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Minadakis N, Kaderli L, Horvath R, Bourgeois Y, Xu W, Thieme M, Woods DP, Roulin AC. Polygenic architecture of flowering time and its relationship with local environments in the grass Brachypodium distachyon. Genetics 2024; 227:iyae042. [PMID: 38504651 PMCID: PMC11075549 DOI: 10.1093/genetics/iyae042] [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: 01/12/2024] [Revised: 01/12/2024] [Accepted: 03/07/2024] [Indexed: 03/21/2024] Open
Abstract
Synchronizing the timing of reproduction with the environment is crucial in the wild. Among the multiple mechanisms, annual plants evolved to sense their environment, the requirement of cold-mediated vernalization is a major process that prevents individuals from flowering during winter. In many annual plants including crops, both a long and short vernalization requirement can be observed within species, resulting in so-called early-(spring) and late-(winter) flowering genotypes. Here, using the grass model Brachypodium distachyon, we explored the link between flowering-time-related traits (vernalization requirement and flowering time), environmental variation, and diversity at flowering-time genes by combining measurements under greenhouse and outdoor conditions. These experiments confirmed that B. distachyon natural accessions display large differences regarding vernalization requirements and ultimately flowering time. We underline significant, albeit quantitative effects of current environmental conditions on flowering-time-related traits. While disentangling the confounding effects of population structure on flowering-time-related traits remains challenging, population genomics analyses indicate that well-characterized flowering-time genes may contribute significantly to flowering-time variation and display signs of polygenic selection. Flowering-time genes, however, do not colocalize with genome-wide association peaks obtained with outdoor measurements, suggesting that additional genetic factors contribute to flowering-time variation in the wild. Altogether, our study fosters our understanding of the polygenic architecture of flowering time in a natural grass system and opens new avenues of research to investigate the gene-by-environment interaction at play for this trait.
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Affiliation(s)
- Nikolaos Minadakis
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Lars Kaderli
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Robert Horvath
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRD, 34 000 Montpellier, France
| | - Wenbo Xu
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Michael Thieme
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Daniel P Woods
- Department of Plant Sciences, University of California-Davis, 104 Robbins Hall, Davis, CA 95616, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
| | - Anne C Roulin
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstr. 107, 8008 Zürich, Switzerland
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Ludwig E, Sumner J, Berry J, Polydore S, Ficor T, Agnew E, Haines K, Greenham K, Fahlgren N, Mockler TC, Gehan MA. Natural variation in Brachypodium distachyon responses to combined abiotic stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1676-1701. [PMID: 37483133 DOI: 10.1111/tpj.16387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 06/26/2023] [Accepted: 07/05/2023] [Indexed: 07/25/2023]
Abstract
The demand for agricultural production is becoming more challenging as climate change increases global temperature and the frequency of extreme weather events. This study examines the phenotypic variation of 149 accessions of Brachypodium distachyon under drought, heat, and the combination of stresses. Heat alone causes the largest amounts of tissue damage while the combination of stresses causes the largest decrease in biomass compared to other treatments. Notably, Bd21-0, the reference line for B. distachyon, did not have robust growth under stress conditions, especially the heat and combined drought and heat treatments. The climate of origin was significantly associated with B. distachyon responses to the assessed stress conditions. Additionally, a GWAS found loci associated with changes in plant height and the amount of damaged tissue under stress. Some of these SNPs were closely located to genes known to be involved in responses to abiotic stresses and point to potential causative loci in plant stress response. However, SNPs found to be significantly associated with a response to heat or drought individually are not also significantly associated with the combination of stresses. This, with the phenotypic data, suggests that the effects of these abiotic stresses are not simply additive, and the responses to the combined stresses differ from drought and heat alone.
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Affiliation(s)
- Ella Ludwig
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Joshua Sumner
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Jeffrey Berry
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
- Bayer Crop Sciences, St. Louis, Missouri, 63017, USA
| | - Seth Polydore
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Tracy Ficor
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Erica Agnew
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Kristina Haines
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Kathleen Greenham
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
- University of Minnesota, St. Paul, Minnesota, 55108, USA
| | - Noah Fahlgren
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
| | - Malia A Gehan
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132, USA
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3
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Rodrigues AP, Pais IP, Leitão AE, Dubberstein D, Lidon FC, Marques I, Semedo JN, Rakocevic M, Scotti-Campos P, Campostrini E, Rodrigues WP, Simões-Costa MC, Reboredo FH, Partelli FL, DaMatta FM, Ribeiro-Barros AI, Ramalho JC. Uncovering the wide protective responses in Coffea spp. leaves to single and superimposed exposure of warming and severe water deficit. FRONTIERS IN PLANT SCIENCE 2024; 14:1320552. [PMID: 38259931 PMCID: PMC10801242 DOI: 10.3389/fpls.2023.1320552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/30/2023] [Indexed: 01/24/2024]
Abstract
Climate changes boosted the frequency and severity of drought and heat events, with aggravated when these stresses occur simultaneously, turning crucial to unveil the plant response mechanisms to such harsh conditions. Therefore, plant responses/resilience to single and combined exposure to severe water deficit (SWD) and heat were assessed in two cultivars of the main coffee-producing species: Coffea arabica cv. Icatu and C. canephora cv. Conilon Clone 153 (CL153). Well-watered plants (WW) were exposed to SWD under an adequate temperature of 25/20°C (day/night), and thereafter submitted to a gradual increase up to 42/30°C, and a 14-d recovery period (Rec14). Greater protective response was found to single SWD than to single 37/28°C and/or 42/30°C (except for HSP70) in both cultivars, but CL153-SWD plants showed the larger variations of leaf thermal imaging crop water stress index (CWSI, 85% rise at 37/28°C) and stomatal conductance index (IG, 66% decline at 25/20°C). Both cultivars revealed great resilience to SWD and/or 37/28°C, but a tolerance limit was surpassed at 42/30°C. Under stress combination, Icatu usually displayed lower impacts on membrane permeability, and PSII function, likely associated with various responses, usually mostly driven by drought (but often kept or even strengthened under SWD and 42/30°C). These included the photoprotective zeaxanthin and lutein, antioxidant enzymes (superoxide dismutase, Cu,Zn-SOD; ascorbate peroxidase, APX), HSP70, arabinose and mannitol (involving de novo sugar synthesis), contributing to constrain lipoperoxidation. Also, only Icatu showed a strong reinforcement of glutathione reductase activity under stress combination. In general, the activities of antioxidative enzymes declined at 42/30°C (except Cu,Zn-SOD in Icatu and CAT in CL153), but HSP70 and raffinose were maintained higher in Icatu, whereas mannitol and arabinose markedly increased in CL153. Overall, a great leaf plasticity was found, especially in Icatu that revealed greater responsiveness of coordinated protection under all experimental conditions, justifying low PIChr and absence of lipoperoxidation increase at 42/30°C. Despite a clear recovery by Rec14, some aftereffects persisted especially in SWD plants (e.g., membranes), relevant in terms of repeated stress exposure and full plant recovery to stresses.
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Affiliation(s)
- Ana P. Rodrigues
- Laboratório de Interações Planta-Ambiente e Biodiversidade (PlantStress & Biodiversity), Centro de Estudos Florestais (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Oeiras, Lisboa, Portugal
- Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Lisboa, Portugal
| | - Isabel P. Pais
- Unidade de Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Oeiras, Portugal
- Unidade de GeoBiociências, GeoEngenharias e GeoTecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - António E. Leitão
- Laboratório de Interações Planta-Ambiente e Biodiversidade (PlantStress & Biodiversity), Centro de Estudos Florestais (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Oeiras, Lisboa, Portugal
- Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Lisboa, Portugal
- Unidade de GeoBiociências, GeoEngenharias e GeoTecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Danielly Dubberstein
- Laboratório de Interações Planta-Ambiente e Biodiversidade (PlantStress & Biodiversity), Centro de Estudos Florestais (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Oeiras, Lisboa, Portugal
- Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Lisboa, Portugal
- Centro Univ. Norte do Espírito Santo (CEUNES), Dept. Ciências Agrárias e Biológicas (DCAB), Univ. Federal Espírito Santo (UFES), São Mateus, ES, Brazil
- Assistência Técnica e Gerencial em Cafeicultura - Serviço Nacional de Aprendizagem Rural (SENAR), Porto Velho, RO, Brazil
| | - Fernando C. Lidon
- Unidade de GeoBiociências, GeoEngenharias e GeoTecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Isabel Marques
- Laboratório de Interações Planta-Ambiente e Biodiversidade (PlantStress & Biodiversity), Centro de Estudos Florestais (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Oeiras, Lisboa, Portugal
- Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Lisboa, Portugal
| | - José N. Semedo
- Unidade de Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Oeiras, Portugal
- Unidade de GeoBiociências, GeoEngenharias e GeoTecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Miroslava Rakocevic
- Centro Univ. Norte do Espírito Santo (CEUNES), Dept. Ciências Agrárias e Biológicas (DCAB), Univ. Federal Espírito Santo (UFES), São Mateus, ES, Brazil
| | - Paula Scotti-Campos
- Unidade de Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Oeiras, Portugal
- Unidade de GeoBiociências, GeoEngenharias e GeoTecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Eliemar Campostrini
- Setor de Fisiologia Vegetal, Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense, Rio de Janeiro, Brazil
| | - Weverton P. Rodrigues
- Setor de Fisiologia Vegetal, Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense, Rio de Janeiro, Brazil
- Centro de Ciências Agrárias, Naturais e Letras, Universidade Estadual da Região Tocantina do Maranhão, Maranhão, Brazil
| | - Maria Cristina Simões-Costa
- Laboratório de Interações Planta-Ambiente e Biodiversidade (PlantStress & Biodiversity), Centro de Estudos Florestais (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Oeiras, Lisboa, Portugal
- Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Lisboa, Portugal
| | - Fernando H. Reboredo
- Unidade de GeoBiociências, GeoEngenharias e GeoTecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Fábio L. Partelli
- Centro Univ. Norte do Espírito Santo (CEUNES), Dept. Ciências Agrárias e Biológicas (DCAB), Univ. Federal Espírito Santo (UFES), São Mateus, ES, Brazil
| | - Fábio M. DaMatta
- Departamento de Biologia Vegetal, Universidade Federal Viçosa (UFV), Viçosa, MG, Brazil
| | - Ana I. Ribeiro-Barros
- Laboratório de Interações Planta-Ambiente e Biodiversidade (PlantStress & Biodiversity), Centro de Estudos Florestais (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Oeiras, Lisboa, Portugal
- Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Lisboa, Portugal
- Unidade de GeoBiociências, GeoEngenharias e GeoTecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - José C. Ramalho
- Laboratório de Interações Planta-Ambiente e Biodiversidade (PlantStress & Biodiversity), Centro de Estudos Florestais (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Oeiras, Lisboa, Portugal
- Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Lisboa, Portugal
- Unidade de GeoBiociências, GeoEngenharias e GeoTecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
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4
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FitzPatrick JA, Doucet BI, Holt SD, Patterson CM, Kooyers NJ. Unique drought resistance strategies occur among monkeyflower populations spanning an aridity gradient. AMERICAN JOURNAL OF BOTANY 2023; 110:e16207. [PMID: 37347451 DOI: 10.1002/ajb2.16207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/30/2023] [Accepted: 05/01/2023] [Indexed: 06/23/2023]
Abstract
PREMISE Annual plants often exhibit drought-escape and avoidance strategies to cope with limited water availability. Determining the extent of variation and factors underlying the evolution of divergent strategies is necessary for determining population responses to more frequent and severe droughts. METHODS We leveraged five Mimulus guttatus populations collected across an aridity gradient within manipulative drought and quantitative genetics experiments to examine constitutive and terminal-drought induced responses in drought resistance traits. RESULTS Populations varied considerably in drought-escape- and drought-avoidance-associated traits. The most mesic population demonstrated a unique resource conservative strategy. Xeric populations exhibited extreme plasticity when exposed to terminal drought that included flowering earlier at shorter heights, increasing water-use efficiency, and shifting C:N ratios. However, plasticity responses also differed between populations, with two populations slowing growth rates and flowering at earlier nodes and another population increasing growth rate. While nearly all traits were heritable, phenotypic correlations differed substantially between treatments and often, populations. CONCLUSIONS Our results suggest drought resistance strategies of populations may be finely adapted to local patterns of water availability. Substantial plastic responses suggest that xeric populations can already acclimate to drought through plasticity, but populations not frequently exposed to drought may be more vulnerable.
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Affiliation(s)
| | - Braden I Doucet
- Department of Biology, University of Louisiana, Lafayette, LA, 70503, USA
| | - Stacy D Holt
- Department of Biology, University of Louisiana, Lafayette, LA, 70503, USA
| | | | - Nicholas J Kooyers
- Department of Biology, University of Louisiana, Lafayette, LA, 70503, USA
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Khasanova A, Edwards J, Bonnette J, Singer E, Haque T, Juenger TE. Quantitative genetic-by-soil microbiome interactions in a perennial grass affect functional traits. Proc Biol Sci 2023; 290:20221350. [PMID: 36651054 PMCID: PMC9845970 DOI: 10.1098/rspb.2022.1350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Plants interact with diverse microbiomes that can impact plant growth and performance. Recent studies highlight the potential beneficial aspects of plant microbiomes, including the possibility that microbes facilitate the process of local adaptation in their host plants. Microbially mediated local adaptation in plants occurs when local host genotypes have higher fitness than foreign genotypes because of their affiliation with locally beneficial microbes. Here, plant adaptation results from genetic interactions of the host with locally beneficial microbes (e.g. host genotype-by-microbiome interactions). We used a recombinant inbred line (RIL) mapping population derived from upland and lowland ecotypes of the diploid C4 perennial bunch grass Panicum hallii to explore quantitative genetic responses to soil microbiomes focusing on functional root and shoot traits involved in ecotypic divergence. We show that the growth and development of ecotypes and their trait divergence depends on soil microbiomes. Moreover, we find that the genetic architecture is modified by soil microbiomes, revealing important plant genotype-by-microbiome interactions for quantitative traits. We detected a number of quantitative trait loci (QTL) that interact with the soil microbiome. Our results highlight the importance of microbial interactions in ecotypic divergence and trait genetic architecture in C4 perennial grasses.
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Affiliation(s)
- Albina Khasanova
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78712, USA,Lawrence Berkeley National Laboratory, 717 Potter Street, Berkeley, CA 94710, USA
| | - Joseph Edwards
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78712, USA
| | - Jason Bonnette
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78712, USA
| | - Esther Singer
- Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA,Lawrence Berkeley National Laboratory, 717 Potter Street, Berkeley, CA 94710, USA
| | - Taslima Haque
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78712, USA
| | - Thomas E. Juenger
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78712, USA
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6
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Napier JD, Heckman RW, Juenger TE. Gene-by-environment interactions in plants: Molecular mechanisms, environmental drivers, and adaptive plasticity. THE PLANT CELL 2023; 35:109-124. [PMID: 36342220 PMCID: PMC9806611 DOI: 10.1093/plcell/koac322] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/03/2022] [Indexed: 05/13/2023]
Abstract
Plants demonstrate a broad range of responses to environmental shifts. One of the most remarkable responses is plasticity, which is the ability of a single plant genotype to produce different phenotypes in response to environmental stimuli. As with all traits, the ability of plasticity to evolve depends on the presence of underlying genetic diversity within a population. A common approach for evaluating the role of genetic variation in driving differences in plasticity has been to study genotype-by-environment interactions (G × E). G × E occurs when genotypes produce different phenotypic trait values in response to different environments. In this review, we highlight progress and promising methods for identifying the key environmental and genetic drivers of G × E. Specifically, methodological advances in using algorithmic and multivariate approaches to understand key environmental drivers combined with new genomic innovations can greatly increase our understanding about molecular responses to environmental stimuli. These developing approaches can be applied to proliferating common garden networks that capture broad natural environmental gradients to unravel the underlying mechanisms of G × E. An increased understanding of G × E can be used to enhance the resilience and productivity of agronomic systems.
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Affiliation(s)
- Joseph D Napier
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Robert W Heckman
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
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Hasterok R, Catalan P, Hazen SP, Roulin AC, Vogel JP, Wang K, Mur LAJ. Brachypodium: 20 years as a grass biology model system; the way forward? TRENDS IN PLANT SCIENCE 2022; 27:1002-1016. [PMID: 35644781 DOI: 10.1016/j.tplants.2022.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/13/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
It has been 20 years since Brachypodium distachyon was suggested as a model grass species, but ongoing research now encompasses the entire genus. Extensive Brachypodium genome sequencing programmes have provided resources to explore the determinants and drivers of population diversity. This has been accompanied by cytomolecular studies to make Brachypodium a platform to investigate speciation, polyploidisation, perenniality, and various aspects of chromosome and interphase nucleus organisation. The value of Brachypodium as a functional genomic platform has been underscored by the identification of key genes for development, biotic and abiotic stress, and cell wall structure and function. While Brachypodium is relevant to the biofuel industry, its impact goes far beyond that as an intriguing model to study climate change and combinatorial stress.
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Affiliation(s)
- 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 40-032, Poland.
| | - Pilar Catalan
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca 22071, Spain; Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza E-50059, Spain
| | - Samuel P Hazen
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Anne C Roulin
- Department of Plant and Microbial Biology, University of Zürich, Zürich 8008, Switzerland
| | - John P Vogel
- DOE Joint Genome Institute, Berkeley, CA 94720, USA; University California, Berkeley, Berkeley, CA 94720, USA
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong 226019, Jiangsu, China
| | - Luis A J Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Edward Llwyd Building, Aberystwyth SY23 3DA, UK; College of Agronomy, Shanxi Agricultural University, Taiyuan 030801, Shanxi, China.
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8
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Sancho R, Catalán P, Contreras‐Moreira B, Juenger TE, Des Marais DL. Patterns of pan-genome occupancy and gene coexpression under water-deficit in Brachypodium distachyon. Mol Ecol 2022; 31:5285-5306. [PMID: 35976181 PMCID: PMC9804473 DOI: 10.1111/mec.16661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/29/2022] [Accepted: 08/11/2022] [Indexed: 01/05/2023]
Abstract
Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequencing complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome. These analyses demonstrate that many genes are absent from the first reference genomes, whose analysis dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analysed weighted gene coexpression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and the differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable "occupancy" in the pan-genome - genes which are either present in all studied genotypes or missing in some genotypes - show different distributions among coexpression modules. Coexpression analysis united genes expressed in drought-stressed plants into nine modules covering 72 hub genes (87 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 190 hub genes (251 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.
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Affiliation(s)
- Rubén Sancho
- Department of Agricultural and Environmental Sciences, High Polytechnic School of HuescaUniversity of ZaragozaHuescaSpain,Unidad Associada al CSIC, Grupo de BioquímicaGrupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR)ZaragozaSpain
| | - Pilar Catalán
- Department of Agricultural and Environmental Sciences, High Polytechnic School of HuescaUniversity of ZaragozaHuescaSpain,Unidad Associada al CSIC, Grupo de BioquímicaGrupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR)ZaragozaSpain
| | - Bruno Contreras‐Moreira
- Unidad Associada al CSIC, Grupo de BioquímicaGrupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR)ZaragozaSpain,Estación Experimental de Aula Dei‐Consejo Superior de Investigaciones CientíficasZaragozaSpain,Fundación ARAIDZaragozaSpain
| | - Thomas E. Juenger
- Department of Integrative BiologyThe University of Texas at AustinAustinTexasUSA
| | - David L. Des Marais
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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Monroe JG, Cai H, Des Marais DL. Diversity in nonlinear responses to soil moisture shapes evolutionary constraints in Brachypodium. G3 (BETHESDA, MD.) 2021; 11:jkab334. [PMID: 34570202 PMCID: PMC8664479 DOI: 10.1093/g3journal/jkab334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/15/2021] [Indexed: 12/03/2022]
Abstract
Water availability is perhaps the greatest environmental determinant of plant yield and fitness. However, our understanding of plant-water relations is limited because-like many studies of organism-environment interaction-it is primarily informed by experiments considering performance at two discrete levels-wet and dry-rather than as a continuously varying environmental gradient. Here, we used experimental and statistical methods based on function-valued traits to explore genetic variation in responses to a continuous soil moisture gradient in physiological and morphological traits among 10 genotypes across two species of the model grass genus Brachypodium. We find that most traits exhibit significant genetic variation and nonlinear responses to soil moisture variability. We also observe differences in the shape of these nonlinear responses between traits and genotypes. Emergent phenomena arise from this variation including changes in trait correlations and evolutionary constraints as a function of soil moisture. Our results point to the importance of considering diversity in nonlinear organism-environment relationships to understand plastic and evolutionary responses to changing climates.
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Affiliation(s)
- J Grey Monroe
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Haoran Cai
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David L Des Marais
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Arnold Arboretum of Harvard University, Boston, MA 02130, USA
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10
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Decena MA, Gálvez-Rojas S, Agostini F, Sancho R, Contreras-Moreira B, Des Marais DL, Hernandez P, Catalán P. Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses. PLANTS (BASEL, SWITZERLAND) 2021; 10:2664. [PMID: 34961135 PMCID: PMC8709310 DOI: 10.3390/plants10122664] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 06/14/2023]
Abstract
Dehydration proteins (dehydrins, DHNs) confer tolerance to water-stress deficit in plants. We performed a comparative genomics and evolutionary study of DHN genes in four model Brachypodium grass species. Due to limited knowledge on dehydrin expression under water deprivation stress in Brachypodium, we also performed a drought-induced gene expression analysis in 32 ecotypes of the genus' flagship species B. distachyon showing different hydric requirements. Genomic sequence analysis detected 10 types of dehydrin genes (Bdhn) across the Brachypodium species. Domain and conserved motif contents of peptides encoded by Bdhn genes revealed eight protein architectures. Bdhn genes were spread across several chromosomes. Selection analysis indicated that all the Bdhn genes were constrained by purifying selection. Three upstream cis-regulatory motifs (BES1, MYB124, ZAT) were detected in several Bdhn genes. Gene expression analysis demonstrated that only four Bdhn1-Bdhn2, Bdhn3, and Bdhn7 genes, orthologs of wheat, barley, rice, sorghum, and maize genes, were expressed in mature leaves of B. distachyon and that all of them were more highly expressed in plants under drought conditions. Brachypodium dehydrin expression was significantly correlated with drought-response phenotypic traits (plant biomass, leaf carbon and proline contents and water use efficiency increases, and leaf water and nitrogen content decreases) being more pronounced in drought-tolerant ecotypes. Our results indicate that dehydrin type and regulation could be a key factor determining the acquisition of water-stress tolerance in grasses.
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Affiliation(s)
- Maria Angeles Decena
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071 Huesca, Spain; (M.A.D.); (R.S.)
| | - Sergio Gálvez-Rojas
- ETSI Informática, Universidad de Málaga, Blvr Louis Pasteur 35, 29071 Málaga, Spain; (S.G.-R.); (F.A.)
| | - Federico Agostini
- ETSI Informática, Universidad de Málaga, Blvr Louis Pasteur 35, 29071 Málaga, Spain; (S.G.-R.); (F.A.)
- Instituto de Botánica del Nordeste, UNNE-CONICET, Corrientes W3402, Argentina
| | - Ruben Sancho
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071 Huesca, Spain; (M.A.D.); (R.S.)
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, 50018 Zaragoza, Spain;
| | - Bruno Contreras-Moreira
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, 50018 Zaragoza, Spain;
- Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas, Av. Montañana 1005, 50059 Zaragoza, Spain
| | - David L. Des Marais
- Civil and Environmental Engineering Department, Faculty of Environmental and Life Science, Massachusetts Institute of Technology, 15 Vassar Street, Cambridge, MA 02139, USA;
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible, IAS-CSIC, Menendez Pidal Ave, 14004 Córdoba, Spain
| | - Pilar Catalán
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071 Huesca, Spain; (M.A.D.); (R.S.)
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, 50018 Zaragoza, Spain;
- Departamento de Ciencias Agrarias y del Medio Natural, Tomsk State University, 36 Lenin Ave, 634050 Tomsk, Russia
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11
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Deng Y, Bossdorf O, Scheepens JF. Transgenerational effects of temperature fluctuations in Arabidopsis thaliana. AOB PLANTS 2021; 13:plab064. [PMID: 34950444 PMCID: PMC8691168 DOI: 10.1093/aobpla/plab064] [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: 04/21/2021] [Accepted: 10/09/2021] [Indexed: 06/14/2023]
Abstract
Plant stress responses can extend into the following generations, a phenomenon called transgenerational effects. Heat stress, in particular, is known to affect plant offspring, but we do not know to what extent these effects depend on the temporal patterns of the stress, and whether transgenerational responses are adaptive and genetically variable within species. To address these questions, we carried out a two-generation experiment with nine Arabidopsis thaliana genotypes. We subjected the plants to heat stress regimes that varied in timing and frequency, but not in mean temperature, and we then grew the offspring of these plants under controlled conditions as well as under renewed heat stress. The stress treatments significantly carried over to the offspring generation, with timing having stronger effects on plant phenotypes than stress frequency. However, there was no evidence that transgenerational effects were adaptive. The magnitudes of transgenerational effects differed substantially among genotypes, and for some traits the strength of plant responses was significantly associated with the climatic variability at the sites of origin. In summary, timing of heat stress not only directly affects plants, but it can also cause transgenerational effects on offspring phenotypes. Genetic variation in transgenerational effects, as well as correlations between transgenerational effects and climatic variability, indicates that transgenerational effects can evolve, and have probably already done so in the past.
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Affiliation(s)
- Ying Deng
- Institute of Evolution and Ecology, University of Tübingen, Tübingen 72076, Germany
- Natural History Research Center, Shanghai Natural History Museum, Shanghai 200041, China
| | - Oliver Bossdorf
- Institute of Evolution and Ecology, University of Tübingen, Tübingen 72076, Germany
| | - J F Scheepens
- Institute of Evolution and Ecology, University of Tübingen, Tübingen 72076, Germany
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main 60438, Germany
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12
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Azodi CB, Lloyd JP, Shiu SH. The cis-regulatory codes of response to combined heat and drought stress in Arabidopsis thaliana. NAR Genom Bioinform 2020; 2:lqaa049. [PMID: 33575601 PMCID: PMC7671360 DOI: 10.1093/nargab/lqaa049] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/22/2020] [Accepted: 07/06/2020] [Indexed: 11/24/2022] Open
Abstract
Plants respond to their environment by dynamically modulating gene expression. A powerful approach for understanding how these responses are regulated is to integrate information about cis-regulatory elements (CREs) into models called cis-regulatory codes. Transcriptional response to combined stress is typically not the sum of the responses to the individual stresses. However, cis-regulatory codes underlying combined stress response have not been established. Here we modeled transcriptional response to single and combined heat and drought stress in Arabidopsis thaliana. We grouped genes by their pattern of response (independent, antagonistic and synergistic) and trained machine learning models to predict their response using putative CREs (pCREs) as features (median F-measure = 0.64). We then developed a deep learning approach to integrate additional omics information (sequence conservation, chromatin accessibility and histone modification) into our models, improving performance by 6.2%. While pCREs important for predicting independent and antagonistic responses tended to resemble binding motifs of transcription factors associated with heat and/or drought stress, important synergistic pCREs resembled binding motifs of transcription factors not known to be associated with stress. These findings demonstrate how in silico approaches can improve our understanding of the complex codes regulating response to combined stress and help us identify prime targets for future characterization.
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Affiliation(s)
- Christina B Azodi
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - John P Lloyd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
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13
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van Munster M. Impact of Abiotic Stresses on Plant Virus Transmission by Aphids. Viruses 2020; 12:E216. [PMID: 32075208 PMCID: PMC7077179 DOI: 10.3390/v12020216] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/05/2020] [Accepted: 02/08/2020] [Indexed: 01/05/2023] Open
Abstract
Plants regularly encounter abiotic constraints, and plant response to stress has been a focus of research for decades. Given increasing global temperatures and elevated atmospheric CO2 levels and the occurrence of water stress episodes driven by climate change, plant biochemistry, in particular, plant defence responses, may be altered significantly. Environmental factors also have a wider impact, shaping viral transmission processes that rely on a complex set of interactions between, at least, the pathogen, the vector, and the host plant. This review considers how abiotic stresses influence the transmission and spread of plant viruses by aphid vectors, mainly through changes in host physiology status, and summarizes the latest findings in this research field. The direct effects of climate change and severe weather events that impact the feeding behaviour of insect vectors as well as the major traits (e.g., within-host accumulation, disease severity and transmission) of viral plant pathogens are discussed. Finally, the intrinsic capacity of viruses to react to environmental cues in planta and how this may influence viral transmission efficiency is summarized. The clear interaction between biotic (virus) and abiotic stresses is a risk that must be accounted for when modelling virus epidemiology under scenarios of climate change.
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Affiliation(s)
- Manuella van Munster
- INRA, UMR385, CIRAD TA-A54K, Campus International de Baillarguet, CEDEX 05, 34398 Montpellier, France
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14
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Li M, Kennedy A, Huybrechts M, Dochy N, Geuten K. The Effect of Ambient Temperature on Brachypodium distachyon Development. FRONTIERS IN PLANT SCIENCE 2019; 10:1011. [PMID: 31497030 PMCID: PMC6712961 DOI: 10.3389/fpls.2019.01011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/18/2019] [Indexed: 05/05/2023]
Abstract
Due to climate change, the effect of temperature on crops has become a global concern. It has been reported that minor changes in temperature can cause large decreases in crop yield. While not a crop, the model Brachypodium distachyon can help to efficiently investigate ambient temperature responses of temperate grasses, which include wheat and barley. Here, we use different accessions to explore the effect of ambient temperature on Brachypodium phenology. We recorded leaf initiation, heading time, leaf and branch number at heading, seed set time, seed weight, seed size, seed dormancy, and seed germination at different temperatures. We found that warmer temperatures promote leaf initiation so that leaf number at heading is positively correlated to temperature. Heading time is not correlated to temperature but accessions show an optimal temperature at which heading is earliest. Cool temperatures prolong seed maturation which increases seed weight. The progeny seeds of plants grown at these cool ambient temperatures show stronger dormancy, while imbibition of seeds at low temperature improves germination. Among all developmental stages, it is the duration of seed maturation that is most sensitive to temperature. The results we found reveal that temperature responses in Brachypodium are highly conserved with temperate cereals, which makes Brachypodium a good model to explore temperature responsive pathways in temperate grasses.
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Affiliation(s)
| | | | | | | | - Koen Geuten
- Department of Biology, KU Leuven, Leuven, Belgium
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15
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Lenk I, Fisher LHC, Vickers M, Akinyemi A, Didion T, Swain M, Jensen CS, Mur LAJ, Bosch M. Transcriptional and Metabolomic Analyses Indicate that Cell Wall Properties are Associated with Drought Tolerance in Brachypodium distachyon. Int J Mol Sci 2019; 20:E1758. [PMID: 30974727 PMCID: PMC6479473 DOI: 10.3390/ijms20071758] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/03/2019] [Accepted: 04/08/2019] [Indexed: 01/07/2023] Open
Abstract
Brachypodium distachyon is an established model for drought tolerance. We previously identified accessions exhibiting high tolerance, susceptibility and intermediate tolerance to drought; respectively, ABR8, KOZ1 and ABR4. Transcriptomics and metabolomic approaches were used to define tolerance mechanisms. Transcriptional analyses suggested relatively few drought responsive genes in ABR8 compared to KOZ1. Linking these to gene ontology (GO) terms indicated enrichment for "regulated stress response", "plant cell wall" and "oxidative stress" associated genes. Further, tolerance correlated with pre-existing differences in cell wall-associated gene expression including glycoside hydrolases, pectin methylesterases, expansins and a pectin acetylesterase. Metabolomic assessments of the same samples also indicated few significant changes in ABR8 with drought. Instead, pre-existing differences in the cell wall-associated metabolites correlated with drought tolerance. Although other features, e.g., jasmonate signaling were suggested in our study, cell wall-focused events appeared to be predominant. Our data suggests two different modes through which the cell wall could confer drought tolerance: (i) An active response mode linked to stress induced changes in cell wall features, and (ii) an intrinsic mode where innate differences in cell wall composition and architecture are important. Both modes seem to contribute to ABR8 drought tolerance. Identification of the exact mechanisms through which the cell wall confers drought tolerance will be important in order to inform development of drought tolerant crops.
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Affiliation(s)
- Ingo Lenk
- DLF Seeds A/S, Højerupvej 31, 4660 Store Heddinge, Denmark.
| | - Lorraine H C Fisher
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
| | - Martin Vickers
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
| | - Aderemi Akinyemi
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
| | - Thomas Didion
- DLF Seeds A/S, Højerupvej 31, 4660 Store Heddinge, Denmark.
| | - Martin Swain
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
| | | | - Luis A J Mur
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
| | - Maurice Bosch
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
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16
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Fitzpatrick CR, Mustafa Z, Viliunas J. Soil microbes alter plant fitness under competition and drought. J Evol Biol 2019; 32:438-450. [PMID: 30739360 DOI: 10.1111/jeb.13426] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 02/02/2019] [Accepted: 02/05/2019] [Indexed: 01/02/2023]
Abstract
Plants exist across varying biotic and abiotic environments, including variation in the composition of soil microbial communities. The ecological effects of soil microbes on plant communities are well known, whereas less is known about their importance for plant evolutionary processes. In particular, the net effects of soil microbes on plant fitness may vary across environmental contexts and among plant genotypes, setting the stage for microbially mediated plant evolution. Here, we assess the effects of soil microbes on plant fitness and natural selection on flowering time in different environments. We performed two experiments in which we grew Arabidopsis thaliana genotypes replicated in either live or sterilized soil microbial treatments, and across varying levels of either competition (isolation, intraspecific competition or interspecific competition) or watering (well-watered or drought). We found large effects of competition and watering on plant fitness as well as the expression and natural selection of flowering time. Soil microbes increased average plant fitness under interspecific competition and drought and shaped the response of individual plant genotypes to drought. Finally, plant tolerance to either competition or drought was uncorrelated between soil microbial treatments suggesting that the plant traits favoured under environmental stress may depend on the presence of soil microbes. In summary, our experiments demonstrate that soil microbes can have large effects on plant fitness, which depend on both the environment and individual plant genotype. Future work in natural systems is needed for a complete understanding of the evolutionary importance of interactions between plants and soil microorganisms.
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Affiliation(s)
- Connor R Fitzpatrick
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Zainab Mustafa
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Joani Viliunas
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
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17
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Genetic Variation of Growth Traits and Genotype-by-Environment Interactions in Clones of Catalpa bungei and Catalpa fargesii f. duclouxii. FORESTS 2019. [DOI: 10.3390/f10010057] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Clones of Catalpa bungei and Catalpa fargesii f. duclouxii were studied over several years in central China to explore genetic variation in growth traits and to identify clones of high wood yield and high stability. The genetic parameters for height, diameter at breast height (DBH), and stem volume of clones, were estimated. The effect of clone × year on the increment of stem volume in the two species was analyzed by genotype and genotype × environment (GGE) biplot methods. Significant differences in growth traits among clones and between species were found. The growth of C. bungei exceeded that of C. fargesii f. duclouxii after 4 years. Furthermore, from the 5th year, the repeatability and genetic variation coefficient (GCV) of the C. bungei clones were higher than those of the C. fargesii f. duclouxii clones in most cases. The phenotypic variation coefficient (PCV) of the C. fargesii f. duclouxii clones was significantly lower than that of the C. bungei clones. The repeatability of stem volume was intermediate or high in the two species. ANOVA revealed significant effects of the clone by year interaction in these two species. GGE biplot analysis revealed that wood yield and stability were largely independent in C. bungei; clones 22-03, 19-27, and 20-01 were the optimal clones in this species. In contrast, the optimal clones 63 and 128 of C. fargesii f. duclouxii combined the desired characteristics of high yield and high stability. In conclusion, our results indicated that the height and stem volume of C. bungei was under strong genetic control, whereas that of C. fargesii f. duclouxii was influenced by the environment more than by genetic effects. Genetic improvement by clone selection can be expected to be effective, as the repeatability of stem volume was high. Francis and Kannenberg’s method and GGE biplot analysis were used in combination to evaluate the clones. C. bungei clone 22-03 and C. fargesii f. duclouxii clones 63 and 128 were identified as the optimal clones, which exhibited both a high increment of stem volume and high stability.
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18
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Shaar‐Moshe L, Hayouka R, Roessner U, Peleg Z. Phenotypic and metabolic plasticity shapes life-history strategies under combinations of abiotic stresses. PLANT DIRECT 2019; 3:e00113. [PMID: 31245755 PMCID: PMC6508786 DOI: 10.1002/pld3.113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/11/2018] [Accepted: 12/23/2018] [Indexed: 05/23/2023]
Abstract
Plants developed various reversible and non-reversible acclimation mechanisms to cope with the multifaceted nature of abiotic-stress combinations. We hypothesized that in order to endure these stress combinations, plants elicit distinctive acclimation strategies through specific trade-offs between reproduction and defense. To investigate Brachypodium distachyon acclimation strategies to combinations of salinity, drought and heat, we applied a system biology approach, integrating physiological, metabolic, and transcriptional analyses. We analyzed the trade-offs among functional and performance traits, and their effects on plant fitness. A combination of drought and heat resulted in escape strategy, while under a combination of salinity and heat, plants exhibited an avoidance strategy. On the other hand, under combinations of salinity and drought, with or without heat stress, plant fitness (i.e., germination rate of subsequent generation) was severely impaired. These results indicate that under combined stresses, plants' life-history strategies were shaped by the limits of phenotypic and metabolic plasticity and the trade-offs between traits, thereby giving raise to distinct acclimations. Our findings provide a mechanistic understanding of plant acclimations to combinations of abiotic stresses and shed light on the different life-history strategies that can contribute to grass fitness and possibly to their dispersion under changing environments.
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Affiliation(s)
- Lidor Shaar‐Moshe
- The Robert H. Smith Institute of Plant Sciences and Genetics in AgricultureThe Hebrew University of JerusalemRehovotIsrael
| | - Ruchama Hayouka
- The Robert H. Smith Institute of Plant Sciences and Genetics in AgricultureThe Hebrew University of JerusalemRehovotIsrael
| | - Ute Roessner
- School of BioSciencesThe University of MelbourneMelbourneAustralia
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in AgricultureThe Hebrew University of JerusalemRehovotIsrael
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19
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Martínez LM, Fernández-Ocaña A, Rey PJ, Salido T, Amil-Ruiz F, Manzaneda AJ. Variation in functional responses to water stress and differentiation between natural allopolyploid populations in the Brachypodium distachyon species complex. ANNALS OF BOTANY 2018; 121:1369-1382. [PMID: 29893879 PMCID: PMC6007385 DOI: 10.1093/aob/mcy037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/26/2018] [Indexed: 05/21/2023]
Abstract
Background and Aims Some polyploid species show enhanced physiological tolerance to drought compared with their progenitors. However, very few studies have examined the consistency of physiological drought response between genetically differentiated natural polyploid populations, which is key to evaluation of the importance of adaptive evolution after polyploidization in those systems where drought exerts a selective pressure. Methods A comparative functional approach was used to investigate differentiation of drought-tolerance-related traits in the Brachypodium species complex, a model system for grass polyploid adaptive speciation and functional genomics that comprises three closely related annual species: the two diploid parents, B. distachyon and B. stacei, and the allotetraploid derived from them, B. hybridum. Differentiation of drought-tolerance-related traits between ten genetically distinct B. hybridum populations and its ecological correlates was further analysed. Key Results The functional drought response is overall well differentiated between Brachypodium species. Brachypodium hybridum allotetraploids showed a transgressive expression pattern in leaf phytohormone content in response to drought. In contrast, other B. hybridum physiological traits correlated to B. stacei ones. Particularly, proline and water content were the traits that best discriminated these species from B. distachyon under drought. Conclusions After polyploid formation and/or colonization, B. hybridum populations have adaptively diverged physiologically and genetically in response to variations in aridity.
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Affiliation(s)
- Luisa M Martínez
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Ana Fernández-Ocaña
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Pedro J Rey
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Teresa Salido
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Francisco Amil-Ruiz
- Bioinformatics Unit, Central Service for Research Support (SCAI), University of Córdoba, Córdoba, Spain
| | - Antonio J Manzaneda
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
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20
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Ramalho JC, Rodrigues AP, Lidon FC, Marques LMC, Leitão AE, Fortunato AS, Pais IP, Silva MJ, Scotti-Campos P, Lopes A, Reboredo FH, Ribeiro-Barros AI. Stress cross-response of the antioxidative system promoted by superimposed drought and cold conditions in Coffea spp. PLoS One 2018; 13:e0198694. [PMID: 29870563 PMCID: PMC5988331 DOI: 10.1371/journal.pone.0198694] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/23/2018] [Indexed: 12/18/2022] Open
Abstract
The understanding of acclimation strategies to low temperature and water availability is decisive to ensure coffee crop sustainability, since these environmental conditions determine the suitability of cultivation areas. In this context, the impacts of single and combined exposure to drought and cold were evaluated in three genotypes of the two major cropped species, Coffea arabica cv. Icatu, Coffea canephora cv. Apoatã, and the hybrid Obatã. Crucial traits of plant resilience to environmental stresses have been examined: photosynthesis, lipoperoxidation and the antioxidant response. Drought and/or cold promoted leaf dehydration, which was accompanied by stomatal and mesophyll limitations that impaired leaf C-assimilation in all genotypes. However, Icatu showed a lower impact upon stress exposure and a faster and complete photosynthetic recovery. Although lipoperoxidation was increased by drought (Icatu) and cold (all genotypes), it was greatly reduced by stress interaction, especially in Icatu. In fact, although the antioxidative system was reinforced under single drought and cold exposure (e.g., activity of enzymes as Cu,Zn-superoxide dismutase, ascorbate peroxidase, APX, glutathione reductase and catalase, CAT), the stronger increases were observed upon the simultaneous exposure to both stresses, which was accompanied with a transcriptional response of some genes, namely related to APX. Complementary, non-enzyme antioxidant molecules were promoted mostly by cold and the stress interaction, including α-tocopherol (in C. arabica plants), ascorbate (ASC), zeaxanthin, and phenolic compounds (all genotypes). In general, drought promoted antioxidant enzymes activity, whereas cold enhanced the synthesis of both enzyme and non-enzyme antioxidants, the latter likely related to a higher need of antioxidative capability when enzyme reactions were probably quite repressed by low temperature. Icatu showed the wider antioxidative capability, with the triggering of all studied antioxidative molecules by drought (except CAT), cold, and, particularly, stress interaction (except ASC), revealing a clear stress cross-tolerance. This justified the lower impacts on membrane lipoperoxidation and photosynthetic capacity under stress interaction conditions, related to a better ROS control. These findings are also relevant to coffee water management, showing that watering in the cold season should be largely avoided.
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Affiliation(s)
- José C. Ramalho
- Plant-Environment Interactions & Biodiversity Lab (PlantStress&Biodiversity), Linking Landscape, Environment, Agriculture and Food Unit (LEAF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Oeiras, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Ana P. Rodrigues
- Plant-Environment Interactions & Biodiversity Lab (PlantStress&Biodiversity), Linking Landscape, Environment, Agriculture and Food Unit (LEAF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Oeiras, Portugal
| | - Fernando C. Lidon
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Luís M. C. Marques
- Colóides Polimeros e Superficies, Instituto de Tecnologia Química e Biológica (ITQB), Universidade NOVA de Lisboa (UNL), Oeiras, Portugal
| | - A. Eduardo Leitão
- Plant-Environment Interactions & Biodiversity Lab (PlantStress&Biodiversity), Linking Landscape, Environment, Agriculture and Food Unit (LEAF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Oeiras, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Ana S. Fortunato
- Plant-Environment Interactions & Biodiversity Lab (PlantStress&Biodiversity), Linking Landscape, Environment, Agriculture and Food Unit (LEAF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Oeiras, Portugal
| | - Isabel P. Pais
- Unid. Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Oeiras, Portugal
| | - Maria J. Silva
- Plant-Environment Interactions & Biodiversity Lab (PlantStress&Biodiversity), Linking Landscape, Environment, Agriculture and Food Unit (LEAF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Oeiras, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Paula Scotti-Campos
- Unid. Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Oeiras, Portugal
| | - António Lopes
- Colóides Polimeros e Superficies, Instituto de Tecnologia Química e Biológica (ITQB), Universidade NOVA de Lisboa (UNL), Oeiras, Portugal
| | - F. H. Reboredo
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Ana I. Ribeiro-Barros
- Plant-Environment Interactions & Biodiversity Lab (PlantStress&Biodiversity), Linking Landscape, Environment, Agriculture and Food Unit (LEAF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Oeiras, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
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Ecoevolutionary Dynamics of Carbon Cycling in the Anthropocene. Trends Ecol Evol 2018; 33:213-225. [DOI: 10.1016/j.tree.2017.12.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 12/06/2017] [Accepted: 12/13/2017] [Indexed: 11/17/2022]
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Rey PJ, Manzaneda AJ, Alcántara JM. The interplay between aridity and competition determines colonization ability, exclusion and ecological segregation in the heteroploid Brachypodium distachyon species complex. THE NEW PHYTOLOGIST 2017; 215:85-96. [PMID: 28436561 DOI: 10.1111/nph.14574] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 03/15/2017] [Indexed: 06/07/2023]
Abstract
A higher competitive advantage of polyploid plants compared with their parental diploids is frequently invoked to explain their establishment success, colonization of novel environments and cytotypic ecological segregation, yet there is scarce experimental evidence supporting such hypotheses. Here, we investigated whether differential competitive ability of species of the Brachypodium distachyon (Poaceae) species complex, a model system for genomic, ecological and evolutionary studies of temperate grasses, contributes to explaining their ecological segregation as well as their coexistence in diploid/allotetraploid contact zones. We conducted two field experiments in dry and humid localities to evaluate the tolerance to competition of diploids and allotetraploids in densely occupied environments, and to parameterize models of intra- and intercytotype competition as a mechanism for species exclusion/coexistence. We provide experimental evidence supporting the hypothesis that, under natural field conditions, allotetraploids have superior ecological success compared with one of their parental diploids in terms of both colonizing competitive habitats and intercytotypic competition, with the balance of intra/intercytotype competition favoring polyploid population establishment. These findings, together with previous data on ecogeographic segregation and adaptive response to water stress, suggest that the interplay between aridity and competitive outcome determines the ability to colonize competitive environments, the exclusion of diploids, especially in arid localities, and species geographic segregation.
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Affiliation(s)
- Pedro J Rey
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, E 23071, Spain
| | - Antonio J Manzaneda
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, E 23071, Spain
| | - Julio M Alcántara
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, E 23071, Spain
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