PMID: 37666004 PMCID: PMC10809039 DOI: 10.1093/aob/mcad133] [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: 06/05/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
The regulation of flowering time is typically governed by transcription factors or epigenetic modifications. Transcript isoforms can play important roles in flowering regulation. Recently, transcript isoforms were discovered in the key genes, OfAP1 and OfTFL1, of the flowering regulatory network in Osmanthus fragrans. OfAP1-b generates a full-length isoform of OfAP1-b1 as well as an isoform of OfAP1-b2 that lacks the C-terminal domain. Although OfAP1-b2 does not possess an activation domain, it has a complete K domain that allows it to form heterodimers. OfAP1-b2 competes with OfAP1-b1 by binding with OfAGL24 to create non-functional and functional heterodimers. As a result, OfAP1-b1 promotes flowering while OfAP1-b2 delays flowering. OfTFL1 produces two isoforms located in different areas: OfTFL1-1 in the cytoplasm and OfTFL1-2 in the nucleus. When combined with OfFD, OfTFL1-1 does not enter the nucleus to repress AP1 expression, leading to early flowering. Conversely, when combined with OfFD, OfTFL1-2 enters the nucleus to repress AP1 expression, resulting in later flowering. Tissue-specific expression and functional conservation testing of OfAP1 and OfTFL1 support the new model's effectiveness in regulating flowering. Overall, this study provides new insights into regulating flowering time by the competition of isoforms.
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Affiliation(s)
- Yong Li
- College of Life Science, Henan Agricultural University, Zhengzhou 450046, China
- College of Life Science and Technology, Inner Mongolia Normal University, Huhehaote 010022, China
| | - He-Xiao Xia
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Samuel A Cushman
- Northern Arizona University, School of Forestry, Flagstaff, AZ 86011-4084, USA
| | - Heng Zhao
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Peng Guo
- College of Life Science, Henan Agricultural University, Zhengzhou 450046, China
| | - Yan-Pei Liu
- College of Life Science, Henan Agricultural University, Zhengzhou 450046, China
| | - Nan Lin
- College of Life Science, Henan Agricultural University, Zhengzhou 450046, China
| | - Fu-De Shang
- College of Life Science, Henan Agricultural University, Zhengzhou 450046, China
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Kinmonth-Schultz H, Lewandowska-Sabat A, Imaizumi T, Ward JK, Rognli OA, Fjellheim S. Flowering Times of Wild Arabidopsis Accessions From Across Norway Correlate With Expression Levels of FT, CO, and FLC Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:747740. [PMID: 34790213 PMCID: PMC8591261 DOI: 10.3389/fpls.2021.747740] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/30/2021] [Indexed: 06/12/2023]
Abstract
Temperate species often require or flower most rapidly in the long daylengths, or photoperiods, experienced in summer or after prolonged periods of cold temperatures, referred to as vernalization. Yet, even within species, plants vary in the degree of responsiveness to these cues. In Arabidopsis thaliana, CONSTANS (CO) and FLOWERING LOCUS C (FLC) genes are key to photoperiod and vernalization perception and antagonistically regulate FLOWERING LOCUS T (FT) to influence the flowering time of the plants. However, it is still an open question as to how these genes vary in their interactions among wild accessions with different flowering behaviors and adapted to different microclimates, yet this knowledge could improve our ability to predict plant responses in variable natural conditions. To assess the relationships among these genes and to flowering time, we exposed 10 winter-annual Arabidopsis accessions from throughout Norway, ranging from early to late flowering, along with two summer-annual accessions to 14 weeks of vernalization and either 8- or 19-h photoperiods to mimic Norwegian climate conditions, then assessed gene expression levels 3-, 5-, and 8-days post vernalization. CO and FLC explained both FT levels and flowering time (days) but not rosette leaf number at flowering. The correlation between FT and flowering time increased over time. Although vernalization suppresses FLC, FLC was high in the late-flowering accessions. Across accessions, FT was expressed only at low FLC levels and did not respond to CO in the late-flowering accessions. We proposed that FT may only be expressed below a threshold value of FLC and demonstrated that these three genes correlated to flowering times across genetically distinct accessions of Arabidopsis.
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Affiliation(s)
- Hannah Kinmonth-Schultz
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States
| | | | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA, United States
| | - Joy K. Ward
- College of Arts and Sciences, Case Western Reserve University, Cleveland, OH, United States
| | - Odd Arne Rognli
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Siri Fjellheim
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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Kronenberg L, Yates S, Boer MP, Kirchgessner N, Walter A, Hund A. Temperature response of wheat affects final height and the timing of stem elongation under field conditions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:700-717. [PMID: 33057698 PMCID: PMC7853599 DOI: 10.1093/jxb/eraa471] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/10/2020] [Indexed: 05/18/2023]
Abstract
In wheat, temperature affects the timing and intensity of stem elongation. Genetic variation for this process is therefore important for adaptation. This study investigates the genetic response to temperature fluctuations during stem elongation and its relationship to phenology and height. Canopy height of 315 wheat genotypes (GABI wheat panel) was scanned twice weekly in the field phenotyping platform (FIP) of ETH Zurich using a LIDAR. Temperature response was modelled using linear regressions between stem elongation and mean temperature in each measurement interval. This led to a temperature-responsive (slope) and a temperature-irresponsive (intercept) component. The temperature response was highly heritable (H2=0.81) and positively related to a later start and end of stem elongation as well as final height. Genome-wide association mapping revealed three temperature-responsive and four temperature-irresponsive quantitative trait loci (QTLs). Furthermore, putative candidate genes for temperature-responsive QTLs were frequently related to the flowering pathway in Arabidopsis thaliana, whereas temperature-irresponsive QTLs corresponded to growth and reduced height genes. In combination with Rht and Ppd alleles, these loci, together with the loci for the timing of stem elongation, accounted for 71% of the variability in height. This demonstrates how high-throughput field phenotyping combined with environmental covariates can contribute to a smarter selection of climate-resilient crops.
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Affiliation(s)
- Lukas Kronenberg
- Crop Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Martin P Boer
- Biometris, Wageningen University & Research, PB Wageningen, The Netherlands
| | - Norbert Kirchgessner
- Crop Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Achim Walter
- Crop Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Andreas Hund
- Crop Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
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Kronenberg L, Yates S, Boer MP, Kirchgessner N, Walter A, Hund A. Temperature response of wheat affects final height and the timing of stem elongation under field conditions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:700-717. [PMID: 33057698 DOI: 10.1101/756700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/10/2020] [Indexed: 05/29/2023]
Abstract
In wheat, temperature affects the timing and intensity of stem elongation. Genetic variation for this process is therefore important for adaptation. This study investigates the genetic response to temperature fluctuations during stem elongation and its relationship to phenology and height. Canopy height of 315 wheat genotypes (GABI wheat panel) was scanned twice weekly in the field phenotyping platform (FIP) of ETH Zurich using a LIDAR. Temperature response was modelled using linear regressions between stem elongation and mean temperature in each measurement interval. This led to a temperature-responsive (slope) and a temperature-irresponsive (intercept) component. The temperature response was highly heritable (H2=0.81) and positively related to a later start and end of stem elongation as well as final height. Genome-wide association mapping revealed three temperature-responsive and four temperature-irresponsive quantitative trait loci (QTLs). Furthermore, putative candidate genes for temperature-responsive QTLs were frequently related to the flowering pathway in Arabidopsis thaliana, whereas temperature-irresponsive QTLs corresponded to growth and reduced height genes. In combination with Rht and Ppd alleles, these loci, together with the loci for the timing of stem elongation, accounted for 71% of the variability in height. This demonstrates how high-throughput field phenotyping combined with environmental covariates can contribute to a smarter selection of climate-resilient crops.
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Affiliation(s)
- Lukas Kronenberg
- Crop Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Martin P Boer
- Biometris, Wageningen University & Research, PB Wageningen, The Netherlands
| | - Norbert Kirchgessner
- Crop Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Achim Walter
- Crop Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Andreas Hund
- Crop Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
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Chen WW, Xu JM, Jin JF, Lou HQ, Fan W, Yang JL. Genome-Wide Transcriptome Analysis Reveals Conserved and Distinct Molecular Mechanisms of Al Resistance in Buckwheat (Fagopyrum esculentum Moench) Leaves. Int J Mol Sci 2017; 18:ijms18091859. [PMID: 28846612 PMCID: PMC5618508 DOI: 10.3390/ijms18091859] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 11/16/2022] Open
Abstract
Being an Al-accumulating crop, buckwheat detoxifies and tolerates Al not only in roots but also in leaves. While much progress has recently been made toward Al toxicity and resistance mechanisms in roots, little is known about the molecular basis responsible for detoxification and tolerance processes in leaves. Here, we carried out transcriptome analysis of buckwheat leaves in response to Al stress (20 µM, 24 h). We obtained 33,931 unigenes with 26,300 unigenes annotated in the NCBI database, and identified 1063 upregulated and 944 downregulated genes under Al stress. Functional category analysis revealed that genes related to protein translation, processing, degradation and metabolism comprised the biological processes most affected by Al, suggesting that buckwheat leaves maintain flexibility under Al stress by rapidly reprogramming their physiology and metabolism. Analysis of genes related to transcription regulation revealed that a large proportion of chromatin-regulation genes are specifically downregulated by Al stress, whereas transcription factor genes are overwhelmingly upregulated. Furthermore, we identified 78 upregulated and 22 downregulated genes that encode transporters. Intriguingly, only a few genes were overlapped with root Al-regulated transporter genes, which include homologs of AtMATE, ALS1, STAR1, ALS3 and a divalent ion symporter. In addition, we identified a subset of genes involved in development, in which genes associated with flowering regulation were important. Based on these data, it is proposed that buckwheat leaves develop conserved and distinct mechanisms to cope with Al toxicity.
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Affiliation(s)
- Wei Wei Chen
- Research Centre for Plant RNA Signaling , College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada.
| | - Jia Meng Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jian Feng Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - He Qiang Lou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Wei Fan
- College of Resource and Environment, Yunnan Agricultural University, Kunming 650201, China.
| | - Jian Li Yang
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada.
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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Ibañez C, Poeschl Y, Peterson T, Bellstädt J, Denk K, Gogol-Döring A, Quint M, Delker C. Ambient temperature and genotype differentially affect developmental and phenotypic plasticity in Arabidopsis thaliana. BMC PLANT BIOLOGY 2017; 17:114. [PMID: 28683779 PMCID: PMC5501000 DOI: 10.1186/s12870-017-1068-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/25/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Global increase in ambient temperatures constitute a significant challenge to wild and cultivated plant species. Forward genetic analyses of individual temperature-responsive traits have resulted in the identification of several signaling and response components. However, a comprehensive knowledge about temperature sensitivity of different developmental stages and the contribution of natural variation is still scarce and fragmented at best. RESULTS Here, we systematically analyze thermomorphogenesis throughout a complete life cycle in ten natural Arabidopsis thaliana accessions grown under long day conditions in four different temperatures ranging from 16 to 28 °C. We used Q10, GxE, phenotypic divergence and correlation analyses to assess temperature sensitivity and genotype effects of more than 30 morphometric and developmental traits representing five phenotype classes. We found that genotype and temperature differentially affected plant growth and development with variing strengths. Furthermore, overall correlations among phenotypic temperature responses was relatively low which seems to be caused by differential capacities for temperature adaptations of individual accessions. CONCLUSION Genotype-specific temperature responses may be attractive targets for future forward genetic approaches and accession-specific thermomorphogenesis maps may aid the assessment of functional relevance of known and novel regulatory components.
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Affiliation(s)
- Carla Ibañez
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Yvonne Poeschl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06099 Halle (Saale), Germany
| | - Tom Peterson
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Julia Bellstädt
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Kathrin Denk
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Andreas Gogol-Döring
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06099 Halle (Saale), Germany
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Carolin Delker
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
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Hill CB, Li C. Genetic Architecture of Flowering Phenology in Cereals and Opportunities for Crop Improvement. FRONTIERS IN PLANT SCIENCE 2016; 7:1906. [PMID: 28066466 PMCID: PMC5165254 DOI: 10.3389/fpls.2016.01906] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/01/2016] [Indexed: 05/21/2023]
Abstract
Cereal crop species including bread wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rice (Oryza sativa L.), and maize (Zea mays L.) provide the bulk of human nutrition and agricultural products for industrial use. These four cereals are central to meet future demands of food supply for an increasing world population under a changing climate. A prerequisite for cereal crop production is the transition from vegetative to reproductive and grain-filling phases starting with flower initiation, a key developmental switch tightly regulated in all flowering plants. Although studies in the dicotyledonous model plant Arabidopsis thaliana build the foundations of our current understanding of plant phenology genes and regulation, the availability of genome assemblies with high-confidence sequences for rice, maize, and more recently bread wheat and barley, now allow the identification of phenology-associated gene orthologs in monocots. Together with recent advances in next-generation sequencing technologies, QTL analysis, mutagenesis, complementation analysis, and RNA interference, many phenology genes have been functionally characterized in cereal crops and conserved as well as functionally divergent genes involved in flowering were found. Epigenetic and other molecular regulatory mechanisms that respond to environmental and endogenous triggers create an enormous plasticity in flowering behavior among cereal crops to ensure flowering is only induced under optimal conditions. In this review, we provide a summary of recent discoveries of flowering time regulators with an emphasis on four cereal crop species (bread wheat, barley, rice, and maize), in particular, crop-specific regulatory mechanisms and genes. In addition, pleiotropic effects on agronomically important traits such as grain yield, impact on adaptation to new growing environments and conditions, genetic sequence-based selection and targeted manipulation of phenology genes, as well as crop growth simulation models for predictive crop breeding, are discussed.
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Affiliation(s)
- Camilla B. Hill
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, PerthWA, Australia
- *Correspondence: Chengdao Li, Camilla B. Hill,
| | - Chengdao Li
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, PerthWA, Australia
- Department of Agriculture and Food Western Australia, South PerthWA, Australia
- *Correspondence: Chengdao Li, Camilla B. Hill,
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