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Mejia S, Santos JLB, Noutsos C. Comprehensive Genome-Wide Natural Variation and Expression Analysis of Tubby-like Proteins Gene Family in Brachypodium distachyon. PLANTS (BASEL, SWITZERLAND) 2024; 13:987. [PMID: 38611516 PMCID: PMC11013449 DOI: 10.3390/plants13070987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024]
Abstract
The Tubby-like proteins (TLPs) gene family is a group of transcription factors found in both animals and plants. In this study, we identified twelve B. distachyon TLPs, divided into six groups based on conserved domains and evolutionary relationships. We predicted cis-regulatory elements involved in light, hormone, and biotic and abiotic stresses. The expression patterns in response to light and hormones revealed that BdTLP3, 4, 7, and 14 are involved in light responses, and BdTLP1 is involved in ABA responses. Furthermore, BdTLP2, 7, 9, and 13 are expressed throughout vegetative and reproductive stages, whereas BdTLP1, 3, 5, and 14 are expressed at germinating grains and early vegetative development, and BdTLP4, 6, 8, and 10 are expressed at the early reproduction stage. The natural variation in the eleven most diverged B. distachyon lines revealed high conservation levels of BdTLP1-6 to high variation in BdTLP7-14 proteins. Based on diversifying selection, we identified amino acids in BdTLP1, 3, 8, and 13, potentially substantially affecting protein functions. This analysis provided valuable information for further functional studies to understand the regulation, pathways involved, and mechanism of BdTLPs.
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Affiliation(s)
- Sendi Mejia
- Biological Sciences Department, Suny Old Westbury, Old Westbury, NY 11568, USA
- Botany and Plant Pathology Department, Purdue University, West Lafayette, IN 47907, USA
| | | | - Christos Noutsos
- Biological Sciences Department, Suny Old Westbury, Old Westbury, NY 11568, USA
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2
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Woods DP, Li W, Sibout R, Shao M, Laudencia-Chingcuanco D, Vogel JP, Dubcovsky J, Amasino RM. PHYTOCHROME C regulation of photoperiodic flowering via PHOTOPERIOD1 is mediated by EARLY FLOWERING 3 in Brachypodium distachyon. PLoS Genet 2023; 19:e1010706. [PMID: 37163541 PMCID: PMC10171608 DOI: 10.1371/journal.pgen.1010706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/17/2023] [Indexed: 05/12/2023] Open
Abstract
Daylength sensing in many plants is critical for coordinating the timing of flowering with the appropriate season. Temperate climate-adapted grasses such as Brachypodium distachyon flower during the spring when days are becoming longer. The photoreceptor PHYTOCHROME C is essential for long-day (LD) flowering in B. distachyon. PHYC is required for the LD activation of a suite of genes in the photoperiod pathway including PHOTOPERIOD1 (PPD1) that, in turn, result in the activation of FLOWERING LOCUS T (FT1)/FLORIGEN, which causes flowering. Thus, B. distachyon phyC mutants are extremely delayed in flowering. Here we show that PHYC-mediated activation of PPD1 occurs via EARLY FLOWERING 3 (ELF3), a component of the evening complex in the circadian clock. The extreme delay of flowering of the phyC mutant disappears when combined with an elf3 loss-of-function mutation. Moreover, the dampened PPD1 expression in phyC mutant plants is elevated in phyC/elf3 mutant plants consistent with the rapid flowering of the double mutant. We show that loss of PPD1 function also results in reduced FT1 expression and extremely delayed flowering consistent with results from wheat and barley. Additionally, elf3 mutant plants have elevated expression levels of PPD1, and we show that overexpression of ELF3 results in delayed flowering associated with a reduction of PPD1 and FT1 expression, indicating that ELF3 represses PPD1 transcription consistent with previous studies showing that ELF3 binds to the PPD1 promoter. Indeed, PPD1 is the main target of ELF3-mediated flowering as elf3/ppd1 double mutant plants are delayed flowering. Our results indicate that ELF3 operates downstream from PHYC and acts as a repressor of PPD1 in the photoperiod flowering pathway of B. distachyon.
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Affiliation(s)
- Daniel P. Woods
- Dept. Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Weiya Li
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Richard Sibout
- Institut Jean-Pierre Bourgin, UMR1318 INRAE-AgroParisTech, Versailles Cedex, France
- UR1268 BIA, INRAE, Nantes, France
| | - Mingqin Shao
- DOE Joint Genome Institute, Berkeley, California, United States of America
| | - Debbie Laudencia-Chingcuanco
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, California, United States of America
| | - John P. Vogel
- DOE Joint Genome Institute, Berkeley, California, United States of America
| | - Jorge Dubcovsky
- Dept. Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Richard M. Amasino
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States of America
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, United States of America
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3
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Raissig MT, Woods DP. The wild grass Brachypodium distachyon as a developmental model system. Curr Top Dev Biol 2022; 147:33-71. [PMID: 35337454 DOI: 10.1016/bs.ctdb.2021.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The arrival of cheap and high-throughput sequencing paired with efficient gene editing technologies allows us to use non-traditional model systems and mechanistically approach biological phenomena beyond what was conceivable just a decade ago. Venturing into different model systems enables us to explore for example clade-specific environmental responses to changing climates or the genetics and development of clade-specific organs, tissues and cell types. We-both early career researchers working with the wild grass model Brachypodium distachyon-want to use this review to (1) highlight why we think B. distachyon is a fantastic grass developmental model system, (2) summarize the tools and resources that have enabled discoveries made in B. distachyon, and (3) discuss a handful of developmental biology vignettes made possible by using B. distachyon as a model system. Finally, we want to conclude by (4) relating our personal stories with this emerging model system and (5) share what we think is important to consider before starting work with an emerging model system.
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Affiliation(s)
- Michael T Raissig
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany; Institute of Plant Sciences, University of Bern, Bern, Switzerland.
| | - Daniel P Woods
- Department of Plant Sciences, University of California, Davis, CA, United States; Howard Hughes Medical Institute, Chevy Chase, MD, United States.
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4
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Sancho R, Inda LA, Díaz-Pérez A, Des Marais DL, Gordon S, Vogel JP, Lusinska J, Hasterok R, Contreras-Moreira B, Catalán P. Tracking the ancestry of known and 'ghost' homeologous subgenomes in model grass Brachypodium polyploids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1535-1558. [PMID: 34951515 DOI: 10.1111/tpj.15650] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 12/10/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Rubén Sancho
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - Luis A Inda
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, Zaragoza, Spain
| | - Antonio Díaz-Pérez
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain
- Instituto de Genética, Facultad de Agronomía, Universidad Central de Venezuela, Caracas, Venezuela
| | | | - Sean Gordon
- DOE Joint Genome Institute, Berkeley, California, USA
| | - John P Vogel
- DOE Joint Genome Institute, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Joanna Lusinska
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Bruno Contreras-Moreira
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
- Department of Genetics and Plant Breeding, Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
| | - Pilar Catalán
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
- Tomsk State University, Tomsk, Russia
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5
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Woods DP, Dong Y, Bouché F, Mayer K, Varner L, Ream TS, Thrower N, Wilkerson C, Cartwright A, Sibout R, Laudencia-Chingcuanco D, Vogel J, Amasino RM. Mutations in the predicted DNA polymerase subunit POLD3 result in more rapid flowering of Brachypodium distachyon. THE NEW PHYTOLOGIST 2020; 227:1725-1735. [PMID: 32173866 DOI: 10.1111/nph.16546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 02/18/2020] [Indexed: 06/10/2023]
Abstract
The timing of reproduction is a critical developmental decision in the life cycle of many plant species. Fine mapping of a rapid-flowering mutant was done using whole-genome sequence data from bulked DNA from a segregating F2 mapping populations. The causative mutation maps to a gene orthologous with the third subunit of DNA polymerase δ (POLD3), a previously uncharacterized gene in plants. Expression analyses of POLD3 were conducted via real time qPCR to determine when and in what tissues the gene is expressed. To better understand the molecular basis of the rapid-flowering phenotype, transcriptomic analyses were conducted in the mutant vs wild-type. Consistent with the rapid-flowering mutant phenotype, a range of genes involved in floral induction and flower development are upregulated in the mutant. Our results provide the first characterization of the developmental and gene expression phenotypes that result from a lesion in POLD3 in plants.
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Affiliation(s)
- Daniel P Woods
- Laboratory of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, WI, 53706, USA
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, University of Wisconsin, 433 Babcock Dr., Madison, WI, 53706, USA
| | - Yinxin Dong
- Department of Biochemistry, University of Wisconsin, 433 Babcock Dr., Madison, WI, 53706, USA
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Frédéric Bouché
- Department of Biochemistry, University of Wisconsin, 433 Babcock Dr., Madison, WI, 53706, USA
| | - Kevin Mayer
- Laboratory of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, WI, 53706, USA
| | - Leah Varner
- Department of Biochemistry, University of Wisconsin, 433 Babcock Dr., Madison, WI, 53706, USA
| | - Thomas S Ream
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, University of Wisconsin, 433 Babcock Dr., Madison, WI, 53706, USA
| | - Nicholas Thrower
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, 53706, USA
- Department of Plant Biology and Department of Molecular Biology and Biochemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Curtis Wilkerson
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, 53706, USA
- Department of Plant Biology and Department of Molecular Biology and Biochemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Amy Cartwright
- United States Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Richard Sibout
- INRAE, UR BIA, F-44316, Nantes, France
- Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | | | - John Vogel
- United States Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- University of California Berkeley, Berkeley, CA, 94704, USA
| | - Richard M Amasino
- Laboratory of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, WI, 53706, USA
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, University of Wisconsin, 433 Babcock Dr., Madison, WI, 53706, USA
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6
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Gladala‐Kostarz A, Doonan JH, Bosch M. Mechanical stimulation in Brachypodium distachyon: Implications for fitness, productivity, and cell wall properties. PLANT, CELL & ENVIRONMENT 2020; 43:1314-1330. [PMID: 31955437 PMCID: PMC7318644 DOI: 10.1111/pce.13724] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/18/2019] [Accepted: 01/10/2020] [Indexed: 05/06/2023]
Abstract
Mechanical stimulation, including exposure to wind, is a common environmental variable for plants. However, knowledge about the morphogenetic response of the grasses (Poaceae) to mechanical stimulation and impact on relevant agronomic traits is very limited. Two natural accessions of Brachypodium distachyon were exposed to wind and mechanical treatments. We surveyed a wide range of stem-related traits to determine the effect of the two treatments on plant growth, development, and stem biomass properties. Both treatments induced significant quantitative changes across multiple scales, from the whole plant down to cellular level. The two treatments resulted in shorter stems, reduced biomass, increased tissue rigidity, delayed flowering, and reduced seed yield in both accessions. Among changes in cell wall-related features, a substantial increase in lignin content and pectin methylesterase activity was most notable. Mechanical stimulation also reduced the enzymatic sugar release from the cell wall, thus increasing biomass recalcitrance. Notably, treatments had a distinct and opposite effect on vascular bundle area in the two accessions, suggesting genetic variation in modulating these responses to mechanical stimulation. Our findings highlight that exposure of grasses to mechanical stimulation is a relevant environmental factor affecting multiple traits important for their utilization in food, feed, and bioenergy applications.
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Affiliation(s)
- Agnieszka Gladala‐Kostarz
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | - John H. Doonan
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
- National Plant Phenomics Centre, Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
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7
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Ding Y, Shi Y, Yang S. Molecular Regulation of Plant Responses to Environmental Temperatures. MOLECULAR PLANT 2020; 13:544-564. [PMID: 32068158 DOI: 10.1016/j.molp.2020.02.004] [Citation(s) in RCA: 282] [Impact Index Per Article: 70.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 05/19/2023]
Abstract
Temperature is a key factor governing the growth and development, distribution, and seasonal behavior of plants. The entire plant life cycle is affected by environmental temperatures. Plants grow rapidly and exhibit specific changes in morphology under mild average temperature conditions, a response termed thermomorphogenesis. When exposed to chilling or moist chilling low temperatures, flowering or seed germination is accelerated in some plant species; these processes are known as vernalization and cold stratification, respectively. Interestingly, once many temperate plants are exposed to chilling temperatures for some time, they can acquire the ability to resist freezing stress, a process termed cold acclimation. In the face of global climate change, heat stress has emerged as a frequent challenge, which adversely affects plant growth and development. In this review, we summarize and discuss recent progress in dissecting the molecular mechanisms regulating plant thermomorphogenesis, vernalization, and responses to extreme temperatures. We also discuss the remaining issues that are crucial for understanding the interactions between plants and temperature.
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Affiliation(s)
- Yanglin Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yiting Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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8
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Cao S, Luo X, Xie L, Gao C, Wang D, Holt BF, Lin H, Chu C, Xia X. The florigen interactor BdES43 represses flowering in the model temperate grass Brachypodium distachyon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:262-275. [PMID: 31782581 DOI: 10.1111/tpj.14622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 10/25/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023]
Abstract
FLOWERING LOCUS T (FT) protein, physiologically florigen, has been identified as a system integrator of numerous flowering time pathways in many studies, and its homologs are found throughout the plant lineage. It is important to uncover how precisely florigenic homologs contribute to flowering initiation and how these factors interact genetically. Here we dissected the function of Brachypodium FT orthologs BdFTL1 and BdFTL2 using overexpression and gene-editing experiments. Transgenic assays showed that both BdFTL1 and BdFTL2 could promote flowering, whereas BdFTL2 was essential for flowering initiation. Notably, BdFTL1 is subject to alternative splicing (AS), and its transcriptional level and AS are significantly affected by BdFTL2. Additionally, BdFTL2 could bind with the PHD-containing protein BdES43, an H3K4me3 reader. Furthermore, BdES43 was antagonistic to BdFTL2 in flowering initiation in a transcription-dependent manner and significantly affected BdFTL1 expression. BdFTL2, BdES43 and H3K4me3 also had highly similar distribution patterns within the BdFTL1 locus, indicating their interplay in regulating target genes. Taken together, florigen BdFTL2 functions as a potential epigenetic effector of BdFTL1 by interacting with a BdES43-H3K4me3 complex. This finding provides an additional insight for the regulatory mechanism underlying the multifaceted roles of florigen.
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Affiliation(s)
- Shuanghe Cao
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xumei Luo
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Li Xie
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Caixia Gao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Daowen Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Ben F Holt
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA
| | - Hao Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Chengcai Chu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
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9
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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: 12] [Impact Index Per Article: 3.0] [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.
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10
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Luo X, He Y. Experiencing winter for spring flowering: A molecular epigenetic perspective on vernalization. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:104-117. [PMID: 31829495 DOI: 10.1111/jipb.12896] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 12/10/2019] [Indexed: 05/17/2023]
Abstract
Many over-wintering plants, through vernalization, overcome a block to flowering and thus acquire competence to flower in the following spring after experiencing prolonged cold exposure or winter cold. The vernalization pathways in different angiosperm lineages appear to have convergently evolved to adapt to temperate climates. Molecular and epigenetic mechanisms for vernalization regulation have been well studied in the crucifer model plant Arabidopsis thaliana. Here, we review recent progresses on the vernalization pathway in Arabidopsis. In addition, we summarize current molecular and genetic understandings of vernalization regulation in temperate grasses including wheat and Brachypodium, two monocots from Pooideae, followed by a brief discussion on divergence of the vernalization pathways between Brassicaceae and Pooideae.
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Affiliation(s)
- Xiao Luo
- National Key Laboratory of Plant Molecular Genetics & Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yuehui He
- National Key Laboratory of Plant Molecular Genetics & Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Sciences, Shanghai, 201602, China
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11
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Martin SL, Parent JS, Laforest M, Page E, Kreiner JM, James T. Population Genomic Approaches for Weed Science. PLANTS (BASEL, SWITZERLAND) 2019; 8:E354. [PMID: 31546893 PMCID: PMC6783936 DOI: 10.3390/plants8090354] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/12/2019] [Accepted: 09/14/2019] [Indexed: 12/16/2022]
Abstract
Genomic approaches are opening avenues for understanding all aspects of biological life, especially as they begin to be applied to multiple individuals and populations. However, these approaches typically depend on the availability of a sequenced genome for the species of interest. While the number of genomes being sequenced is exploding, one group that has lagged behind are weeds. Although the power of genomic approaches for weed science has been recognized, what is needed to implement these approaches is unfamiliar to many weed scientists. In this review we attempt to address this problem by providing a primer on genome sequencing and provide examples of how genomics can help answer key questions in weed science such as: (1) Where do agricultural weeds come from; (2) what genes underlie herbicide resistance; and, more speculatively, (3) can we alter weed populations to make them easier to control? This review is intended as an introduction to orient weed scientists who are thinking about initiating genome sequencing projects to better understand weed populations, to highlight recent publications that illustrate the potential for these methods, and to provide direction to key tools and literature that will facilitate the development and execution of weed genomic projects.
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Affiliation(s)
- Sara L Martin
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Jean-Sebastien Parent
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Martin Laforest
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada.
| | - Eric Page
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Harrow, ON N0R 1G0, Canada.
| | - Julia M Kreiner
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
| | - Tracey James
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
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12
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Onda Y, Inoue K, Sawada Y, Shimizu M, Takahagi K, Uehara-Yamaguchi Y, Hirai MY, Garvin DF, Mochida K. Genetic Variation for Seed Metabolite Levels in Brachypodium distachyon. Int J Mol Sci 2019; 20:ijms20092348. [PMID: 31083584 PMCID: PMC6540107 DOI: 10.3390/ijms20092348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/27/2019] [Indexed: 12/27/2022] Open
Abstract
Metabolite composition and concentrations in seed grains are important traits of cereals. To identify the variation in the seed metabolotypes of a model grass, namely Brachypodium distachyon, we applied a widely targeted metabolome analysis to forty inbred lines of B. distachyon and examined the accumulation patterns of 183 compounds in the seeds. By comparing the metabolotypes with the population structure of these lines, we found signature metabolites that represent different accumulation patterns for each of the three B. distachyon subpopulations. Moreover, we found that thirty-seven metabolites exhibited significant differences in their accumulation between the lines Bd21 and Bd3-1. Using a recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21, we identified the quantitative trait loci (QTLs) linked with this variation in the accumulation of thirteen metabolites. Our metabolite QTL analysis illustrated that different genetic factors may presumably regulate the accumulation of 4-pyridoxate and pyridoxamine in vitamin B6 metabolism. Moreover, we found two QTLs on chromosomes 1 and 4 that affect the accumulation of an anthocyanin, chrysanthemin. These QTLs genetically interacted to regulate the accumulation of this compound. This study demonstrates the potential for metabolite QTL mapping in B. distachyon and provides new insights into the genetic dissection of metabolomic traits in temperate grasses.
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Affiliation(s)
- Yoshihiko Onda
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yuji Sawada
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Minami Shimizu
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Kotaro Takahagi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yukiko Uehara-Yamaguchi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Masami Y Hirai
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - David F Garvin
- Plant Science Research Unit, United States Department of Agriculture, Agricultural Research Service, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Institute of Plant Science and Resource, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan.
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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13
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Divergent roles of FT-like 9 in flowering transition under different day lengths in Brachypodium distachyon. Nat Commun 2019; 10:812. [PMID: 30778068 PMCID: PMC6379408 DOI: 10.1038/s41467-019-08785-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/24/2019] [Accepted: 01/30/2019] [Indexed: 12/13/2022] Open
Abstract
Timing of reproductive transition is precisely modulated by environmental cues in flowering plants. Facultative long-day plants, including Arabidopsis and temperate grasses, trigger rapid flowering in long-day conditions (LDs) and delay flowering under short-day conditions (SDs). Here, we characterize a SD-induced FLOWERING LOCUS T ortholog, FT-like 9 (FTL9), that promotes flowering in SDs but inhibits flowering in LDs in Brachypodium distachyon. Mechanistically, like photoperiod-inductive FT1, FTL9 can interact with FD1 to form a flowering activation complex (FAC), but the floral initiation efficiency of FTL9-FAC is much lower than that of FT1-FAC, thereby resulting in a positive role for FTL9 in promoting floral transition when FT1 is not expressed, but a dominant-negative role when FT1 accumulates significantly. We also find that CONSTANS 1 (CO1) can suppress FTL9 in addition to stimulate FT1 to enhance accelerated flowering under LDs. Our findings on the antagonistic functions of FTL9 under different day-length environments will contribute to understanding the multifaceted roles of FT in fine-tune modulation of photoperiodic flowering in plants. Plant flowering time is modified by day length. Here the authors show that the model grass Brachypodium distachyon expresses different homologs of FT in short and long days to produce floral activator complexes with altered activities contributing to photoperiod-dependence of flowering time.
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14
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Wilson PB, Streich JC, Murray KD, Eichten SR, Cheng R, Aitken NC, Spokas K, Warthmann N, Gordon SP, Vogel JP, Borevitz JO. Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate. Genetics 2019; 211:317-331. [PMID: 30446522 PMCID: PMC6325704 DOI: 10.1534/genetics.118.301589] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 11/08/2018] [Indexed: 01/29/2023] Open
Abstract
The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translation to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and genotyped by sequencing. Overall, 1897 samples were classified into two diploid or allopolyploid species, and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines was selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22, and 47 QTL were identified for flowering time, early vigor, and energy traits, respectively. The results highlight the genomic structure of the Brachypodium species complex, and the diploid lines provided a resource that allows complex trait dissection within this grass model species.
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Affiliation(s)
- Pip B Wilson
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Jared C Streich
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Kevin D Murray
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Steve R Eichten
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Riyan Cheng
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
- Department of Psychiatry, University of California San Diego, La Jolla, California 92093
| | - Nicola C Aitken
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
- Ecogenomics and Bioinformatics Lab, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Kurt Spokas
- Soil and Water Management, Agricultural Research Service, United States Department of Agricutlture (USDA), St. Paul, Minnesota 55108
| | - Norman Warthmann
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Sean P Gordon
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598
| | - John P Vogel
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598
| | - Justin O Borevitz
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
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15
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Omidvar V, Dugyala S, Li F, Rottschaefer SM, Miller ME, Ayliffe M, Moscou MJ, Kianian SF, Figueroa M. Detection of Race-Specific Resistance Against Puccinia coronata f. sp. avenae in Brachypodium Species. PHYTOPATHOLOGY 2018; 108:1443-1454. [PMID: 29923800 DOI: 10.1094/phyto-03-18-0084-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Oat crown rust caused by Puccinia coronata f. sp. avenae is the most destructive foliar disease of cultivated oat. Characterization of genetic factors controlling resistance responses to Puccinia coronata f. sp. avenae in nonhost species could provide new resources for developing disease protection strategies in oat. We examined symptom development and fungal colonization levels of a collection of Brachypodium distachyon and B. hybridum accessions infected with three North American P. coronata f. sp. avenae isolates. Our results demonstrated that colonization phenotypes are dependent on both host and pathogen genotypes, indicating a role for race-specific responses in these interactions. These responses were independent of the accumulation of reactive oxygen species. Expression analysis of several defense-related genes suggested that salicylic acid and ethylene-mediated signaling but not jasmonic acid are components of resistance reaction to P. coronata f. sp. avenae. Our findings provide the basis to conduct a genetic inheritance study to examine whether effector-triggered immunity contributes to nonhost resistance to P. coronata f. sp. avenae in Brachypodium spp.
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Affiliation(s)
- Vahid Omidvar
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Sheshanka Dugyala
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Feng Li
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Susan M Rottschaefer
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Marisa E Miller
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Mick Ayliffe
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Matthew J Moscou
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Shahryar F Kianian
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Melania Figueroa
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
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16
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Bettgenhaeuser J, Gardiner M, Spanner R, Green P, Hernández-Pinzón I, Hubbard A, Ayliffe M, Moscou MJ. The genetic architecture of colonization resistance in Brachypodium distachyon to non-adapted stripe rust (Puccinia striiformis) isolates. PLoS Genet 2018; 14:e1007637. [PMID: 30265666 PMCID: PMC6161849 DOI: 10.1371/journal.pgen.1007637] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 08/15/2018] [Indexed: 12/19/2022] Open
Abstract
Multilayered defense responses ensure that plants are hosts to only a few adapted pathogens in the environment. The host range of a plant pathogen depends on its ability to fully overcome plant defense barriers, with failure at any single step sufficient to prevent life cycle completion of the pathogen. Puccinia striiformis, the causal agent of stripe rust (=yellow rust), is an agronomically important obligate biotrophic fungal pathogen of wheat and barley. It is generally unable to complete its life cycle on the non-adapted wild grass species Brachypodium distachyon, but natural variation exists for the degree of hyphal colonization by Puccinia striiformis. Using three B. distachyon mapping populations, we identified genetic loci conferring colonization resistance to wheat-adapted and barley-adapted isolates of P. striiformis. We observed a genetic architecture composed of two major effect QTLs (Yrr1 and Yrr3) restricting the colonization of P. striiformis. Isolate specificity was observed for Yrr1, whereas Yrr3 was effective against all tested P. striiformis isolates. Plant immune receptors of the nucleotide binding, leucine-rich repeat (NB-LRR) encoding gene family are present at the Yrr3 locus, whereas genes of this family were not identified at the Yrr1 locus. While it has been proposed that resistance to adapted and non-adapted pathogens are inherently different, the observation of (1) a simple genetic architecture of colonization resistance, (2) isolate specificity of major and minor effect QTLs, and (3) NB-LRR encoding genes at the Yrr3 locus suggest that factors associated with resistance to adapted pathogens are also critical for non-adapted pathogens.
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Affiliation(s)
| | | | | | - Phon Green
- The Sainsbury Laboratory, Norwich, United Kingdom
| | | | - Amelia Hubbard
- National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Matthew J. Moscou
- The Sainsbury Laboratory, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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17
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Lomax A, Woods DP, Dong Y, Bouché F, Rong Y, Mayer KS, Zhong X, Amasino RM. An ortholog of CURLY LEAF/ENHANCER OF ZESTE like-1 is required for proper flowering in Brachypodium distachyon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:871-882. [PMID: 29314414 DOI: 10.1111/tpj.13815] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/29/2017] [Accepted: 12/04/2017] [Indexed: 05/22/2023]
Abstract
Many plants require prolonged exposure to cold to acquire the competence to flower. The process by which cold exposure results in competence is known as vernalization. In Arabidopsis thaliana, vernalization leads to the stable repression of the floral repressor FLOWERING LOCUS C via chromatin modification, including an increase of trimethylation on lysine 27 of histone H3 (H3K27me3) by Polycomb Repressive Complex 2 (PRC2). Vernalization in pooids is associated with the stable induction of a floral promoter, VERNALIZATION 1 (VRN1). From a screen for mutants with a reduced vernalization requirement in the model grass Brachypodium distachyon, we identified two recessive alleles of ENHANCER OF ZESTE-LIKE 1 (EZL1). EZL1 is orthologous to A. thaliana CURLY LEAF 1, a gene that encodes the catalytic subunit of PRC2. B. distachyon ezl1 mutants flower rapidly without vernalization in long-day (LD) photoperiods; thus, EZL1 is required for the proper maintenance of the vegetative state prior to vernalization. Transcriptomic studies in ezl1 revealed mis-regulation of thousands of genes, including ectopic expression of several floral homeotic genes in leaves. Loss of EZL1 results in the global reduction of H3K27me3 and H3K27me2, consistent with this gene making a major contribution to PRC2 activity in B. distachyon. Furthermore, in ezl1 mutants, the flowering genes VRN1 and AGAMOUS (AG) are ectopically expressed and have reduced H3K27me3. Artificial microRNA knock-down of either VRN1 or AG in ezl1-1 mutants partially restores wild-type flowering behavior in non-vernalized plants, suggesting that ectopic expression in ezl1 mutants may contribute to the rapid-flowering phenotype.
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Affiliation(s)
- Aaron Lomax
- Laboratory of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, WI, 53706, USA
- Department of Biochemistry, University of Wisconsin, 433 Babcock Dr., Madison, WI, 53706, USA
| | - Daniel P Woods
- Laboratory of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, WI, 53706, USA
- Department of Biochemistry, University of Wisconsin, 433 Babcock Dr., Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yinxin Dong
- Department of Biochemistry, University of Wisconsin, 433 Babcock Dr., Madison, WI, 53706, USA
| | - Frédéric Bouché
- Department of Biochemistry, University of Wisconsin, 433 Babcock Dr., Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ying Rong
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Kevin S Mayer
- Laboratory of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, Madison, WI, 53705, USA
| | - Xuehua Zhong
- Laboratory of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, Madison, WI, 53705, USA
| | - Richard M Amasino
- Laboratory of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, WI, 53706, USA
- Department of Biochemistry, University of Wisconsin, 433 Babcock Dr., Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
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18
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Establishment of a vernalization requirement in Brachypodium distachyon requires REPRESSOR OF VERNALIZATION1. Proc Natl Acad Sci U S A 2017; 114:6623-6628. [PMID: 28584114 DOI: 10.1073/pnas.1700536114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A requirement for vernalization, the process by which prolonged cold exposure provides competence to flower, is an important adaptation to temperate climates that ensures flowering does not occur before the onset of winter. In temperate grasses, vernalization results in the up-regulation of VERNALIZATION1 (VRN1) to establish competence to flower; however, little is known about the mechanism underlying repression of VRN1 in the fall season, which is necessary to establish a vernalization requirement. Here, we report that a plant-specific gene containing a bromo-adjacent homology and transcriptional elongation factor S-II domain, which we named REPRESSOR OF VERNALIZATION1 (RVR1), represses VRN1 before vernalization in Brachypodium distachyon That RVR1 is upstream of VRN1 is supported by the observations that VRN1 is precociously elevated in an rvr1 mutant, resulting in rapid flowering without cold exposure, and the rapid-flowering rvr1 phenotype is dependent on VRN1 The precocious VRN1 expression in rvr1 is associated with reduced levels of the repressive chromatin modification H3K27me3 at VRN1, which is similar to the reduced VRN1 H3K27me3 in vernalized plants. Furthermore, the transcriptome of vernalized wild-type plants overlaps with that of nonvernalized rvr1 plants, indicating loss of rvr1 is similar to the vernalized state at a molecular level. However, loss of rvr1 results in more differentially expressed genes than does vernalization, indicating that RVR1 may be involved in processes other than vernalization despite a lack of any obvious pleiotropy in the rvr1 mutant. This study provides an example of a role for this class of plant-specific genes.
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19
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Bouché F, Woods DP, Amasino RM. Winter Memory throughout the Plant Kingdom: Different Paths to Flowering. PLANT PHYSIOLOGY 2017; 173:27-35. [PMID: 27756819 PMCID: PMC5210730 DOI: 10.1104/pp.16.01322] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 09/21/2016] [Indexed: 05/18/2023]
Abstract
Molecular mechanisms contribute to the memory of winter in different plant groups.
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Affiliation(s)
- Frédéric Bouché
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706 (F.B., D.P.W., R.M.A.); and
- United States Department of Energy Great Lakes Bioenergy Research Center, Madison, Wisconsin 53726 (D.P.W., R.M.A.)
| | - Daniel P Woods
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706 (F.B., D.P.W., R.M.A.); and
- United States Department of Energy Great Lakes Bioenergy Research Center, Madison, Wisconsin 53726 (D.P.W., R.M.A.)
| | - Richard M Amasino
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706 (F.B., D.P.W., R.M.A.); and
- United States Department of Energy Great Lakes Bioenergy Research Center, Madison, Wisconsin 53726 (D.P.W., R.M.A.)
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20
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Amasino RM, Cheung AY, Dresselhaus T, Kuhlemeier C. Focus on Flowering and Reproduction. PLANT PHYSIOLOGY 2017; 173:1-4. [PMID: 28049854 PMCID: PMC5210767 DOI: 10.1104/pp.16.01867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Richard M Amasino
- Guest Editor
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Alice Y Cheung
- Associate Editor
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003
| | - Thomas Dresselhaus
- Guest Editor
- Cell Biology and Plant Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Cris Kuhlemeier
- Monitoring Editor
- Institute of Plant Sciences, University of Bern, 3013 Bern, Switzerland
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21
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Woods DP, Bednarek R, Bouché F, Gordon SP, Vogel JP, Garvin DF, Amasino RM. Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon. PLANT PHYSIOLOGY 2017; 173:269-279. [PMID: 27742753 PMCID: PMC5210718 DOI: 10.1104/pp.16.01178] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/10/2016] [Indexed: 05/03/2023]
Abstract
The transition to reproductive development is a crucial step in the plant life cycle, and the timing of this transition is an important factor in crop yields. Here, we report new insights into the genetic control of natural variation in flowering time in Brachypodium distachyon, a nondomesticated pooid grass closely related to cereals such as wheat (Triticum spp.) and barley (Hordeum vulgare L.). A recombinant inbred line population derived from a cross between the rapid-flowering accession Bd21 and the delayed-flowering accession Bd1-1 were grown in a variety of environmental conditions to enable exploration of the genetic architecture of flowering time. A genotyping-by-sequencing approach was used to develop SNP markers for genetic map construction, and quantitative trait loci (QTLs) that control differences in flowering time were identified. Many of the flowering-time QTLs are detected across a range of photoperiod and vernalization conditions, suggesting that the genetic control of flowering within this population is robust. The two major QTLs identified in undomesticated B. distachyon colocalize with VERNALIZATION1/PHYTOCHROME C and VERNALIZATION2, loci identified as flowering regulators in the domesticated crops wheat and barley. This suggests that variation in flowering time is controlled in part by a set of genes broadly conserved within pooid grasses.
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Affiliation(s)
- Daniel P Woods
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.B., F.B., R.M.A.)
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (S.P.G., J.P.V.); and
- USDA-ARS Plant Science Research Unit, University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, Minnesota 55108 (D.F.G.)
| | - Ryland Bednarek
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.B., F.B., R.M.A.)
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (S.P.G., J.P.V.); and
- USDA-ARS Plant Science Research Unit, University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, Minnesota 55108 (D.F.G.)
| | - Frédéric Bouché
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.B., F.B., R.M.A.)
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (S.P.G., J.P.V.); and
- USDA-ARS Plant Science Research Unit, University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, Minnesota 55108 (D.F.G.)
| | - Sean P Gordon
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.B., F.B., R.M.A.)
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (S.P.G., J.P.V.); and
- USDA-ARS Plant Science Research Unit, University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, Minnesota 55108 (D.F.G.)
| | - John P Vogel
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.B., F.B., R.M.A.)
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (S.P.G., J.P.V.); and
- USDA-ARS Plant Science Research Unit, University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, Minnesota 55108 (D.F.G.)
| | - David F Garvin
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.)
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.B., F.B., R.M.A.)
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (S.P.G., J.P.V.); and
- USDA-ARS Plant Science Research Unit, University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, Minnesota 55108 (D.F.G.)
| | - Richard M Amasino
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.);
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.M.A.);
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (D.P.W., R.B., F.B., R.M.A.);
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598 (S.P.G., J.P.V.); and
- USDA-ARS Plant Science Research Unit, University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, Minnesota 55108 (D.F.G.)
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Fisher LHC, Han J, Corke FMK, Akinyemi A, Didion T, Nielsen KK, Doonan JH, Mur LAJ, Bosch M. Linking Dynamic Phenotyping with Metabolite Analysis to Study Natural Variation in Drought Responses of Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2016; 7:1751. [PMID: 27965679 PMCID: PMC5126067 DOI: 10.3389/fpls.2016.01751] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/07/2016] [Indexed: 05/23/2023]
Abstract
Drought is an important environmental stress limiting the productivity of major crops worldwide. Understanding drought tolerance and possible mechanisms for improving drought resistance is therefore a prerequisite to develop drought-tolerant crops that produce significant yields with reduced amounts of water. Brachypodium distachyon (Brachypodium) is a key model species for cereals, forage grasses, and energy grasses. In this study, initial screening of a Brachypodium germplasm collection consisting of 138 different ecotypes exposed to progressive drought, highlighted the natural variation in morphology, biomass accumulation, and responses to drought stress. A core set of ten ecotypes, classified as being either tolerant, susceptible or intermediate, in response to drought stress, were exposed to mild or severe (respectively, 15 and 0% soil water content) drought stress and phenomic parameters linked to growth and color changes were assessed. When exposed to severe drought stress, phenotypic data and metabolite profiling combined with multivariate analysis revealed a remarkable consistency in separating the selected ecotypes into their different pre-defined drought tolerance groups. Increases in several metabolites, including for the phytohormones jasmonic acid and salicylic acid, and TCA-cycle intermediates, were positively correlated with biomass yield and with reduced yellow pixel counts; suggestive of delayed senescence, both key target traits for crop improvement to drought stress. While metabolite analysis also separated ecotypes into the distinct tolerance groupings after exposure to mild drought stress, similar analysis of the phenotypic data failed to do so, confirming the value of metabolomics to investigate early responses to drought stress. The results highlight the potential of combining the analyses of phenotypic and metabolic responses to identify key mechanisms and markers associated with drought tolerance in both the Brachypodium model plant as well as agronomically important crops.
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Affiliation(s)
- Lorraine H. C. Fisher
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Jiwan Han
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Fiona M. K. Corke
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Aderemi Akinyemi
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | | | | | - John H. Doonan
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Luis A. J. Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
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