1
|
Li Y, Jin L, Liu X, He C, Bi S, Saeed S, Yan W. Epigenetic control on transcription of vernalization genes and whole-genome gene expression profile induced by vernalization in common wheat. PLANT DIVERSITY 2024; 46:386-394. [PMID: 38798730 PMCID: PMC11119517 DOI: 10.1016/j.pld.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/10/2024] [Accepted: 02/27/2024] [Indexed: 05/29/2024]
Abstract
Vernalization is necessary for winter wheat to flower. However, it is unclear whether vernalization is also required for spring wheat, which is frequently sown in fall, and what molecular mechanisms underlie the vernalization response in wheat varieties. In this study, we examined the molecular mechanisms that regulate vernalization response in winter and spring wheat varieties. For this purpose, we determined how major vernalization genes (VRN1, VRN2, and VRN3) respond to vernalization in these varieties and whether modifications to histones play a role in changes in gene expression. We also identified genes that are differentially regulated in response to vernalization in winter and spring wheat varieties. We found that in winter wheat, but not in spring wheat, VRN1 expression decreases when returned to warm temperature following vernalization. This finding may be associated with differences between spring and winter wheat in the levels of tri-methylation of lysine 27 on histone H3 (H3K27me3) and tri-methylation of lysine 4 on histone H3 (H3K4me3) at the VRN1 gene. Analysis of winter wheat transcriptomes before and after vernalization revealed that vernalization influences the expression of several genes, including those involved in leucine catabolism, cysteine biosynthesis, and flavonoid biosynthesis. These findings provide new candidates for further study on the mechanism of vernalization regulation in wheat.
Collapse
Affiliation(s)
- Yunzhen Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Liujie Jin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyu Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Siteng Bi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Sulaiman Saeed
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Wu L, Li G, Li D, Dong C, Zhang X, Zhang L, Yang Z, Kong X, Xia C, Chen J, Liu X. Identification and functional analysis of a chromosome 2D fragment harboring TaFPF1 gene with the potential for yield improvement using a late heading wheat mutant. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:92. [PMID: 38568320 DOI: 10.1007/s00122-024-04593-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024]
Abstract
KEY MESSAGE A chromosome fragment influencing wheat heading and grain size was identified using mapping of m406 mutant. The study of TaFPF1 in this fragment provides more insights into wheat yield improvement. In recent years, wheat production has faced formidable challenges driven by rapid population growth and climate change, emphasizing the importance of improving specific agronomic traits such as heading date, spike length, and grain size. To identify potential genes for improving these traits, we screened a wheat EMS mutant library and identified a mutant, designated m406, which exhibited a significantly delayed heading date compared to the wild-type. Intriguingly, the mutant also displayed significantly longer spike and larger grain size. Genetic analysis revealed that a single recessive gene was responsible for the delayed heading. Surprisingly, a large 46.58 Mb deletion at the terminal region of chromosome arm 2DS in the mutant was identified through fine mapping and fluorescence in situ hybridization. Thus, the phenotypes of the mutant m406 are controlled by a group of linked genes. This deletion encompassed 917 annotated high-confidence genes, including the previously studied wheat genes Ppd1 and TaDA1, which could affect heading date and grain size. Multiple genes in this region probably contribute to the phenotypes of m406. We further investigated the function of TaFPF1 using gene editing. TaFPF1 knockout mutants showed delayed heading and increased grain size. Moreover, we identified the direct upstream gene of TaFPF1 and investigated its relationship with other important flowering genes. Our study not only identified more genes affecting heading and grain development within this deleted region but also highlighted the potential of combining these genes for improvement of wheat traits.
Collapse
Affiliation(s)
- Lifen Wu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, Sichuan, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chunhao Dong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xueying Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, Sichuan, China
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chuan Xia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jingtang Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China.
| | - Xu Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China.
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
4
|
Bobadilla LK, Tranel PJ. Predicting the unpredictable: the regulatory nature and promiscuity of herbicide cross resistance. PEST MANAGEMENT SCIENCE 2024; 80:235-244. [PMID: 37595061 DOI: 10.1002/ps.7728] [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: 07/14/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/20/2023]
Abstract
The emergence of herbicide-resistant weeds is a significant threat to modern agriculture. Cross resistance, a phenomenon where resistance to one herbicide confers resistance to another, is a particular concern owing to its unpredictability. Nontarget-site (NTS) cross resistance is especially challenging to predict, as it arises from genes that encode enzymes that do not directly involve the herbicide target site and can affect multiple herbicides. Recent advancements in genomic and structural biology techniques could provide new venues for predicting NTS resistance in weed species. In this review, we present an overview of the latest approaches that could be used. We discuss the use of genomic and epigenomics techniques such as ATAC-seq and DAP-seq to identify transcription factors and cis-regulatory elements associated with resistance traits. Enzyme/protein structure prediction and docking analysis are discussed as an initial step for predicting herbicide binding affinities with key enzymes to identify candidates for subsequent in vitro validation. We also provide example analyses that can be deployed toward elucidating cross resistance and its regulatory patterns. Ultimately, our review provides important insights into the latest scientific advancements and potential directions for predicting and managing herbicide cross resistance in weeds. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Collapse
Affiliation(s)
- Lucas K Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| |
Collapse
|
5
|
Madrigal Y, Alzate JF, Pabón-Mora N. Evolution of major flowering pathway integrators in Orchidaceae. PLANT REPRODUCTION 2023:10.1007/s00497-023-00482-7. [PMID: 37823912 DOI: 10.1007/s00497-023-00482-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/10/2023] [Indexed: 10/13/2023]
Abstract
The Orchidaceae is a mega-diverse plant family with ca. 29,000 species with a large variety of life forms that can colonize transitory habitats. Despite this diversity, little is known about their flowering integrators in response to specific environmental factors. During the reproductive transition in flowering plants a vegetative apical meristem (SAM) transforms into an inflorescence meristem (IM) that forms bracts and flowers. In model grasses, like rice, a flowering genetic regulatory network (FGRN) controlling reproductive transitions has been identified, but little is known in the Orchidaceae. In order to analyze the players of the FRGN in orchids, we performed comprehensive phylogenetic analyses of CONSTANS-like/CONSTANS-like 4 (COL/COL4), FLOWERING LOCUS D (FD), FLOWERING LOCUS C/FRUITFULL (FLC/FUL) and SUPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) gene lineages. In addition to PEBP and AGL24/SVP genes previously analyzed, here we identify an increase of orchid homologs belonging to COL4, and FUL gene lineages in comparison with other monocots, including grasses, due to orchid-specific gene lineage duplications. Contrariwise, local duplications in Orchidaceae are less frequent in the COL, FD and SOC1 gene lineages, which points to a retention of key functions under strong purifying selection in essential signaling factors. We also identified changes in the protein sequences after such duplications, variation in the evolutionary rates of resulting paralogous clades and targeted expression of isolated homologs in different orchids. Interestingly, vernalization-response genes like VERNALIZATION1 (VRN1) and FLOWERING LOCUS C (FLC) are completely lacking in orchids, or alternatively are reduced in number, as is the case of VERNALIZATION2/GHD7 (VRN2). Our findings point to non-canonical factors sensing temperature changes in orchids during reproductive transition. Expression data of key factors gathered from Elleanthus auratiacus, a terrestrial orchid in high Andean mountains allow us to characterize which copies are actually active during flowering. Altogether, our data lays down a comprehensive framework to assess gene function of a restricted number of homologs identified more likely playing key roles during the flowering transition, and the changes of the FGRN in neotropical orchids in comparison with temperate grasses.
Collapse
Affiliation(s)
- Yesenia Madrigal
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F Alzate
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
| | - Natalia Pabón-Mora
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia.
| |
Collapse
|
6
|
Rodríguez Del Río Á, Monteagudo A, Contreras-Moreira B, Kiss T, Mayer M, Karsai I, Igartua E, Casas AM. Diversity of gene expression responses to light quality in barley. Sci Rep 2023; 13:17143. [PMID: 37816785 PMCID: PMC10564772 DOI: 10.1038/s41598-023-44263-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 10/05/2023] [Indexed: 10/12/2023] Open
Abstract
Light quality influence on barley development is poorly understood. We exposed three barley genotypes with either sensitive or insensitive response to two light sources producing different light spectra, fluorescent bulbs, and metal halide lamps, keeping constant light intensity, duration, and temperature. Through RNA-seq, we identified the main genes and pathways involved in the genotypic responses. A first analysis identified genotypic differences in gene expression of development-related genes, including photoreceptors and flowering time genes. Genes from the vernalization pathway of light quality-sensitive genotypes were affected by fluorescent light. In particular, vernalization-related repressors reacted differently: HvVRN2 did not experience relevant changes, whereas HvOS2 expression increased under fluorescent light. To identify the genes primarily related to light quality responses, and avoid the confounding effect of plant developmental stage, genes influenced by development were masked in a second analysis. Quantitative expression levels of PPD-H1, which influenced HvVRN1 and HvFT1, explained genotypic differences in development. Upstream mechanisms (light signaling and circadian clock) were also altered, but no specific genes linking photoreceptors and the photoperiod pathway were identified. The variety of light-quality sensitivities reveals the presence of possible mechanisms of adaptation of winter and facultative barley to latitudinal variation in light quality, which deserves further research.
Collapse
Affiliation(s)
- Álvaro Rodríguez Del Río
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
- Centro de Biotecnología y Genómica de Plantas, UPM/INIA-CSIC, Madrid, Spain
| | - Arantxa Monteagudo
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
| | - Bruno Contreras-Moreira
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
- Fundación ARAID, Zaragoza, Spain
| | - Tibor Kiss
- Centre for Agriculture Research ELKH (ATK), Martonvásár, Hungary
- Center for Research and Development, Food and Wine Center of Excellence, Eszterházy Károly Catholic University, Eger, Hungary
| | - Marianna Mayer
- Centre for Agriculture Research ELKH (ATK), Martonvásár, Hungary
| | - Ildikó Karsai
- Centre for Agriculture Research ELKH (ATK), Martonvásár, Hungary
| | - Ernesto Igartua
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain.
| | - Ana M Casas
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
| |
Collapse
|
7
|
Contreras-Moreira B, Saraf S, Naamati G, Casas AM, Amberkar SS, Flicek P, Jones AR, Dyer S. GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation. Genome Biol 2023; 24:223. [PMID: 37798615 PMCID: PMC10552430 DOI: 10.1186/s13059-023-03071-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/21/2023] [Indexed: 10/07/2023] Open
Abstract
Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent identifiers hamper their exploration. To address this, we define pangenes, which summarize a species coding potential and link back to original annotations. The protocol get_pangenes performs whole genome alignments (WGA) to call syntenic gene models based on coordinate overlaps. A benchmark with small and large plant genomes shows that pangenes recapitulate phylogeny-based orthologies and produce complete soft-core gene sets. Moreover, WGAs support lift-over and help confirm gene presence-absence variation. Source code and documentation: https://github.com/Ensembl/plant-scripts .
Collapse
Affiliation(s)
- Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
- Estación Experimental Aula Dei-CSIC, 50059, Zaragoza, Spain.
| | - Shradha Saraf
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Ana M Casas
- Estación Experimental Aula Dei-CSIC, 50059, Zaragoza, Spain
| | - Sandeep S Amberkar
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Andrew R Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| |
Collapse
|
8
|
Liu S, Chen S, Zhou Y, Shen Y, Qin Z, Wu L. VERNALIZATION1 represses FLOWERING PROMOTING FACTOR1-LIKE1 in leaves for timely flowering in Brachypodium distachyon. THE PLANT CELL 2023; 35:3697-3711. [PMID: 37378548 PMCID: PMC10533335 DOI: 10.1093/plcell/koad190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/01/2023] [Accepted: 06/26/2023] [Indexed: 06/29/2023]
Abstract
FLOWERING PROMOTING FACTOR1 (FPF1), a small protein without any known domains, promotes flowering in several plants; however, its functional mechanism remains unknown. Here, we characterized 2 FPF1-like proteins, FPL1 and FPL7, which, in contrast, function as flowering repressors in Brachypodium distachyon. FPL1 and FPL7 interact with the components of the florigen activation complex (FAC) and inhibit FAC activity to restrict expression of its critical target, VERNALIZATION1 (VRN1), in leaves, thereby preventing overaccumulation of FLOWERING LOCUS T1 (FT1) at the juvenile stage. Further, VRN1 can directly bind to the FPL1 promoter and repress FPL1 expression; hence, as VRN1 gradually accumulates during the late vegetative stage, FAC is released. This accurate feedback regulation of FPL1 by VRN1 allows proper FT1 expression in leaves and ensures sufficient FAC formation in shoot apical meristems to trigger timely flowering. Overall, we define a sophisticated modulatory loop for flowering initiation in a temperate grass, providing insights toward resolving the molecular basis underlying fine-tuning flowering time in plants.
Collapse
Affiliation(s)
- Shu Liu
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Siyi Chen
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yang Zhou
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuxin Shen
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhengrui Qin
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Liang Wu
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Hainan Yazhou Bay Seed Laboratory, Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China
| |
Collapse
|
9
|
Gramzow L, Sharma R, Theißen G. Evolutionary Dynamics of FLC-like MADS-Box Genes in Brassicaceae. PLANTS (BASEL, SWITZERLAND) 2023; 12:3281. [PMID: 37765445 PMCID: PMC10536770 DOI: 10.3390/plants12183281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
MADS-box genes encode transcription factors that play important roles in the development and evolution of plants. There are more than a dozen clades of MADS-box genes in angiosperms, of which those with functions in the specification of floral organ identity are especially well-known. From what has been elucidated in the model plant Arabidopsis thaliana, the clade of FLC-like MADS-box genes, comprising FLC-like genes sensu strictu and MAF-like genes, are somewhat special among the MADS-box genes of plants since FLC-like genes, especially MAF-like genes, show unusual evolutionary dynamics, in that they generate clusters of tandemly duplicated genes. Here, we make use of the latest genomic data of Brassicaceae to study this remarkable feature of the FLC-like genes in a phylogenetic context. We have identified all FLC-like genes in the genomes of 29 species of Brassicaceae and reconstructed the phylogeny of these genes employing a Maximum Likelihood method. In addition, we conducted selection analyses using PAML. Our results reveal that there are three major clades of FLC-like genes in Brassicaceae that all evolve under purifying selection but with remarkably different strengths. We confirm that the tandem arrangement of MAF-like genes in the genomes of Brassicaceae resulted in a high rate of duplications and losses. Interestingly, MAF-like genes also seem to be prone to transposition. Considering the role of FLC-like genes sensu lato (s.l.) in the timing of floral transition, we hypothesize that this rapid evolution of the MAF-like genes was a main contributor to the successful adaptation of Brassicaceae to different environments.
Collapse
Affiliation(s)
- Lydia Gramzow
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | | | | |
Collapse
|
10
|
Huang X, Wang J, Xia L, Chen C, Wang M, Lu J, Lu T, Li K, Liang R, He X, Luo C. Functional studies of four MiFPF genes in mango revealed their function in promoting flowering in transgenic Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2023; 285:153994. [PMID: 37105044 DOI: 10.1016/j.jplph.2023.153994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/19/2023] [Accepted: 04/20/2023] [Indexed: 05/22/2023]
Abstract
Flowering promoting factor (FPF) genes play a substantial regulatory role in the process of flowering. In the present study, four MiFPF genes, namely, MiFPF1, MiFPF2, MiFPF3a, and MiFPF3b, were obtained from mango (Mangifera indica L.). Tissue expression analysis showed that MiFPFs were expressed in all mango tissues. Specifically, MiFPF1 and MiFPF2 were highly expressed in leaves, while MiFPF3a and MiFPF3b were highly expressed in flowers and buds. The four MiFPF proteins localize to the nucleus. Overexpression of MiFPFs in transgenic Arabidopsis resulted in early flowering and upregulated the expression of APETAL1 (AP1), FLOWERING LOCUS D (FD) and FLOWERING LOCUS T (FT). MiFPF genes increased the root growth of transgenic Arabidopsis plants under gibberellin treatment. BiFC assays showed that MiFPFs can interact with several DELLA proteins. Taken together, our results demonstrate that the MiFPF gene was involved not only in promoting flowering but also in increasing root growth under gibberellin (GA3) treatment.
Collapse
Affiliation(s)
- Xing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Jingzun Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Liming Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Canni Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Meng Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Jiamei Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Tingting Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Kaijiang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Rongzhen Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Xinhua He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China.
| | - Cong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China.
| |
Collapse
|
11
|
Gao H, Suo X, Zhao L, Ma X, Cheng R, Wang G, Zhang H. Molecular evolution, diversification, and expression assessment of MADS gene family in Setaria italica, Setaria viridis, and Panicum virgatum. PLANT CELL REPORTS 2023; 42:1003-1024. [PMID: 37012438 DOI: 10.1007/s00299-023-03009-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/20/2023] [Indexed: 05/12/2023]
Abstract
KEY MESSAGE This paper sheds light on the evolution and expression patterns of MADS genes in Setaria and Panicum virgatum. SiMADS51 and SiMADS64 maybe involved in the ABA-dependent pathway of drought response. The MADS gene family is a key regulatory factor family that controls growth, reproduction, and response to abiotic stress in plants. However, the molecular evolution of this family is rarely reported. Here, a total of 265 MADS genes were identified in Setaria italica (foxtail millet), Setaria viridis (green millet), and Panicum virgatum (switchgrass) and analyzed by bioinformatics, including physicochemical characteristics, subcellular localization, chromosomal position and duplicate, motif distribution, genetic structure, genetic evolvement, and expression patterns. Phylogenetic analysis was used to categorize these genes into M and MIKC types. The distribution of motifs and gene structure were similar for the corresponding types. According to a collinearity study, the MADS genes have been mostly conserved during evolution. The principal cause of their expansion is segmental duplication. However, the MADS gene family tends to shrink in foxtail millet, green millet, and switchgrass. The MADS genes were subjected to purifying selection, but several positive selection sites were also identified in three species. And most of the promoters of MADS genes contain cis-elements related to stress and hormonal response. RNA-seq and quantitative Real-time PCR (qRT-PCR) analysis also were examined. SiMADS genes expression levels are considerably changed in reaction to various treatments, following qRT-PCR analysis. This sheds fresh light on the evolution and expansion of the MADS family in foxtail millet, green millet, and switchgrass, and lays the foundation for further research on their functions.
Collapse
Affiliation(s)
- Hui Gao
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Department of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, Hebei, China
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Xiaoman Suo
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Department of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, Hebei, China
| | - Ling Zhao
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Xinlei Ma
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Department of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, Hebei, China
| | - Ruhong Cheng
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
| | - Genping Wang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
| | - Haoshan Zhang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
- Chinese Academy of Agricultural Sciences Institute of Crop Sciences, Beijing, 100081, China.
| |
Collapse
|
12
|
Wang F, Zhou Z, Zhu L, Gu Y, Guo B, Lv C, Zhu J, Xu R. Genome-wide analysis of the MADS-box gene family involved in salt and waterlogging tolerance in barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1178065. [PMID: 37229117 PMCID: PMC10203460 DOI: 10.3389/fpls.2023.1178065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/07/2023] [Indexed: 05/27/2023]
Abstract
MADS-box transcription factors are crucial members of regulatory networks underlying multiple developmental pathways and abiotic stress regulatory networks in plants. Studies on stress resistance-related functions of MADS-box genes are very limited in barley. To gain insight into this gene family and elucidate their roles in salt and waterlogging stress resistance, we performed genome-wide identification, characterization and expression analysis of MADS-box genes in barley. A whole-genome survey of barley revealed 83 MADS-box genes, which were categorized into type I (Mα, Mβ and Mγ) and type II (AP1, SEP1, AGL12, STK, AGL16, SVP and MIKC*) lineages based on phylogeny, protein motif structure. Twenty conserved motifs were determined and each HvMADS contained one to six motifs. We also found tandem repeat duplication was the driven force for HvMADS gene family expansion. Additionally, the co-expression regulatory network of 10 and 14 HvMADS genes was predicted in response to salt and waterlogging stress, and we proposed HvMADS11,13 and 35 as candidate genes for further exploration of the functions in abiotic stress. The extensive annotations and transcriptome profiling reported in this study ultimately provides the basis for MADS functional characterization in genetic engineering of barley and other gramineous crops.
Collapse
|
13
|
Chirivì D, Betti C. Molecular Links between Flowering and Abiotic Stress Response: A Focus on Poaceae. PLANTS (BASEL, SWITZERLAND) 2023; 12:331. [PMID: 36679044 PMCID: PMC9866591 DOI: 10.3390/plants12020331] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Extreme temperatures, drought, salinity and soil pollution are the most common types of abiotic stresses crops can encounter in fields; these variations represent a general warning to plant productivity and survival, being more harmful when in combination. Plant response to such conditions involves the activation of several molecular mechanisms, starting from perception to signaling, transcriptional reprogramming and protein modifications. This can influence the plant's life cycle and development to different extents. Flowering developmental transition is very sensitive to environmental stresses, being critical to reproduction and to agricultural profitability for crops. The Poacee family contains some of the most widespread domesticated plants, such as wheat, barley and rice, which are commonly referred to as cereals and represent a primary food source. In cultivated Poaceae, stress-induced modifications of flowering time and development cause important yield losses by directly affecting seed production. At the molecular level, this reflects important changes in gene expression and protein activity. Here, we present a comprehensive overview on the latest research investigating the molecular pathways linking flowering control to osmotic and temperature extreme conditions in agronomically relevant monocotyledons. This aims to provide hints for biotechnological strategies that can ensure agricultural stability in ever-changing climatic conditions.
Collapse
|
14
|
Wheat genomic study for genetic improvement of traits in China. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1718-1775. [PMID: 36018491 DOI: 10.1007/s11427-022-2178-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.
Collapse
|
15
|
Preston JC, Fjellheim S. Flowering time runs hot and cold. PLANT PHYSIOLOGY 2022; 190:5-18. [PMID: 35274728 PMCID: PMC9434294 DOI: 10.1093/plphys/kiac111] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/13/2022] [Indexed: 05/16/2023]
Abstract
Evidence suggests that anthropogenically-mediated global warming results in accelerated flowering for many plant populations. However, the fact that some plants are late flowering or unaffected by warming, underscores the complex relationship between phase change, temperature, and phylogeny. In this review, we present an emerging picture of how plants sense temperature changes, and then discuss the independent recruitment of ancient flowering pathway genes for the evolution of ambient, low, and high temperature-regulated reproductive development. As well as revealing areas of research required for a better understanding of how past thermal climates have shaped global patterns of plasticity in plant phase change, we consider the implications for these phenological thermal responses in light of climate change.
Collapse
Affiliation(s)
| | - Siri Fjellheim
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås 1430, Norway
| |
Collapse
|
16
|
Cha JK, O'Connor K, Alahmad S, Lee JH, Dinglasan E, Park H, Lee SM, Hirsz D, Kwon SW, Kwon Y, Kim KM, Ko JM, Hickey LT, Shin D, Dixon LE. Speed vernalization to accelerate generation advance in winter cereal crops. MOLECULAR PLANT 2022; 15:1300-1309. [PMID: 35754174 DOI: 10.1016/j.molp.2022.06.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/02/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
There are many challenges facing the development of high-yielding, nutritious crops for future environments. One limiting factor is generation time, which prolongs research and plant breeding timelines. Recent advances in speed breeding protocols have dramatically reduced generation time for many short-day and long-day species by optimizing light and temperature conditions during plant growth. However, winter crops with a vernalization requirement still require up to 6-10 weeks in low-temperature conditions before the transition to reproductive development. Here, we tested a suite of environmental conditions and protocols to investigate whether the vernalization process can be accelerated. We identified a vernalization method consisting of exposing seeds at the soil surface to an extended photoperiod of 22 h day:2 h night at 10°C with transfer to speed breeding conditions that dramatically reduces generation time in both winter wheat (Triticum aestivum) and winter barley (Hordeum vulgare). Implementation of the speed vernalization protocol followed by speed breeding allowed the completion of up to five generations per year for winter wheat or barley, whereas only two generations can be typically completed under standard vernalization and plant growth conditions. The speed vernalization protocol developed in this study has great potential to accelerate biological research and breeding outcomes for winter crops.
Collapse
Affiliation(s)
- Jin-Kyung Cha
- National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Kathryn O'Connor
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Samir Alahmad
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Jong-Hee Lee
- National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Eric Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Hyeonjin Park
- National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - So-Myeong Lee
- National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Dominique Hirsz
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Soon-Wook Kwon
- Department of Plant Bioscience, Pusan National University, Miryang 60463, Korea
| | - Youngho Kwon
- National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Kyeong-Min Kim
- National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Jong-Min Ko
- National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia.
| | - Dongjin Shin
- National Institute of Crop Science, RDA, Miryang 50424, Korea.
| | - Laura E Dixon
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| |
Collapse
|
17
|
Fernández-Calleja M, Ciudad FJ, Casas AM, Igartua E. Hybrids Provide More Options for Fine-Tuning Flowering Time Responses of Winter Barley. FRONTIERS IN PLANT SCIENCE 2022; 13:827701. [PMID: 35432439 PMCID: PMC9011329 DOI: 10.3389/fpls.2022.827701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Crop adaptation requires matching resource availability to plant development. Tight coordination of the plant cycle with prevailing environmental conditions is crucial to maximizing yield. It is expected that winters in temperate areas will become warmer, so the vernalization requirements of current cultivars can be desynchronized with the environment's vernalizing potential. Therefore, current phenological ideotypes may not be optimum for future climatic conditions. Major genes conferring vernalization sensitivity and phenological responses in barley (Hordeum vulgare L.) are known, but some allelic combinations remain insufficiently evaluated. Furthermore, there is a lack of knowledge about flowering time in a hybrid context. To honor the promise of increased yield potentials, hybrid barley phenology must be studied, and the knowledge deployed in new cultivars. A set of three male and two female barley lines, as well as their six F1 hybrids, were studied in growth chambers, subjected to three vernalization treatments: complete (8 weeks), moderate (4 weeks), and low (2 weeks). Development was recorded up to flowering, and expression of major genes was assayed at key stages. We observed a gradation in responses to vernalization, mostly additive, concentrated in the phase until the initiation of stem elongation, and proportional to the allele constitution and dosage present in VRN-H1. These responses were further modulated by the presence of PPD-H2. The duration of the late reproductive phase presented more dominance toward earliness and was affected by the rich variety of alleles at VRN-H3. Our results provide further opportunities for fine-tuning total and phasal growth duration in hybrid barley, beyond what is currently feasible in inbred cultivars.
Collapse
Affiliation(s)
- Miriam Fernández-Calleja
- Department of Genetics and Plant Production, Aula Dei Experimental Station - Spanish National Research Council (EEAD-CSIC), Zaragoza, Spain
| | - Francisco J. Ciudad
- Agricultural Technology Institute of Castilla and León (ITACYL), Valladolid, Spain
| | - Ana M. Casas
- Department of Genetics and Plant Production, Aula Dei Experimental Station - Spanish National Research Council (EEAD-CSIC), Zaragoza, Spain
| | - Ernesto Igartua
- Department of Genetics and Plant Production, Aula Dei Experimental Station - Spanish National Research Council (EEAD-CSIC), Zaragoza, Spain
| |
Collapse
|
18
|
Fritsche S, Rippel Salgado L, Boron AK, Hanning KR, Donaldson LA, Thorlby G. Transcriptional Regulation of Pine Male and Female Cone Initiation and Development: Key Players Identified Through Comparative Transcriptomics. Front Genet 2022; 13:815093. [PMID: 35368695 PMCID: PMC8971679 DOI: 10.3389/fgene.2022.815093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/24/2022] [Indexed: 11/24/2022] Open
Abstract
With long reproductive timescales, large complex genomes, and a lack of reliable reference genomes, understanding gene function in conifers is extremely challenging. Consequently, our understanding of which genetic factors influence the development of reproductive structures (cones) in monoecious conifers remains limited. Genes with inferred roles in conifer reproduction have mostly been identified through homology and phylogenetic reconstruction with their angiosperm counterparts. We used RNA-sequencing to generate transcriptomes of the early morphological stages of cone development in the conifer species Pinus densiflora and used these to gain a deeper insight into the transcriptional changes during male and female cone development. Paired-end Illumina sequencing was used to generate transcriptomes from non-reproductive tissue and male and female cones at four time points with a total of 382.82 Gbp of data generated. After assembly and stringent filtering, a total of 37,164 transcripts were retrieved, of which a third were functionally annotated using the Mercator plant pipeline. Differentially expressed gene (DEG) analysis resulted in the identification of 172,092 DEGs in the nine tissue types. This, alongside GO gene enrichment analyses, pinpointed transcripts putatively involved in conifer reproductive structure development, including co-orthologs of several angiosperm flowering genes and several that have not been previously reported in conifers. This study provides a comprehensive transcriptome resource for male and early female cone development in the gymnosperm species Pinus densiflora. Characterisation of this resource has allowed the identification of potential key players and thus provides valuable insights into the molecular regulation of reproductive structure development in monoecious conifers.
Collapse
Affiliation(s)
- Steffi Fritsche
- Forest Genetics and Biotechnology, Scion, Rotorua, New Zealand
| | - Leonardo Rippel Salgado
- Forest Genetics and Biotechnology, Scion, Rotorua, New Zealand
- Molecular and Digital Breeding, The New Zealand Institute for Plant and Food Research, Te Puke, New Zealand
| | | | | | | | - Glenn Thorlby
- Forest Genetics and Biotechnology, Scion, Rotorua, New Zealand
- *Correspondence: Glenn Thorlby,
| |
Collapse
|
19
|
Time-course transcriptome profiling revealed the specific expression patterns of MADS-box genes associated with the distinct developmental processes between winter and spring wheat. Gene 2022; 809:146030. [PMID: 34673213 DOI: 10.1016/j.gene.2021.146030] [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: 01/08/2021] [Revised: 07/02/2021] [Accepted: 10/14/2021] [Indexed: 11/23/2022]
Abstract
The shoot apex is a region where new cells are produced and elongate. The developmental state of the wheat shoot apex under low temperature affects its cold resistance. In this study, the morphology of shoot apex before overwintering was characterized for 24 wheat line with different winter and spring characteristics. Our research showed that the shoot apex of autumn-sown spring wheat lines reached the temperature sensitive double-ridge stage before overwintering, whereas shoot apex of winter wheat lines are found in temperature-insensitive vegetative or elongation stages. In order to explore how gene expression is associated with shoot apex differentiation in winter and spring wheat, we used strand-specific RNA sequencing to profile the gene expression patterns at four time-points between 14 after germination and 45 days after germination in the winter wheat cultivar Dongnongdongmai No. 1 (DM1) and in the spring wheat cultivar China Spring (CS). We identified 11,848 differentially expressed genes between the two cultivars. Most up-regulated genes in CS were involved in energy metabolism and transport during the seedling stage, whereas up-regulated genes in DM1 were involved in protein and DNA synthesis. MADS-box genes affect plant growth and development. In this study, MADS-boxes with differential expression between CS and DM1 were screened and evolutionary tree analysis was conducted. During all sampling periods, CS highly expressed MADS-box genes that induce flowering promotion genes such as VRN1, VRT and AG, while lowly expressed MADS-box genes that induce flowering-inhibiting homologous genes such as SVP. TaVRN1 composition in DM1 and CS was vrn-A1, vrn-B1, and Vrn-D1b. Analysis of the sequence of TaVRN1 (TraesCS5A01G391700) from DM1 and CS revealed 5 SNP differences in the promoter regions and 3 SNP deletions in the intron regions. The expression levels of cold resistant genes in DM1 were significantly higher than those in CS at seedling stage (neither DM1 nor CS experienced cold in this study), including CBF, cold induced protein,acid desaturase and proline rich proteins. Additionally, the expression levels of auxin-related genes were significantly higher in CS than those in DM1 at 45 days after germination. Our study identified candidate genes associated with the process of differentiation of the shoot apex in winter and spring wheat at the seedling stage and also raised an internal stress tolerance model for winter wheat to endogenously anticipate the coming stressful conditions in winter.
Collapse
|
20
|
Raza Q, Riaz A, Atif RM, Hussain B, Rana IA, Ali Z, Budak H, Alaraidh IA. Genome-Wide Diversity of MADS-Box Genes in Bread Wheat is Associated with its Rapid Global Adaptability. Front Genet 2022; 12:818880. [PMID: 35111207 PMCID: PMC8801776 DOI: 10.3389/fgene.2021.818880] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022] Open
Abstract
MADS-box gene family members play multifarious roles in regulating the growth and development of crop plants and hold enormous promise for bolstering grain yield potential under changing global environments. Bread wheat (Triticum aestivum L.) is a key stable food crop around the globe. Until now, the available information concerning MADS-box genes in the wheat genome has been insufficient. Here, a comprehensive genome-wide analysis identified 300 high confidence MADS-box genes from the publicly available reference genome of wheat. Comparative phylogenetic analyses with Arabidopsis and rice MADS-box genes classified the wheat genes into 16 distinct subfamilies. Gene duplications were mainly identified in subfamilies containing unbalanced homeologs, pointing towards a potential mechanism for gene family expansion. Moreover, a more rapid evolution was inferred for M-type genes, as compared with MIKC-type genes, indicating their significance in understanding the evolutionary history of the wheat genome. We speculate that subfamily-specific distal telomeric duplications in unbalanced homeologs facilitate the rapid adaptation of wheat to changing environments. Furthermore, our in-silico expression data strongly proposed MADS-box genes as active guardians of plants against pathogen insurgency and harsh environmental conditions. In conclusion, we provide an entire complement of MADS-box genes identified in the wheat genome that could accelerate functional genomics efforts and possibly facilitate bridging gaps between genotype-to-phenotype relationships through fine-tuning of agronomically important traits.
Collapse
Affiliation(s)
- Qasim Raza
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Pakistan
- *Correspondence: Qasim Raza, ; Ibrahim A. Alaraidh,
| | - Awais Riaz
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Pakistan
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
- Precision Agriculture and Analytics Lab, National Centre for Big Data and Cloud Computing, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Babar Hussain
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Iqrar Ahmad Rana
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Hikmet Budak
- Montana BioAgriculture, Inc., Missoula, MT, United States
| | - Ibrahim A. Alaraidh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
- *Correspondence: Qasim Raza, ; Ibrahim A. Alaraidh,
| |
Collapse
|
21
|
Bahrani H, Båga M, Larsen J, Graf RJ, Laroche A, Chibbar RN. The Relationships between Plant Developmental Traits and Winter Field Survival in Rye (Secale cereale L.). PLANTS 2021; 10:plants10112455. [PMID: 34834817 PMCID: PMC8625450 DOI: 10.3390/plants10112455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 11/17/2022]
Abstract
Overwintering cereals accumulate low temperature tolerance (LTT) during cold acclimation in the autumn. Simultaneously, the plants adjust to the colder season by making developmental changes at the shoot apical meristem. These processes lead to higher winter hardiness in winter rye varieties (Secale cereale L.) adapted to Northern latitudes as compared to other cereal crops. To dissect the winter-hardiness trait in rye, a panel of 96 genotypes of different origins and growth habits was assessed for winter field survival (WFS), LTT, and six developmental traits. Best Linear Unbiased Estimates for WFS determined from five field trials correlated strongly with LTT (r = 0.90, p < 0.001); thus, cold acclimation efficiency was the major contributor to WFS. WFS also correlated strongly (p < 0.001) with final leaf number (r = 0.80), prostrate growth habit (r = 0.61), plant height (r = 0.34), but showed weaker associations with top internode length (r = 0.30, p < 0.01) and days to anthesis (r = 0.25, p < 0.05). The heritability estimates (h2) for WFS-associated traits ranged from 0.45 (prostrate growth habit) to 0.81 (final leaf number) and were overall higher than for WFS (h2 = 0.48). All developmental traits associated with WFS and LTT are postulated to be regulated by phytohormone levels at shoot apical meristem.
Collapse
Affiliation(s)
- Hirbod Bahrani
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada; (H.B.); (M.B.)
| | - Monica Båga
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada; (H.B.); (M.B.)
| | - Jamie Larsen
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Harrow, ON N0R 1G0, Canada;
| | - Robert J. Graf
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (R.J.G.); (A.L.)
| | - Andre Laroche
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (R.J.G.); (A.L.)
| | - Ravindra N. Chibbar
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada; (H.B.); (M.B.)
- Correspondence:
| |
Collapse
|
22
|
Hirsz D, Dixon LE. The Roles of Temperature-Related Post-Transcriptional Regulation in Cereal Floral Development. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112230. [PMID: 34834593 PMCID: PMC8620327 DOI: 10.3390/plants10112230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/02/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Temperature is a critical environmental signal in the regulation of plant growth and development. The temperature signal varies across a daily 24 h period, between seasons and stochastically depending on local environmental events. Extracting important information from these complex signals has led plants to evolve multiple temperature responsive regulatory mechanisms at the molecular level. In temperate cereals, we are starting to identify and understand these molecular mechanisms. In addition, we are developing an understanding of how this knowledge can be used to increase the robustness of crop yield in response to significant changes in local and global temperature patterns. To enable this, it is becoming apparent that gene regulation, regarding expression and post-transcriptional regulation, is crucial. Large transcriptomic studies are identifying global changes in spliced transcript variants and regulatory non-coding RNAs in response to seasonal and stress temperature signals in many of the cereal crops. Understanding the functions of these variants and targets of the non-coding RNAs will greatly increase how we enable the adaptation of crops. This review considers our current understanding and areas for future development.
Collapse
|
23
|
Penfield S, Warner S, Wilkinson L. Molecular responses to chilling in a warming climate and their impacts on plant reproductive development and yield. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab375. [PMID: 34409451 DOI: 10.1093/jxb/erab375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Indexed: 06/13/2023]
Abstract
Responses to prolonged winter chilling are universal in temperate plants which use seasonal temperature cues in the seed, vegetative and reproductive phases to align development with the earth's orbit. Climate change is driving a decline in reliable winter chill and affecting the sub-tropical extent of cultivation for temperate over-wintering crops. Here we explore molecular aspects of plant responses to winter chill including seasonal bud break and flowering, and how variation in the intensity of winter chilling or de-vernalisation can lead to effects on post-chilling plant development, including that of structures necessary for crop yields.
Collapse
Affiliation(s)
- Steven Penfield
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Samuel Warner
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Laura Wilkinson
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| |
Collapse
|
24
|
Sharma N, Geuten K, Giri BS, Varma A. The molecular mechanism of vernalization in Arabidopsis and cereals: role of Flowering Locus C and its homologs. PHYSIOLOGIA PLANTARUM 2020; 170:373-383. [PMID: 32623749 DOI: 10.1111/ppl.13163] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/25/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
Winter varieties of plants can flower only after exposure to prolonged cold. This phenomenon is known as vernalization and has been widely studied in the model plant Arabidopsis thaliana as well as in monocots. Through the repression of floral activator genes, vernalization prevents flowering in winter. In Arabidopsis, FLOWERING LOCUS C or FLC is the key repressor during vernalization, while in monocots vernalization is regulated through VRN1, VRN2 and VRN3 (or FLOWERING LOCUS T). Interestingly, VRN genes are not homologous to FLC but FLC homologs are found to have a significant role in vernalization response in cereals. The presence of FLC homologs in monocots opens new dimensions to understand, compare and retrace the evolution of vernalization pathways between monocots and dicots. In this review, we discuss the molecular mechanism of vernalization-induced flowering along with epigenetic regulations in Arabidopsis and temperate cereals. A better understanding of cold-induced flowering will be helpful in crop breeding strategies to modify the vernalization requirement of economically important temperate cereals.
Collapse
Affiliation(s)
- Neha Sharma
- Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Koen Geuten
- Department of Biology, KU Leuven, Leuven, B-3001, Belgium
| | - Balendu Shekhar Giri
- Department of Chemical Engineering and Technology, Indian Institute of Technology (IIT-BHU), Varanasi, Uttar Pradesh, 221005, India
| | - Ajit Varma
- Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, 201313, India
| |
Collapse
|
25
|
Jacott CN, Boden SA. Feeling the heat: developmental and molecular responses of wheat and barley to high ambient temperatures. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5740-5751. [PMID: 32667992 PMCID: PMC7540836 DOI: 10.1093/jxb/eraa326] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/10/2020] [Indexed: 05/22/2023]
Abstract
The increasing demand for global food security in the face of a warming climate is leading researchers to investigate the physiological and molecular responses of cereals to rising ambient temperatures. Wheat and barley are temperate cereals whose yields are adversely affected by high ambient temperatures, with each 1 °C increase above optimum temperatures reducing productivity by 5-6%. Reproductive development is vulnerable to high-temperature stress, which reduces yields by decreasing grain number and/or size and weight. In recent years, analysis of early inflorescence development and genetic pathways that control the vegetative to floral transition have elucidated molecular processes that respond to rising temperatures, including those involved in the vernalization- and photoperiod-dependent control of flowering. In comparison, our understanding of genes that underpin thermal responses during later developmental stages remains poor, thus highlighting a key area for future research. This review outlines the responses of developmental genes to warmer conditions and summarizes our knowledge of the reproductive traits of wheat and barley influenced by high temperatures. We explore ways in which recent advances in wheat and barley research capabilities could help identify genes that underpin responses to rising temperatures, and how improved knowledge of the genetic regulation of reproduction and plant architecture could be used to develop thermally resilient cultivars.
Collapse
Affiliation(s)
- Catherine N Jacott
- Department of Crop Genetics, John Innes Centre, Colney Lane, Norwich, UK
| | - Scott A Boden
- Department of Crop Genetics, John Innes Centre, Colney Lane, Norwich, UK
- School of Agriculture, Food and Wine, Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, SA, Australia
- Correspondence:
| |
Collapse
|
26
|
Osnato M, Matias-Hernandez L, Aguilar-Jaramillo AE, Kater MM, Pelaz S. Genes of the RAV Family Control Heading Date and Carpel Development in Rice. PLANT PHYSIOLOGY 2020; 183:1663-1680. [PMID: 32554473 PMCID: PMC7401134 DOI: 10.1104/pp.20.00562] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/03/2020] [Indexed: 05/11/2023]
Abstract
In plants, correct formation of reproductive organs is critical for successful seedset and perpetuation of the species. Plants have evolved different molecular mechanisms to coordinate flower and seed development at the proper time of the year. Among the plant-specific RELATED TO ABI3 AND VP1 (RAV) family of transcription factors, only TEMPRANILLO1 (TEM1) and TEM2 have been shown to affect reproductive development in Arabidopsis (Arabidopsis thaliana). They negatively regulate the floral transition through direct repression of FLOWERING LOCUS T and GIBBERELLIN 3-OXIDASE1/2, encoding major components of the florigen. Here we identify RAV genes from rice (Oryza sativa), and unravel their regulatory roles in key steps of reproductive development. Our data strongly suggest that, like TEMs, OsRAV9/OsTEM1 has a conserved function as a repressor of photoperiodic flowering upstream of the floral activators OsMADS14 and Hd3a, through a mechanism reminiscent of that one underlying floral transition in temperate cereals. Furthermore, OsRAV11 and OsRAV12 may have acquired a new function in the differentiation of the carpel and the control of seed size, acting downstream of floral homeotic factors. Alternatively, this function may have been lost in Arabidopsis. Our data reveal conservation of RAV gene function in the regulation of flowering time in monocotyledonous and dicotyledonous plants, but also unveil roles in the development of rice gynoecium.
Collapse
Affiliation(s)
- Michela Osnato
- Centre for Research in Agricultural Genomics, Centro de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universidad Autónoma de Barcelona-Universidad de Barcelona, Campus Universidad Autónoma de Barcelona, 08193 Barcelona, Spain
- Department BioSciences, University of Milan, 20133 Milan, Italy
| | - Luis Matias-Hernandez
- Centre for Research in Agricultural Genomics, Centro de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universidad Autónoma de Barcelona-Universidad de Barcelona, Campus Universidad Autónoma de Barcelona, 08193 Barcelona, Spain
| | - Andrea Elizabeth Aguilar-Jaramillo
- Centre for Research in Agricultural Genomics, Centro de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universidad Autónoma de Barcelona-Universidad de Barcelona, Campus Universidad Autónoma de Barcelona, 08193 Barcelona, Spain
| | - Martin M Kater
- Department BioSciences, University of Milan, 20133 Milan, Italy
| | - Soraya Pelaz
- Centre for Research in Agricultural Genomics, Centro de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universidad Autónoma de Barcelona-Universidad de Barcelona, Campus Universidad Autónoma de Barcelona, 08193 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| |
Collapse
|
27
|
Phenology and related traits for wheat adaptation. Heredity (Edinb) 2020; 125:417-430. [PMID: 32457509 PMCID: PMC7784700 DOI: 10.1038/s41437-020-0320-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 11/09/2022] Open
Abstract
Wheat is a major food crop, with around 765 million tonnes produced globally. The largest wheat producers include the European Union, China, India, Russia, United States, Canada, Pakistan, Australia, Ukraine and Argentina. Cultivation of wheat across such diverse global environments with variation in climate, biotic and abiotic stresses, requires cultivars adapted to a range of growing conditions. One intrinsic way that wheat achieves adaptation is through variation in phenology (seasonal timing of the lifecycle) and related traits (e.g., those affecting plant architecture). It is important to understand the genes that underlie this variation, and how they interact with each other, other traits and the growing environment. This review summarises the current understanding of phenology and developmental traits that adapt wheat to different environments. Examples are provided to illustrate how different combinations of alleles can facilitate breeding of wheat varieties with optimal crop performance for different growing regions or farming systems.
Collapse
|
28
|
Kennedy A, Geuten K. The Role of FLOWERING LOCUS C Relatives in Cereals. FRONTIERS IN PLANT SCIENCE 2020; 11:617340. [PMID: 33414801 PMCID: PMC7783157 DOI: 10.3389/fpls.2020.617340] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/02/2020] [Indexed: 05/12/2023]
Abstract
FLOWERING LOCUS C (FLC) is one of the best characterized genes in plant research and is integral to vernalization-dependent flowering time regulation. Yet, despite the abundance of information on this gene and its relatives in Arabidopsis thaliana, the role FLC genes play in other species, in particular cereal crops and temperate grasses, remains elusive. This has been due in part to the comparative reduced availability of bioinformatic and mutant resources in cereals but also on the dominant effect in cereals of the VERNALIZATION (VRN) genes on the developmental process most associated with FLC in Arabidopsis. The strong effect of the VRN genes has led researchers to believe that the entire process of vernalization must have evolved separately in Arabidopsis and cereals. Yet, since the confirmation of the existence of FLC-like genes in monocots, new light has been shed on the roles these genes play in both vernalization and other mechanisms to fine tune development in response to specific environmental conditions. Comparisons of FLC gene function and their genetic and epigenetic regulation can now be made between Arabidopsis and cereals and how they overlap and diversify is coming into focus. With the advancement of genome editing techniques, further study on these genes is becoming increasingly easier, enabling us to investigate just how essential FLC-like genes are to modulating flowering time behavior in cereals.
Collapse
|
29
|
Qian C, Yan X, Shi Y, Yin H, Chang Y, Chen J, Ingvarsson PK, Nevo E, Ma XF. Adaptive signals of flowering time pathways in wild barley from Israel over 28 generations. Heredity (Edinb) 2020; 124:62-76. [PMID: 31527784 PMCID: PMC6906298 DOI: 10.1038/s41437-019-0264-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 01/06/2023] Open
Abstract
Flowering time is one of the most critical traits for plants' life cycles, which is influenced by various environment changes, such as global warming. Previous studies have suggested that to guarantee reproductive success, plants have shifted flowering times to adapt to global warming. Although many studies focused on the molecular mechanisms of early flowering, little was supported by the repeated sampling at different time points through the changing climate. To fully dissect the temporal and spatial evolutionary genetics of flowering time, we investigated nucleotide variation in ten flowering time candidate genes and nine reference genes for the same ten wild-barley populations sampled 28 years apart (1980-2008). The overall genetic differentiation was significantly greater in the descendant populations (2008) compared with the ancestral populations (1980); however, local adaptation tests failed to detect any single-nucleotide polymorphism (SNP)/indel under spatial-diversifying selection at either time point. By contrast, the WFABC (Wright-Fisher ABC-based approach) that detected 54 SNPs/indels was under strong selection during the past 28 generations. Moreover, all these 54 alleles were segregated in the ancestral populations, but fixed in the descendent populations. Among the top ten SNPs/indels, seven were located in genes of FT1 (FLOWERING TIME LOCUS T 1), CO1 (CONSTANS-LIKE PROTEIN 1), and VRN-H2 (VERNALIZATION-H2), which have been documented to be associated with flowering time regulation in barley cultivars. This study might suggest that all ten populations have undergone parallel evolution over the past few decades in response to global warming, and even an overwhelming local adaptation and ecological differentiation.
Collapse
Affiliation(s)
- Chaoju Qian
- Department of Ecology and Agriculture Research, Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
| | - Xia Yan
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Yong Shi
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Hengxia Yin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China
| | - Yuxiao Chang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 450002, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, SE-750 07, Uppsala, Sweden
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel.
| | - Xiao-Fei Ma
- Department of Ecology and Agriculture Research, Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China.
| |
Collapse
|
30
|
Genetic and Molecular Control of Floral Organ Identity in Cereals. Int J Mol Sci 2019; 20:ijms20112743. [PMID: 31167420 PMCID: PMC6600504 DOI: 10.3390/ijms20112743] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 12/22/2022] Open
Abstract
Grasses represent a major family of monocots comprising mostly cereals. When compared to their eudicot counterparts, cereals show a remarkable morphological diversity. Understanding the molecular basis of floral organ identity and inflorescence development is crucial to gain insight into the grain development for yield improvement purposes in cereals, however, the exact genetic mechanism of floral organogenesis remains elusive due to their complex inflorescence architecture. Extensive molecular analyses of Arabidopsis and other plant genera and species have established the ABCDE floral organ identity model. According to this model, hierarchical combinatorial activities of A, B, C, D, and E classes of homeotic genes regulate the identity of different floral organs with partial conservation and partial diversification between eudicots and cereals. Here, we review the developmental role of A, B, C, D, and E gene classes and explore the recent advances in understanding the floral development and subsequent organ specification in major cereals with reference to model plants. Furthermore, we discuss the evolutionary relationships among known floral organ identity genes. This comparative overview of floral developmental genes and associated regulatory factors, within and between species, will provide a thorough understanding of underlying complex genetic and molecular control of flower development and floral organ identity, which can be helpful to devise innovative strategies for grain yield improvement in cereals.
Collapse
|
31
|
Monteagudo A, Igartua E, Contreras-Moreira B, Gracia MP, Ramos J, Karsai I, Casas AM. Fine-tuning of the flowering time control in winter barley: the importance of HvOS2 and HvVRN2 in non-inductive conditions. BMC PLANT BIOLOGY 2019; 19:113. [PMID: 30909882 PMCID: PMC6434887 DOI: 10.1186/s12870-019-1727-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/19/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND In winter barley plants, vernalization and photoperiod cues have to be integrated to promote flowering. Plant development and expression of different flowering promoter (HvVRN1, HvCO2, PPD-H1, HvFT1, HvFT3) and repressor (HvVRN2, HvCO9 and HvOS2) genes were evaluated in two winter barley varieties under: (1) natural increasing photoperiod, without vernalization, and (2) under short day conditions in three insufficient vernalization treatments. These challenging conditions were chosen to capture non-optimal and natural responses, representative of those experienced in the Mediterranean area. RESULTS In absence of vernalization and under increasing photoperiods, HvVRN2 expression increased with day-length, mainly between 12 and 13 h photoperiods in our latitudes. The flowering promoter gene in short days, HvFT3, was only expressed after receiving induction of cold or plant age, which was associated with low transcript levels of HvVRN2 and HvOS2. Under the sub-optimal conditions here described, great differences in development were found between the two winter barley varieties used in the study. Delayed development in 'Barberousse' was associated with increased expression levels of HvOS2. Novel variation for HvCO9 and HvOS2 is reported and might explain such differences. CONCLUSIONS The balance between the expression of flowering promoters and repressor genes regulates the promotion towards flowering or the maintenance of the vegetative state. HvOS2, an ortholog of FLC, appears as a strong candidate to mediate in the vernalization response of barley. Natural variation found would help to exploit the plasticity in development to obtain better-adapted varieties for current and future climate conditions.
Collapse
Affiliation(s)
- Arantxa Monteagudo
- Aula Dei Experimental Station (EEAD-CSIC), Avda. Montañana 1005, E-50059 Zaragoza, Spain
| | - Ernesto Igartua
- Aula Dei Experimental Station (EEAD-CSIC), Avda. Montañana 1005, E-50059 Zaragoza, Spain
| | - Bruno Contreras-Moreira
- Aula Dei Experimental Station (EEAD-CSIC), Avda. Montañana 1005, E-50059 Zaragoza, Spain
- Fundación ARAID, Zaragoza, Spain
| | - M. Pilar Gracia
- Aula Dei Experimental Station (EEAD-CSIC), Avda. Montañana 1005, E-50059 Zaragoza, Spain
| | - Javier Ramos
- Aula Dei Experimental Station (EEAD-CSIC), Avda. Montañana 1005, E-50059 Zaragoza, Spain
| | - Ildikó Karsai
- Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, H-2462 Hungary
| | - Ana M. Casas
- Aula Dei Experimental Station (EEAD-CSIC), Avda. Montañana 1005, E-50059 Zaragoza, Spain
| |
Collapse
|
32
|
Shi C, Zhao L, Zhang X, Lv G, Pan Y, Chen F. Gene regulatory network and abundant genetic variation play critical roles in heading stage of polyploidy wheat. BMC PLANT BIOLOGY 2019; 19:6. [PMID: 30606101 PMCID: PMC6318890 DOI: 10.1186/s12870-018-1591-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 12/05/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND The extensive adaptability of polyploidy wheat is attributed to its complex genome, and accurately controlling heading stage is a prime target in wheat breeding process. Wheat heading stage is an essential growth and development processes since it starts at a crucial point in the transition from vegetative phase to reproductive phase. MAIN BODY Heading stage is mainly decided by vernalization, photoperiod, hormone (like gibberellic acid, GA), and earliness per se (Eps). As a polyploidy species, common wheat possesses the abundant genetic variation, such as allelic variation, copy number variation etc., which have a strong effect on regulation of wheat growth and development. Therefore, understanding genetic manipulation of heading stage is pivotal for controlling the heading stage in wheat. In this review, we summarized the recent advances in the genetic regulatory mechanisms and abundant variation in genetic diversity controlling heading stage in wheat, as well as the interaction mechanism of different signals and the contribution of different genetic variation. We first summarized the genes involved in vernalization, photoperoid and other signals cross-talk with each other to control wheat heading stage, then the abundant genetic variation related to signal components associated with wheat heading stage was also elaborated in detail. CONCLUSION Our knowledge of the regulatory network of wheat heading can be used to adjust the duration of the growth phase for the purpose of acclimatizing to different geographical environments.
Collapse
Affiliation(s)
- Chaonan Shi
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
| | - Lei Zhao
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
| | - Xiangfen Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
| | - Guoguo Lv
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
| | - Yubo Pan
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 China
| |
Collapse
|
33
|
Jiao F, Pahwa K, Manning M, Dochy N, Geuten K. Cold Induced Antisense Transcription of FLOWERING LOCUS C in Distant Grasses. FRONTIERS IN PLANT SCIENCE 2019; 10:72. [PMID: 30774642 PMCID: PMC6367677 DOI: 10.3389/fpls.2019.00072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/17/2019] [Indexed: 05/02/2023]
Abstract
Functional conservation of RNAs between different species is a key argument for their importance. While few long non-coding RNAs are conserved at the sequence level, many long non-coding RNAs have been identified that only share a position relative to other genes. It remains largely unknown whether and how these lncRNAs are conserved beyond their position. In Arabidopsis thaliana, the lncRNA COOLAIR is transcribed antisense from FLOWERING LOCUS C (FLC) in response to cold. Despite relatively low sequence similarity, the COOLAIR expression pattern and in vitro RNA secondary structure are highly conserved across the family Brassicaceae, which originated some 50 mya. It is unclear, however, whether COOLAIR functions in distantly related species such as monocots, which diverged some 150 mya. Here, we identified antisense lncRNAs from FLC homologs in various monocot species that share no sequence similarity with A. thaliana COOLAIR. Yet similar to COOLAIR, we found that BdODDSOC1 antisense (BdCOOLAIR1) and BdODDSOC2 antisense (BdCOOLAIR2) are induced by cold in a Brachypodium distachyon winter accession. Across B. distachyon accessions, the sequences of BdCOOLAIR1 and BdCOOLAIR2 are less conserved than exons but more conserved than flanking regions, suggesting a function for the transcript itself. Knock down of the BdODDSOC2 non-overlapping BdCOOLAIR2 transcript did not show a morphological phenotype, but did result in significantly higher BdODDSOC2 expression during cold, indicating that BdCOOLAIR2 performs a role in cis in the rate of BdODDSOC2 silencing. This functional similarity between eudicot and monocot species reveals ancient conservation or convergent evolution of FLC antisense transcription. Either scenario supports its functional importance.
Collapse
|
34
|
Castelán-Muñoz N, Herrera J, Cajero-Sánchez W, Arrizubieta M, Trejo C, García-Ponce B, Sánchez MDLP, Álvarez-Buylla ER, Garay-Arroyo A. MADS-Box Genes Are Key Components of Genetic Regulatory Networks Involved in Abiotic Stress and Plastic Developmental Responses in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:853. [PMID: 31354752 PMCID: PMC6636334 DOI: 10.3389/fpls.2019.00853] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 06/13/2019] [Indexed: 05/05/2023]
Abstract
Plants, as sessile organisms, adapt to different stressful conditions, such as drought, salinity, extreme temperatures, and nutrient deficiency, via plastic developmental and growth responses. Depending on the intensity and the developmental phase in which it is imposed, a stress condition may lead to a broad range of responses at the morphological, physiological, biochemical, and molecular levels. Transcription factors are key components of regulatory networks that integrate environmental cues and concert responses at the cellular level, including those that imply a stressful condition. Despite the fact that several studies have started to identify various members of the MADS-box gene family as important molecular components involved in different types of stress responses, we still lack an integrated view of their role in these processes. In this review, we analyze the function and regulation of MADS-box gene family members in response to drought, salt, cold, heat, and oxidative stress conditions in different developmental processes of several plants. In addition, we suggest that MADS-box genes are key components of gene regulatory networks involved in plant responses to stress and plant developmental plasticity in response to seasonal changes in environmental conditions.
Collapse
Affiliation(s)
- Natalia Castelán-Muñoz
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Postgrado en Recursos Genéticos y Productividad-Fisiología Vegetal, Colegio de Postgraduados, Texcoco, Mexico
| | - Joel Herrera
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Wendy Cajero-Sánchez
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Maite Arrizubieta
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carlos Trejo
- Postgrado en Botánica, Colegio de Postgraduados, Texcoco, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Adriana Garay-Arroyo
| |
Collapse
|
35
|
Xu S, Chong K. Remembering winter through vernalisation. NATURE PLANTS 2018; 4:997-1009. [PMID: 30478363 DOI: 10.1038/s41477-018-0301-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 10/12/2018] [Indexed: 05/10/2023]
Abstract
Vernalisation is the programmed physiological process in which prolonged cold-exposure provides competency to flower in plants; widely found in winter and biennial species, such as Arabidopsis, fruit trees, vegetables and wheat. This phenomenon is regulated by diverse genetic networks, and memory of vernalisation in a life cycle mainly depends on epigenetic mechanisms. However, less is known about how to count winter-dosage for flowering in plants. Here, we compare the vernalisation genetic framework between the dicots Arabidopsis, temperate grasses, wheat, barley and Brachypodium. We discuss vernalisation mechanisms involving crosstalk between phosphorylation and O-GlcNAcylation modification of key proteins, and epigenetic modifications of the key gene VRN1 in wheat. We also highlight the potential evolutionary origins of vernalisation in various species. Current progress toward understanding the regulation of vernalisation requirements provides insight that will inform the design of molecular breeding strategies for winter crops.
Collapse
Affiliation(s)
- Shujuan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
36
|
Schilling S, Pan S, Kennedy A, Melzer R. MADS-box genes and crop domestication: the jack of all traits. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1447-1469. [PMID: 29474735 DOI: 10.1093/jxb/erx479] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/10/2018] [Indexed: 05/25/2023]
Abstract
MADS-box genes are key regulators of virtually every aspect of plant reproductive development. They play especially prominent roles in flowering time control, inflorescence architecture, floral organ identity determination, and seed development. The developmental and evolutionary importance of MADS-box genes is widely acknowledged. However, their role during flowering plant domestication is less well recognized. Here, we provide an overview illustrating that MADS-box genes have been important targets of selection during crop domestication and improvement. Numerous examples from a diversity of crop plants show that various developmental processes have been shaped by allelic variations in MADS-box genes. We propose that new genomic and genome editing resources provide an excellent starting point for further harnessing the potential of MADS-box genes to improve a variety of reproductive traits in crops. We also suggest that the biophysics of MADS-domain protein-protein and protein-DNA interactions, which is becoming increasingly well characterized, makes them especially suited to exploit coding sequence variations for targeted breeding approaches.
Collapse
Affiliation(s)
- Susanne Schilling
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Sirui Pan
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Alice Kennedy
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Rainer Melzer
- School of Biology and Environmental Science, University College Dublin, Irel
| |
Collapse
|
37
|
Tanaka C, Itoh T, Iwasaki Y, Mizuno N, Nasuda S, Murai K. Direct interaction between VRN1 protein and the promoter region of the wheat FT gene. Genes Genet Syst 2018; 93:25-29. [DOI: 10.1266/ggs.17-00041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Chihiro Tanaka
- Department of Bioscience and Biotechnology, Fukui Prefectural University
| | - Takafumi Itoh
- Department of Bioscience and Biotechnology, Fukui Prefectural University
| | - Yukimoto Iwasaki
- Department of Bioscience and Biotechnology, Fukui Prefectural University
| | | | | | - Koji Murai
- Department of Bioscience and Biotechnology, Fukui Prefectural University
| |
Collapse
|
38
|
Zhong J, Robbett M, Poire A, Preston JC. Successive evolutionary steps drove Pooideae grasses from tropical to temperate regions. THE NEW PHYTOLOGIST 2018; 217:925-938. [PMID: 29091285 DOI: 10.1111/nph.14868] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/22/2017] [Indexed: 06/07/2023]
Abstract
Angiosperm adaptations to seasonally cold climates have occurred multiple times independently. However, the observation that less than half of all angiosperm families are represented in temperate latitudes suggests internal constraints on the evolution of cold tolerance/avoidance strategies. Similar to angiosperms as a whole, grasses are primarily tropical, but one major clade, subfamily Pooideae, radiated extensively within temperate regions. It is posited that this Pooideae niche transition was facilitated by an early origin of long-term cold responsiveness around the base of the subfamily, and that a set of more ancient pathways enabled evolution of seasonal cold tolerance. To test this, we compared transcriptome-level responses of disparate Pooideae to short-/long-term cold and with those previously known in the subtropical grass rice (Ehrhartoideae). Analyses identified several highly conserved cold-responsive 'orthogroups' within our focal Pooideae species that originated successively during the diversification of land plants, predominantly via gene duplication. The majority of conserved Pooideae cold-responsive genes appear to have ancient roles in stress responses, with most of the orthogroups also being sensitive to cold in rice. However, a subgroup of genes was likely co-opted de novo early in the Pooideae. These results highlight a plausible stepwise evolutionary trajectory for cold adaptations across Pooideae.
Collapse
Affiliation(s)
- Jinshun Zhong
- Department of Plant Biology, University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT, 05405, USA
| | - Meghan Robbett
- Department of Plant Biology, University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT, 05405, USA
| | - Alfonso Poire
- Department of Plant Biology, University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT, 05405, USA
| | - Jill C Preston
- Department of Plant Biology, University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT, 05405, USA
| |
Collapse
|
39
|
Bloomer RH, Dean C. Fine-tuning timing: natural variation informs the mechanistic basis of the switch to flowering in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5439-5452. [PMID: 28992087 DOI: 10.1093/jxb/erx270] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The evolution of diverse life history strategies has allowed Arabidopsis thaliana to adapt to worldwide locations, spanning a range of latitudinal and environmental conditions. Arabidopsis thaliana accessions are either vernalization-requiring winter annuals or rapid cyclers, with extensive natural variation in vernalization requirement and response. Genetic and molecular analysis of this variation has enhanced our understanding of the mechanisms involved in life history determination, with translation to both natural and crop systems in the Brassicaceae and beyond.
Collapse
Affiliation(s)
- R H Bloomer
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - C Dean
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| |
Collapse
|
40
|
Wang HM, Tong CG, Jang S. Current progress in orchid flowering/flower development research. PLANT SIGNALING & BEHAVIOR 2017; 12:e1322245. [PMID: 28448202 PMCID: PMC5501233 DOI: 10.1080/15592324.2017.1322245] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 04/19/2017] [Indexed: 05/31/2023]
Abstract
Genetic pathways relevant to flowering of Arabidopsis are under the control of environmental cues such as day length and temperatures, and endogenous signals including phytohormones and developmental aging. However, genes and even regulatory pathways for flowering identified in crops show divergence from those of Arabidopsis and often do not have functional equivalents to Arabidopsis and/or existing species- or genus-specific regulators and show modified or novel pathways. Orchids are the largest, most highly evolved flowering plants, and form an extremely peculiar group of plants. Here, we briefly summarize the flowering pathways of Arabidopsis, rice and wheat and present them alongside recent discoveries/progress in orchid flowering and flower developmental processes including our transgenic Phalaenopsis orchids for LEAFY overexpression. Potential biotechnological applications in flowering/flower development of orchids with potential target genes are also discussed from an interactional and/or comparative viewpoint.
Collapse
Affiliation(s)
- Hsin-Mei Wang
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Chii-Gong Tong
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Seonghoe Jang
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
- Institute of Tropical Plant Science, National Cheng Kung University, Tainan, Taiwan
| |
Collapse
|
41
|
Gol L, Tomé F, von Korff M. Floral transitions in wheat and barley: interactions between photoperiod, abiotic stresses, and nutrient status. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1399-1410. [PMID: 28431134 DOI: 10.1093/jxb/erx055] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The timing of plant reproduction has a large impact on yield in crop plants. Reproductive development in temperate cereals comprises two major developmental transitions. During spikelet initiation, the identity of the shoot meristem switches from the vegetative to the reproductive stage and spikelet primordia are formed on the apex. Subsequently, floral morphogenesis is initiated, a process strongly affected by environmental variation. Recent studies in cereal grasses have suggested that this later phase of inflorescence development controls floret survival and abortion, and is therefore crucial for yield. Here, we provide a synthesis of the early morphological and the more recent genetic studies on shoot development in wheat and barley. The review explores how photoperiod, abiotic stress, and nutrient signalling interact with shoot development, and pinpoints genetic factors that mediate development in response to these environmental cues. We anticipate that research in these areas will be important in understanding adaptation of cereal grasses to changing climate conditions.
Collapse
Affiliation(s)
- Leonard Gol
- Max Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
| | - Filipa Tomé
- Max Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
- Institute of Plant Genetics, Heinrich-Heine-University, D-40225 Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences 'From Complex Traits towards Synthetic Modules', D-40225 Düsseldorf, Germany
| | - Maria von Korff
- Max Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
- Institute of Plant Genetics, Heinrich-Heine-University, D-40225 Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences 'From Complex Traits towards Synthetic Modules', D-40225 Düsseldorf, Germany
| |
Collapse
|
42
|
Sharma N, Ruelens P, D'hauw M, Maggen T, Dochy N, Torfs S, Kaufmann K, Rohde A, Geuten K. A Flowering Locus C Homolog Is a Vernalization-Regulated Repressor in Brachypodium and Is Cold Regulated in Wheat. PLANT PHYSIOLOGY 2017; 173:1301-1315. [PMID: 28034954 PMCID: PMC5291021 DOI: 10.1104/pp.16.01161] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/22/2016] [Indexed: 05/18/2023]
Abstract
Winter cereals require prolonged cold to transition from vegetative to reproductive development. This process, referred to as vernalization, has been extensively studied in Arabidopsis (Arabidopsis thaliana). In Arabidopsis, a key flowering repressor called FLOWERING LOCUS C (FLC) quantitatively controls the vernalization requirement. By contrast, in cereals, the vernalization response is mainly regulated by the VERNALIZATION genes, VRN1 and VRN2 Here, we characterize ODDSOC2, a recently identified FLC ortholog in monocots, knowing that it belongs to the FLC lineage. By studying its expression in a diverse set of Brachypodium accessions, we find that it is a good predictor of the vernalization requirement. Analyses of transgenics demonstrated that BdODDSOC2 functions as a vernalization-regulated flowering repressor. In most Brachypodium accessions BdODDSOC2 is down-regulated by cold, and in one of the winter accessions in which this down-regulation was evident, BdODDSOC2 responded to cold before BdVRN1. When stably down-regulated, the mechanism is associated with spreading H3K27me3 modifications at the BdODDSOC2 chromatin. Finally, homoeolog-specific gene expression analyses identify TaAGL33 and its splice variant TaAGL22 as the FLC orthologs in wheat (Triticum aestivum) behaving most similar to Brachypodium ODDSOC2 Overall, our study suggests that ODDSOC2 is not only phylogenetically related to FLC in eudicots but also functions as a flowering repressor in the vernalization pathway of Brachypodium and likely other temperate grasses. These insights could prove useful in breeding efforts to refine the vernalization requirement of temperate cereals and adapt varieties to changing climates.
Collapse
Affiliation(s)
- Neha Sharma
- Department of Biology, KU Leuven, B-3001 Leuven, Belgium (N.S., P.R., N.D., S.T., K.G.)
- Bayer Crop Science, B-9052 Gent, Belgium (M.D., T.M., A.R.); and
- Institute for Biochemistry and Biology, Potsdam University, 14476 Potsdam-Golm, Germany (K.K.)
| | - Philip Ruelens
- Department of Biology, KU Leuven, B-3001 Leuven, Belgium (N.S., P.R., N.D., S.T., K.G.)
- Bayer Crop Science, B-9052 Gent, Belgium (M.D., T.M., A.R.); and
- Institute for Biochemistry and Biology, Potsdam University, 14476 Potsdam-Golm, Germany (K.K.)
| | - Mariëlla D'hauw
- Department of Biology, KU Leuven, B-3001 Leuven, Belgium (N.S., P.R., N.D., S.T., K.G.)
- Bayer Crop Science, B-9052 Gent, Belgium (M.D., T.M., A.R.); and
- Institute for Biochemistry and Biology, Potsdam University, 14476 Potsdam-Golm, Germany (K.K.)
| | - Thomas Maggen
- Department of Biology, KU Leuven, B-3001 Leuven, Belgium (N.S., P.R., N.D., S.T., K.G.)
- Bayer Crop Science, B-9052 Gent, Belgium (M.D., T.M., A.R.); and
- Institute for Biochemistry and Biology, Potsdam University, 14476 Potsdam-Golm, Germany (K.K.)
| | - Niklas Dochy
- Department of Biology, KU Leuven, B-3001 Leuven, Belgium (N.S., P.R., N.D., S.T., K.G.)
- Bayer Crop Science, B-9052 Gent, Belgium (M.D., T.M., A.R.); and
- Institute for Biochemistry and Biology, Potsdam University, 14476 Potsdam-Golm, Germany (K.K.)
| | - Sanne Torfs
- Department of Biology, KU Leuven, B-3001 Leuven, Belgium (N.S., P.R., N.D., S.T., K.G.)
- Bayer Crop Science, B-9052 Gent, Belgium (M.D., T.M., A.R.); and
- Institute for Biochemistry and Biology, Potsdam University, 14476 Potsdam-Golm, Germany (K.K.)
| | - Kerstin Kaufmann
- Department of Biology, KU Leuven, B-3001 Leuven, Belgium (N.S., P.R., N.D., S.T., K.G.)
- Bayer Crop Science, B-9052 Gent, Belgium (M.D., T.M., A.R.); and
- Institute for Biochemistry and Biology, Potsdam University, 14476 Potsdam-Golm, Germany (K.K.)
| | - Antje Rohde
- Department of Biology, KU Leuven, B-3001 Leuven, Belgium (N.S., P.R., N.D., S.T., K.G.)
- Bayer Crop Science, B-9052 Gent, Belgium (M.D., T.M., A.R.); and
- Institute for Biochemistry and Biology, Potsdam University, 14476 Potsdam-Golm, Germany (K.K.)
| | - Koen Geuten
- Department of Biology, KU Leuven, B-3001 Leuven, Belgium (N.S., P.R., N.D., S.T., K.G.);
- Bayer Crop Science, B-9052 Gent, Belgium (M.D., T.M., A.R.); and
- Institute for Biochemistry and Biology, Potsdam University, 14476 Potsdam-Golm, Germany (K.K.)
| |
Collapse
|
43
|
Bouché F, Woods DP, Amasino RM. Winter Memory throughout the Plant Kingdom: Different Paths to Flowering. PLANT PHYSIOLOGY 2017; 173:27-35. [PMID: 27756819 PMCID: PMC5210730 DOI: 10.1104/pp.16.01322] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 09/21/2016] [Indexed: 05/18/2023]
Abstract
Molecular mechanisms contribute to the memory of winter in different plant groups.
Collapse
Affiliation(s)
- Frédéric Bouché
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706 (F.B., D.P.W., R.M.A.); and
- United States Department of Energy Great Lakes Bioenergy Research Center, Madison, Wisconsin 53726 (D.P.W., R.M.A.)
| | - Daniel P Woods
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706 (F.B., D.P.W., R.M.A.); and
- United States Department of Energy Great Lakes Bioenergy Research Center, Madison, Wisconsin 53726 (D.P.W., R.M.A.)
| | - Richard M Amasino
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706 (F.B., D.P.W., R.M.A.); and
- United States Department of Energy Great Lakes Bioenergy Research Center, Madison, Wisconsin 53726 (D.P.W., R.M.A.)
| |
Collapse
|
44
|
Ejaz M, von Korff M. The Genetic Control of Reproductive Development under High Ambient Temperature. PLANT PHYSIOLOGY 2017; 173:294-306. [PMID: 28049855 PMCID: PMC5210726 DOI: 10.1104/pp.16.01275] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/03/2016] [Indexed: 05/20/2023]
Abstract
Ambient temperature has a large impact on reproductive development and grain yield in temperate cereals. However, little is known about the genetic control of development under different ambient temperatures. Here, we demonstrate that in barley (Hordeum vulgare), high ambient temperatures accelerate or delay reproductive development depending on the photoperiod response gene PHOTOPERIOD1 (Ppd-H1) and its upstream regulator EARLY FLOWERING3 (HvELF3). A natural mutation in Ppd-H1 prevalent in spring barley delayed floral development and reduced the number of florets and seeds per spike, while the wild-type Ppd-H1 or a mutant Hvelf3 allele accelerated floral development and maintained the seed number under high ambient temperatures. High ambient temperature delayed the expression phase and reduced the amplitude of clock genes and repressed the floral integrator gene FLOWERING LOCUS T1 independently of the genotype. Ppd-H1-dependent variation in flowering time under different ambient temperatures correlated with relative expression levels of the BARLEY MADS-box genes VERNALIZATION1 (HvVRN1), HvBM3, and HvBM8 in the leaf. Finally, we show that Ppd-H1 interacts with regulatory variation at HvVRN1. Ppd-H1 only accelerated floral development in the background of a spring HvVRN1 allele with a deletion in the regulatory intron. The full-length winter Hvvrn1 allele was strongly down-regulated, and flowering was delayed by high temperatures irrespective of Ppd-H1 Our findings demonstrate that the photoperiodic and vernalization pathways interact to control flowering time and floret fertility in response to ambient temperature in barley.
Collapse
Affiliation(s)
- Mahwish Ejaz
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (M.E., M.v.K.)
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany (M.E., M.v.K.); and
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules," 40225 Düsseldorf, Germany (M.v.K.)
| | - Maria von Korff
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (M.E., M.v.K.);
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany (M.E., M.v.K.); and
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules," 40225 Düsseldorf, Germany (M.v.K.)
| |
Collapse
|
45
|
Osborn HL, Alonso-Cantabrana H, Sharwood RE, Covshoff S, Evans JR, Furbank RT, von Caemmerer S. Effects of reduced carbonic anhydrase activity on CO2 assimilation rates in Setaria viridis: a transgenic analysis. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:299-310. [PMID: 27702996 PMCID: PMC5853810 DOI: 10.1093/jxb/erw357] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/05/2016] [Indexed: 05/22/2023]
Abstract
In C4 species, the major β-carbonic anhydrase (β-CA) localized in the mesophyll cytosol catalyses the hydration of CO2 to HCO3-, which phosphoenolpyruvate carboxylase uses in the first step of C4 photosynthesis. To address the role of CA in C4 photosynthesis, we generated transgenic Setaria viridis depleted in β-CA. Independent lines were identified with as little as 13% of wild-type CA. No photosynthetic defect was observed in the transformed lines at ambient CO2 partial pressure (pCO2). At low pCO2, a strong correlation between CO2 assimilation rates and CA hydration rates was observed. C18O16O isotope discrimination was used to estimate the mesophyll conductance to CO2 diffusion from the intercellular air space to the mesophyll cytosol (gm) in control plants, which allowed us to calculate CA activities in the mesophyll cytosol (Cm). This revealed a strong relationship between the initial slope of the response of the CO2 assimilation rate to cytosolic pCO2 (ACm) and cytosolic CA activity. However, the relationship between the initial slope of the response of CO2 assimilation to intercellular pCO2 (ACi) and cytosolic CA activity was curvilinear. This indicated that in S. viridis, mesophyll conductance may be a contributing limiting factor alongside CA activity to CO2 assimilation rates at low pCO2.
Collapse
Affiliation(s)
- Hannah L Osborn
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Hugo Alonso-Cantabrana
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Robert E Sharwood
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Sarah Covshoff
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - John R Evans
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Robert T Furbank
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Susanne von Caemmerer
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| |
Collapse
|
46
|
Ford B, Deng W, Clausen J, Oliver S, Boden S, Hemming M, Trevaskis B. Barley (Hordeum vulgare) circadian clock genes can respond rapidly to temperature in an EARLY FLOWERING 3-dependent manner. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5517-5528. [PMID: 27580625 PMCID: PMC5049398 DOI: 10.1093/jxb/erw317] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
An increase in global temperatures will impact future crop yields. In the cereal crops wheat and barley, high temperatures accelerate reproductive development, reducing the number of grains per plant and final grain yield. Despite this relationship between temperature and cereal yield, it is not clear what genes and molecular pathways mediate the developmental response to increased temperatures. The plant circadian clock can respond to changes in temperature and is important for photoperiod-dependent flowering, and so is a potential mechanism controlling temperature responses in cereal crops. This study examines the relationship between temperature, the circadian clock, and the expression of flowering-time genes in barley (Hordeum vulgare), a crop model for temperate cereals. Transcript levels of barley core circadian clock genes were assayed over a range of temperatures. Transcript levels of core clock genes CCA1, GI, PRR59, PRR73, PRR95, and LUX are increased at higher temperatures. CCA1 and PRR73 respond rapidly to a decrease in temperature whereas GI and PRR59 respond rapidly to an increase in temperature. The response of GI and the PRR genes to changes in temperature is lost in the elf3 mutant indicating that their response to temperature may be dependent on a functional ELF3 gene.
Collapse
Affiliation(s)
- Brett Ford
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Weiwei Deng
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Jenni Clausen
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Sandra Oliver
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Scott Boden
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Megan Hemming
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Ben Trevaskis
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
| |
Collapse
|
47
|
Kovalchuk N, Chew W, Sornaraj P, Borisjuk N, Yang N, Singh R, Bazanova N, Shavrukov Y, Guendel A, Munz E, Borisjuk L, Langridge P, Hrmova M, Lopato S. The homeodomain transcription factor TaHDZipI-2 from wheat regulates frost tolerance, flowering time and spike development in transgenic barley. THE NEW PHYTOLOGIST 2016; 211:671-87. [PMID: 26990681 DOI: 10.1111/nph.13919] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/02/2016] [Indexed: 05/20/2023]
Abstract
Homeodomain leucine zipper class I (HD-Zip I) transcription factors (TFs) play key roles in the regulation of plant growth and development under stresses. Functions of the TaHDZipI-2 gene isolated from the endosperm of developing wheat grain were revealed. Molecular characterization of TaHDZipI-2 protein included studies of its dimerisation, protein-DNA interactions and gene activation properties using pull-down assays, in-yeast methods and transient expression assays in wheat cells. The analysis of TaHDZipI-2 gene functions was performed using transgenic barley plants. It included comparison of developmental phenotypes, yield components, grain quality, frost tolerance and the levels of expression of potential target genes in transgenic and control plants. Transgenic TaHDZipI-2 lines showed characteristic phenotypic features that included reduced growth rates, reduced biomass, early flowering, light-coloured leaves and narrowly elongated spikes. Transgenic lines produced 25-40% more seeds per spike than control plants, but with 50-60% smaller grain size. In vivo lipid imaging exposed changes in the distribution of lipids between the embryo and endosperm in transgenic seeds. Transgenic lines were significantly more tolerant to frost than control plants. Our data suggest the role of TaHDZipI-2 in controlling several key processes underlying frost tolerance, transition to flowering and spike development.
Collapse
Affiliation(s)
- Nataliya Kovalchuk
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - William Chew
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Pradeep Sornaraj
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Nikolai Borisjuk
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Nannan Yang
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Rohan Singh
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Natalia Bazanova
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Yuri Shavrukov
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Andre Guendel
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, Gatersleben, Germany
| | - Eberhard Munz
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, Gatersleben, Germany
| | - Ljudmilla Borisjuk
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, Gatersleben, Germany
| | - Peter Langridge
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Maria Hrmova
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Sergiy Lopato
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| |
Collapse
|
48
|
Pearce S, Kippes N, Chen A, Debernardi JM, Dubcovsky J. RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways. BMC PLANT BIOLOGY 2016; 16:141. [PMID: 27329140 PMCID: PMC4915087 DOI: 10.1186/s12870-016-0831-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/15/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND In cereal crops such as wheat, an optimal timing of developmental transitions is required to maximize grain yield. Many of these developmental changes are precisely regulated by changes in the duration, intensity or quality of light. Phytochromes are dimeric photoreceptors that absorb light maximally in the red and far-red wavelengths and induce large-scale transcriptional changes in response to variation in light quality. In wheat, PHYC is required for early flowering under long days. However, it is currently unknown whether this function requires the presence of PHYB. In this study, we characterized the role of PHYB in wheat development and used RNA-seq to analyze and compare the transcriptomes of phyB-null and phyC-null TILLING mutants. RESULTS Under long-day photoperiods, phyB-null plants exhibit a severe delay in flowering comparable to the delay observed in phyC-null plants. These results demonstrate that both genes are required for the induction of wheat flowering under long days. Using replicated RNA-seq studies we identified 82 genes that are significantly up or down regulated in both the phyB-null and phyC-null mutant relative to their respective wild-type controls. Among these genes are several well-characterized positive regulators of flowering, including PPD1, FT1 and VRN1. Eight-fold more genes were differentially regulated only in the phyB-null mutant (2202) than only in the phyC-null mutant (261). The PHYB-regulated genes were enriched in components of the auxin, gibberellin and brassinosteroid biosynthesis and signaling pathways, and in transcription factors with putative roles in regulating vegetative development and shade-avoidance responses. Several genes involved in abiotic stress tolerance pathways were also found to be regulated by PHYB. CONCLUSIONS PHYB and PHYC are both required for the photoperiodic induction of wheat flowering, whereas PHYB alone regulates a large number of genes involved in hormone biosynthesis and signaling, shade-avoidance response, and abiotic stress tolerance. Our analysis provides a comprehensive overview of the PHYB- and PHYC-mediated transcriptional changes during light signaling, and an initial step towards the dissection of this regulatory gene network in wheat. This further dissection will be required to explore the individual phytochrome-mediated developmental responses and to evaluate their potential to improve wheat adaptation to changing environments.
Collapse
Affiliation(s)
- Stephen Pearce
- />Department of Plant Sciences, University of California, Davis, CA 95616 USA
- />Present Address: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Nestor Kippes
- />Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Andrew Chen
- />Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | | | - Jorge Dubcovsky
- />Department of Plant Sciences, University of California, Davis, CA 95616 USA
- />Howard Hughes Medical Institute, Chevy Chase, MD 20815 USA
| |
Collapse
|
49
|
Woods DP, McKeown MA, Dong Y, Preston JC, Amasino RM. Evolution of VRN2/Ghd7-Like Genes in Vernalization-Mediated Repression of Grass Flowering. PLANT PHYSIOLOGY 2016; 170:2124-35. [PMID: 26848096 PMCID: PMC4825116 DOI: 10.1104/pp.15.01279] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 02/02/2016] [Indexed: 05/03/2023]
Abstract
Flowering of many plant species is coordinated with seasonal environmental cues such as temperature and photoperiod. Vernalization provides competence to flower after prolonged cold exposure, and a vernalization requirement prevents flowering from occurring prior to winter. In winter wheat (Triticum aestivum) and barley (Hordeum vulgare), three genes VRN1, VRN2, and FT form a regulatory loop that regulates the initiation of flowering. Prior to cold exposure, VRN2 represses FT. During cold, VRN1 expression increases, resulting in the repression of VRN2, which in turn allows activation of FT during long days to induce flowering. Here, we test whether the circuitry of this regulatory loop is conserved across Pooideae, consistent with their niche transition from the tropics to the temperate zone. Our phylogenetic analyses of VRN2-like genes reveal a duplication event occurred before the diversification of the grasses that gave rise to a CO9 and VRN2/Ghd7 clade and support orthology between wheat/barley VRN2 and rice (Oryza sativa) Ghd7 Our Brachypodium distachyon VRN1 and VRN2 knockdown and overexpression experiments demonstrate functional conservation of grass VRN1 and VRN2 in the promotion and repression of flowering, respectively. However, expression analyses in a range of pooids demonstrate that the cold repression of VRN2 is unique to core Pooideae such as wheat and barley. Furthermore, VRN1 knockdown in B. distachyon demonstrates that the VRN1-mediated suppression of VRN2 is not conserved. Thus, the VRN1-VRN2 feature of the regulatory loop appears to have evolved late in the diversification of temperate grasses.
Collapse
Affiliation(s)
- Daniel P Woods
- Laboratory of Genetics, U.S. Department of Energy Great Lakes Bioenergy Research Center (D.P.W., R.M.A.), and Department of Biochemistry (D.P.W., Y.D., R.M.A.), University of Wisconsin, Madison, Wisconsin 53706;Department of Plant Biology, University of Vermont, Burlington, Vermont 05405 (M.A.M., J.C.P.); andCollege of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China (Y.D.)
| | - Meghan A McKeown
- Laboratory of Genetics, U.S. Department of Energy Great Lakes Bioenergy Research Center (D.P.W., R.M.A.), and Department of Biochemistry (D.P.W., Y.D., R.M.A.), University of Wisconsin, Madison, Wisconsin 53706;Department of Plant Biology, University of Vermont, Burlington, Vermont 05405 (M.A.M., J.C.P.); andCollege of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China (Y.D.)
| | - Yinxin Dong
- Laboratory of Genetics, U.S. Department of Energy Great Lakes Bioenergy Research Center (D.P.W., R.M.A.), and Department of Biochemistry (D.P.W., Y.D., R.M.A.), University of Wisconsin, Madison, Wisconsin 53706;Department of Plant Biology, University of Vermont, Burlington, Vermont 05405 (M.A.M., J.C.P.); andCollege of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China (Y.D.)
| | - Jill C Preston
- Laboratory of Genetics, U.S. Department of Energy Great Lakes Bioenergy Research Center (D.P.W., R.M.A.), and Department of Biochemistry (D.P.W., Y.D., R.M.A.), University of Wisconsin, Madison, Wisconsin 53706;Department of Plant Biology, University of Vermont, Burlington, Vermont 05405 (M.A.M., J.C.P.); andCollege of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China (Y.D.)
| | - Richard M Amasino
- Laboratory of Genetics, U.S. Department of Energy Great Lakes Bioenergy Research Center (D.P.W., R.M.A.), and Department of Biochemistry (D.P.W., Y.D., R.M.A.), University of Wisconsin, Madison, Wisconsin 53706;Department of Plant Biology, University of Vermont, Burlington, Vermont 05405 (M.A.M., J.C.P.); andCollege of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China (Y.D.)
| |
Collapse
|
50
|
Cuesta-Marcos A, Muñoz-Amatriaín M, Filichkin T, Karsai I, Trevaskis B, Yasuda S, Hayes P, Sato K. The Relationships between Development and Low Temperature Tolerance in Barley Near Isogenic Lines Differing for Flowering Behavior. PLANT & CELL PHYSIOLOGY 2015; 56:2312-24. [PMID: 26443377 DOI: 10.1093/pcp/pcv147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/28/2015] [Indexed: 05/25/2023]
Abstract
Flowering time, vernalization requirement, photoperiod sensitivity and low temperature tolerance are key traits in the Triticeae. We characterized a set of isogenic genetic stocks-representing single and pairwise substitutions of spring alleles at the VRN-H1, VRN-H2 and VRN-H3 loci in a winter barley background-at the structural, functional and phenotypic levels. High density mapping with reference to the barley genome sequence confirmed that in all cases target VRN alleles were present in the near isogenic lines (NILs) and allowed estimates of introgression size (at the genetic and physical levels) and gene content. Expression data corroborated the structural and phenotypic results. The latter confirmed that substitution of a spring allele at any of the VRN loci is sufficient to eliminate vernalization requirement. There was no significant change in low temperature tolerance with substitution of a spring allele at VRN-H2, but there were significant losses in cold tolerance with substitutions at VRN-H1 and VRN-H3. Reductions in cold tolerance are ascribed to an accelerated transition from the vegetative to reproductive state. The set of NILs will be a rich resource for understanding the genetics of vernalization, low temperature tolerance and other traits encoded/regulated by genes within the introgressed intervals.
Collapse
Affiliation(s)
- Alfonso Cuesta-Marcos
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA These authors contributed equally to this work
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA These authors contributed equally to this work
| | - Tanya Filichkin
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA
| | - Ildikó Karsai
- MTA ATK, Martonvásár, Brunszvik u. 2. H-2462, Hungary
| | - Ben Trevaskis
- CSIRO, Agriculture Flagship, Canberra, 2601, Australia
| | - Shozo Yasuda
- Institute of Plant Science and Resources, Okayama University, 2-20-1, Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Patrick Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, 2-20-1, Chuo, Kurashiki, Okayama, 710-0046, Japan
| |
Collapse
|