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Abdelrahman M, Gorafi YSA, Sulieman S, Jogaiah S, Gupta A, Tsujimoto H, Nguyen HT, Herrera-Estrella L, Tran LSP. Wild grass-derived alleles represent a genetic architecture for the resilience of modern common wheat to stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38935838 DOI: 10.1111/tpj.16887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024]
Abstract
This review explores the integration of wild grass-derived alleles into modern bread wheat breeding to tackle the challenges of climate change and increasing food demand. With a focus on synthetic hexaploid wheat, this review highlights the potential of genetic variability in wheat wild relatives, particularly Aegilops tauschii, for improving resilience to multifactorial stresses like drought, heat, and salinity. The evolutionary journey of wheat (Triticum spp.) from diploid to hexaploid species is examined, revealing significant genetic contributions from wild grasses. We also emphasize the importance of understanding incomplete lineage sorting in the genomic evolution of wheat. Grasping this information is crucial as it can guide breeders in selecting the appropriate alleles from the gene pool of wild relatives to incorporate into modern wheat varieties. This approach improves the precision of phylogenetic relationships and increases the overall effectiveness of breeding strategies. This review also addresses the challenges in utilizing the wheat wild genetic resources, such as the linkage drag and cross-compatibility issues. Finally, we culminate the review with future perspectives, advocating for a combined approach of high-throughput phenotyping tools and advanced genomic techniques to comprehensively understand the genetic and regulatory architectures of wheat under stress conditions, paving the way for more precise and efficient breeding strategies.
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Affiliation(s)
- Mostafa Abdelrahman
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, 79409, Texas, USA
| | - Yasir Serag Alnor Gorafi
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kitashirakawa, 606-8502, Kyoto, Japan
| | - Saad Sulieman
- Department of Agronomy, Faculty of Agriculture, University of Khartoum, Khartoum North, 13314, Sudan
| | - Sudisha Jogaiah
- Department of Environmental Science, Central University of Kerala, Periye, Kasaragod, 671316, Kerala, India
| | - Aarti Gupta
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, 79409, Texas, USA
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan
| | - Henry T Nguyen
- Division of Plant Sciences and Technology, University of Missouri, Columbia, 65211, Missouri, USA
| | - Luis Herrera-Estrella
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, 79409, Texas, USA
- Unidad de Genomica Avanzada, Centro de Investigación y de Estudios Avanzados del Intituto Politécnico Nacional, Irapuato, 36821, Mexico
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, 79409, Texas, USA
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Alonso R, Muñoz F, Bottini R, Piccoli P, Berli FJ. Effects of Wind Exposure and Deficit Irrigation on Vegetative Growth, Yield Components and Berry Composition of Malbec and Cabernet Sauvignon. PLANTS (BASEL, SWITZERLAND) 2024; 13:1292. [PMID: 38794367 PMCID: PMC11124913 DOI: 10.3390/plants13101292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 04/23/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024]
Abstract
The impact of global warming on Argentine viticulture may result in a geographical shift, with wine-growing regions potentially moving towards the southwest, known as one of the windiest regions in the world. Deficit irrigation is a widely used strategy to control the shoot growth and improve fruit quality attributes, such as berry skin polyphenols. The present study aimed to assess the effects of different wind intensities and irrigation levels, as well as their interactions, on field-grown Vitis vinifera L. cvs. Malbec and Cabernet Sauvignon. The experiment was conducted during two growing seasons with two wind treatments (sheltered and exposed) and two irrigation treatments (well-watered and moderate deficit irrigation) in a multifactorial design. Vegetative growth, stomatal conductance, shoot biomass partition, fruit yield components and berry skin phenolics were evaluated. Our study found that, generally, wind exposure reduced vegetative growth, and deficit irrigation increased the proportion of smaller berries within the bunches. Meanwhile, deficit irrigation and wind exposure additively increased the concentration of berry skin phenolics. Combined stressful conditions enhance biomass partition across the shoot to fruits in Malbec, increasing the weight of bunches and the number of berries. Our findings offer practical implications for vineyard managers in windy regions, providing actionable insights to optimize grapevine cultivation and enhance wine quality.
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Affiliation(s)
- Rodrigo Alonso
- Grupo de Bioquímica Vegetal, Instituto de Biología Agrícola de Mendoza (IBAM), Consejo Nacional de Investigaciones Científicas y Técnicas—Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Almirante Brown 500, Chacras de Coria, Mendoza 5507, Argentina; (F.M.); (P.P.); (F.J.B.)
| | - Flavio Muñoz
- Grupo de Bioquímica Vegetal, Instituto de Biología Agrícola de Mendoza (IBAM), Consejo Nacional de Investigaciones Científicas y Técnicas—Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Almirante Brown 500, Chacras de Coria, Mendoza 5507, Argentina; (F.M.); (P.P.); (F.J.B.)
| | - Rubén Bottini
- Instituto Argentino de Veterinaria, Ambiente y Salud (IAVAS), Universidad Juan Agustín Maza, Av. Acceso Este Lateral Sur 2245, Guaymallén, Mendoza 5519, Argentina;
| | - Patricia Piccoli
- Grupo de Bioquímica Vegetal, Instituto de Biología Agrícola de Mendoza (IBAM), Consejo Nacional de Investigaciones Científicas y Técnicas—Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Almirante Brown 500, Chacras de Coria, Mendoza 5507, Argentina; (F.M.); (P.P.); (F.J.B.)
| | - Federico J. Berli
- Grupo de Bioquímica Vegetal, Instituto de Biología Agrícola de Mendoza (IBAM), Consejo Nacional de Investigaciones Científicas y Técnicas—Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Almirante Brown 500, Chacras de Coria, Mendoza 5507, Argentina; (F.M.); (P.P.); (F.J.B.)
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Hashemi S, Laitinen R, Nikoloski Z. Models and molecular mechanisms for trade-offs in the context of metabolism. Mol Ecol 2024; 33:e16879. [PMID: 36773330 DOI: 10.1111/mec.16879] [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: 08/10/2022] [Revised: 01/19/2023] [Accepted: 02/07/2023] [Indexed: 02/13/2023]
Abstract
Accumulating evidence for trade-offs involving metabolic traits has demonstrated their importance in the evolution of organisms. Metabolic models with different levels of complexity have already been considered when investigating mechanisms that explain various metabolic trade-offs. Here we provide a systematic review of modelling approaches that have been used to study and explain trade-offs between: (i) the kinetic properties of individual enzymes, (ii) rates of metabolic reactions, (iii) the rate and yield of metabolic pathways and networks, (iv) different metabolic objectives in single organisms and in metabolic communities, and (v) metabolic concentrations. In providing insights into the mechanisms underlying these five types of metabolic trade-offs obtained from constraint-based metabolic modelling, we emphasize the relationship of metabolic trade-offs to the classical black box Y-model that provides a conceptual explanation for resource acquisition-allocation trade-offs. In addition, we identify several pressing concerns and offer a perspective for future research in the identification and manipulation of metabolic trade-offs by relying on the toolbox provided by constraint-based metabolic modelling for single organisms and microbial communities.
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Affiliation(s)
- Seirana Hashemi
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Roosa Laitinen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
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4
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Laitinen RAE, Nikoloski Z. Strategies to identify and dissect trade-offs in plants. Mol Ecol 2024; 33:e16780. [PMID: 36380694 DOI: 10.1111/mec.16780] [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: 08/10/2022] [Revised: 10/13/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022]
Abstract
Trade-offs between traits arise and reflect constraints imposed by the environment and physicochemical laws. Trade-off situations are expected to be highly relevant for sessile plants, which have to respond to changes in the environment to ensure survival. Despite increasing interest in determining the genetic and molecular basis of plant trade-offs, there are still gaps and differences with respect to how trade-offs are defined, how they are measured, and how their genetic architecture is dissected. The first step to fill these gaps is to establish what is meant by trade-offs. In this review we provide a classification of the existing definitions of trade-offs according to: (1) the measures used for their quantification, (2) the dependence of trade-offs on environment, and (3) experimental designed used (i.e. a single individual across different environments or a population of individuals in single or multiple environments). We then compare the approaches for quantification of trade-offs based on phenotypic, between-individual, and genetic correlations, and stress the need for developing further quantification indices particularly for trade-offs between multiple traits. Lastly, we highlight the genetic mechanisms underpinning trade-offs and experimental designs that facilitate their discovery in plants, with focus on usage of natural variability. This review also offers a perspective for future research aimed at identification of plant trade-offs, dissection of their genetic architecture, and development of strategies to overcome trade-offs, with applications in crop breeding.
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Affiliation(s)
- Roosa A E Laitinen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
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Rossi N, Powell W, Mackay IJ, Hickey L, Maurer A, Pillen K, Halliday K, Sharma R. Investigating the genetic control of plant development in spring barley under speed breeding conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:115. [PMID: 38691245 PMCID: PMC11063105 DOI: 10.1007/s00122-024-04618-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/08/2024] [Indexed: 05/03/2024]
Abstract
KEY MESSAGE This study found that the genes, PPD-H1 and ELF3, control the acceleration of plant development under speed breeding, with important implications for optimizing the delivery of climate-resilient crops. Speed breeding is a tool to accelerate breeding and research programmes. Despite its success and growing popularity with breeders, the genetic basis of plant development under speed breeding remains unknown. This study explored the developmental advancements of barley genotypes under different photoperiod regimes. A subset of the HEB-25 Nested Association Mapping population was evaluated for days to heading and maturity under two contrasting photoperiod conditions: (1) Speed breeding (SB) consisting of 22 h of light and 2 h of darkness, and (2) normal breeding (NB) consisting of 16 h of light and 8 h of darkness. GWAS revealed that developmental responses under both conditions were largely controlled by two loci: PPDH-1 and ELF3. Allelic variants at these genes determine whether plants display early flowering and maturity under both conditions. At key QTL regions, domesticated alleles were associated with late flowering and maturity in NB and early flowering and maturity in SB, whereas wild alleles were associated with early flowering under both conditions. We hypothesize that this is related to the dark-dependent repression of PPD-H1 by ELF3 which might be more prominent in NB conditions. Furthermore, by comparing development under two photoperiod regimes, we derived an estimate of plasticity for the two traits. Interestingly, plasticity in development was largely attributed to allelic variation at ELF3. Our results have important implications for our understanding and optimization of speed breeding protocols particularly for introgression breeding and the design of breeding programmes to support the delivery of climate-resilient crops.
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Affiliation(s)
- Nicola Rossi
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Wayne Powell
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Ian J Mackay
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Lee Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Andreas Maurer
- Chair of Plant Breeding, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120, Halle, Germany
| | - Klaus Pillen
- Chair of Plant Breeding, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120, Halle, Germany
| | - Karen Halliday
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Rajiv Sharma
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK.
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Schmutz A, Schöb C. Coadaptation of coexisting plants enhances productivity in an agricultural system. Proc Natl Acad Sci U S A 2024; 121:e2305517121. [PMID: 38621135 PMCID: PMC11047107 DOI: 10.1073/pnas.2305517121] [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: 04/05/2023] [Accepted: 03/12/2024] [Indexed: 04/17/2024] Open
Abstract
Growing crops in more diverse crop systems (i.e., intercropping) is one way to produce food more sustainably. Even though intercropping, compared to average monocultures, is generally more productive, the full yield potential of intercropping might not yet have been achieved as modern crop cultivars are bred to be grown in monoculture. Breeding plants for more familiarity in mixtures, i.e., plants that are adapted to more diverse communities (i.e., adaptation) or even to coexist with each other (i.e., coadaptation) might have the potential to sustainably enhance productivity. In this study, the productivity benefits of familiarity through evolutionary adaptation and coevolutionary coadaptation were disentangled in a crop system through an extensive common garden experiment. Furthermore, evolutionary and coevolutionary effects on species-level and community-level productivity were linked to corresponding changes in functional traits. We found evidence for higher productivity and trait convergence with increasing familiarity with the plant communities. Furthermore, our results provide evidence for the coevolution of plants in mixtures leading to higher productivity of coadapted species. However, with the functional traits measured in our study, we could not fully explain the productivity benefits found upon coevolution. Our study investigated coevolution among randomly interacting plants and was able to demonstrate that coadaptation through coevolution of coexisting species in mixtures occurs and promotes ecosystem functioning (i.e., higher productivity). This result is particularly relevant for the diversification of agricultural and forest ecosystems, demonstrating the added value of artificially selecting plants for the communities they are familiar with.
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Affiliation(s)
- Anja Schmutz
- Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zürich, 8092Zurich, Switzerland
| | - Christian Schöb
- Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zürich, 8092Zurich, Switzerland
- Área Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933Móstoles, Madrid, Spain
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7
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Laitinen RAE. Importance of phenotypic plasticity in crop resilience. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:670-673. [PMID: 38307517 PMCID: PMC10837008 DOI: 10.1093/jxb/erad465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
This article comments on:
Guo T, Wei J, Li X, Yu J. 2024. Environmental context of phenotypic plasticity in flowering time in sorghum and rice. Journal of Experimental Botany 75, 1004–1015.
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Affiliation(s)
- Roosa A E Laitinen
- Organismal and Evolutionary Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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8
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Minow MAA, Marand AP, Schmitz RJ. Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits. Annu Rev Genet 2023; 57:297-319. [PMID: 37562412 PMCID: PMC10775913 DOI: 10.1146/annurev-genet-022123-110824] [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] [Indexed: 08/12/2023]
Abstract
The ease and throughput of single-cell genomics have steadily improved, and its current trajectory suggests that surveying single-cell populations will become routine. We discuss the merger of quantitative genetics with single-cell genomics and emphasize how this synergizes with advantages intrinsic to plants. Single-cell population genomics provides increased detection resolution when mapping variants that control molecular traits, including gene expression or chromatin accessibility. Additionally, single-cell population genomics reveals the cell types in which variants act and, when combined with organism-level phenotype measurements, unveils which cellular contexts impact higher-order traits. Emerging technologies, notably multiomics, can facilitate the measurement of both genetic changes and genomic traits in single cells, enabling single-cell genetic experiments. The implementation of single-cell genetics will advance the investigation of the genetic architecture of complex molecular traits and provide new experimental paradigms to study eukaryotic genetics.
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Affiliation(s)
- Mark A A Minow
- Department of Genetics, University of Georgia, Athens, Georgia, USA;
| | | | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, USA;
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9
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Asins MJ, Bullones A, Raga V, Romero-Aranda MR, Espinosa J, Triviño JC, Bernet GP, Traverso JA, Carbonell EA, Claros MG, Belver A. Combining Genetic and Transcriptomic Approaches to Identify Transporter-Coding Genes as Likely Responsible for a Repeatable Salt Tolerance QTL in Citrus. Int J Mol Sci 2023; 24:15759. [PMID: 37958745 PMCID: PMC10650496 DOI: 10.3390/ijms242115759] [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: 09/13/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
The excessive accumulation of chloride (Cl-) in leaves due to salinity is frequently related to decreased yield in citrus. Two salt tolerance experiments to detect quantitative trait loci (QTLs) for leaf concentrations of Cl-, Na+, and other traits using the same reference progeny derived from the salt-tolerant Cleopatra mandarin (Citrus reshni) and the disease-resistant donor Poncirus trifoliata were performed with the aim to identify repeatable QTLs that regulate leaf Cl- (and/or Na+) exclusion across independent experiments in citrus, as well as potential candidate genes involved. A repeatable QTL controlling leaf Cl- was detected in chromosome 6 (LCl-6), where 23 potential candidate genes coding for transporters were identified using the C. clementina genome as reference. Transcriptomic analysis revealed two important candidate genes coding for a member of the nitrate transporter 1/peptide transporter family (NPF5.9) and a major facilitator superfamily (MFS) protein. Cell wall biosynthesis- and secondary metabolism-related processes appeared to play a significant role in differential gene expression in LCl-6. Six likely gene candidates were mapped in LCl-6, showing conserved synteny in C. reshni. In conclusion, markers to select beneficial Cleopatra mandarin alleles of likely candidate genes in LCl-6 to improve salt tolerance in citrus rootstock breeding programs are provided.
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Affiliation(s)
- Maria J. Asins
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain; (V.R.)
| | - Amanda Bullones
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, 29010 Malaga, Spain; (A.B.); (M.G.C.)
| | - Veronica Raga
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain; (V.R.)
| | - Maria R. Romero-Aranda
- Integrative Biology for Plant Stress Group, La Mayora Institute of Subtropical and Mediterranean Horticulture, IHSM-CSIC-UMA, 29750 Malaga, Spain;
| | - Jesus Espinosa
- Department of Stress, Development and Signaling of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (EEZ CSIC), C/Prof. Albareda 1, 18008 Granada, Spain; (J.E.); (A.B.)
| | - Juan C. Triviño
- Sistemas Genómicos S.L., Ronda de Guglielmo Marconi, 6, 46980 Paterna, Spain; (J.C.T.); (G.P.B.)
| | - Guillermo P. Bernet
- Sistemas Genómicos S.L., Ronda de Guglielmo Marconi, 6, 46980 Paterna, Spain; (J.C.T.); (G.P.B.)
| | - Jose A. Traverso
- Department of Cellular Biology, Faculty of Sciences, Universidad de Granada, 18071 Granada, Spain;
| | - Emilio A. Carbonell
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain; (V.R.)
| | - M. Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, 29010 Malaga, Spain; (A.B.); (M.G.C.)
- Integrative Biology for Plant Stress Group, La Mayora Institute of Subtropical and Mediterranean Horticulture, IHSM-CSIC-UMA, 29750 Malaga, Spain;
- CIBER de Enfermedades Raras (CIBERER) U741, 29071 Málaga, Spain
- Institute of Biomedical Research in Málaga (IBIMA), IBIMA-RARE, 29010 Málaga, Spain
| | - Andres Belver
- Department of Stress, Development and Signaling of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (EEZ CSIC), C/Prof. Albareda 1, 18008 Granada, Spain; (J.E.); (A.B.)
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10
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Palacios C, Wang P, Wang N, Brown MA, Capatosto L, Du J, Jiang J, Zhang Q, Dahal N, Lamichhaney S. Genomic Variation, Population History, and Long-Term Genetic Adaptation to High Altitudes in Tibetan Partridge (Perdix hodgsoniae). Mol Biol Evol 2023; 40:msad214. [PMID: 37768198 PMCID: PMC10583571 DOI: 10.1093/molbev/msad214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 09/09/2023] [Accepted: 09/25/2023] [Indexed: 09/29/2023] Open
Abstract
Species residing across elevational gradients display adaptations in response to environmental changes such as oxygen availability, ultraviolet radiation, and temperature. Here, we study genomic variation, gene expression, and long-term adaptation in Tibetan Partridge (Perdix hodgsoniae) populations residing across the elevational gradient of the Tibetan Plateau. We generated a high-quality draft genome and used it to carry out downstream population genomic and transcriptomic analysis. The P. hodgsoniae populations residing across various elevations were genetically distinct, and their phylogenetic clustering was consistent with their geographic distribution. We identified possible evidence of gene flow between populations residing in <3,000 and >4,200 m elevation that is consistent with known habitat expansion of high-altitude populations of P. hodgsoniae to a lower elevation. We identified a 60 kb haplotype encompassing the Estrogen Receptor 1 (ESR1) gene, showing strong genetic divergence between populations of P. hodgsoniae. We identified six single nucleotide polymorphisms within the ESR1 gene fixed for derived alleles in high-altitude populations that are strongly conserved across vertebrates. We also compared blood transcriptome profiles and identified differentially expressed genes (such as GAPDH, LDHA, and ALDOC) that correlated with differences in altitude among populations of P. hodgsoniae. These candidate genes from population genomics and transcriptomics analysis were enriched for neutrophil degranulation and glycolysis pathways, which are known to respond to hypoxia and hence may contribute to long-term adaptation to high altitudes in P. hodgsoniae. Our results highlight Tibetan Partridges as a useful model to study molecular mechanisms underlying long-term adaptation to high altitudes.
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Affiliation(s)
- Catalina Palacios
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Pengcheng Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Nan Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, P. R. China
| | - Megan A Brown
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Lukas Capatosto
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Juan Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Jiahu Jiang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, P. R. China
| | - Qingze Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, P. R. China
| | - Nishma Dahal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP 176061, India
| | - Sangeet Lamichhaney
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
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11
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Tong H, Laitinen RAE, Nikoloski Z. Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2023; 240:426-438. [PMID: 37507350 DOI: 10.1111/nph.19154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023]
Abstract
Plants can rapidly mitigate the effects of suboptimal growth environments by phenotypic plasticity of fitness-traits. While genetic variation for phenotypic plasticity offers the means for breeding climate-resilient crop lines, accurate genomic prediction models for plasticity of fitness-related traits are still lacking. Here, we employed condition- and accession-specific metabolic models for 67 Arabidopsis thaliana accessions to dissect and predict plasticity of rosette growth to changes in nitrogen availability. We showed that specific reactions in photorespiration, linking carbon and nitrogen metabolism, as well as key pathways of central carbon metabolism exhibited substantial genetic variation for flux plasticity. We also demonstrated that, in comparison with a genomic prediction model for fresh weight (FW), genomic prediction of growth plasticity improves the predictability of FW under low nitrogen by 58.9% and by additional 15.4% when further integrating data on plasticity of metabolic fluxes. Therefore, the combination of metabolic and statistical modeling provides a stepping stone in understanding the molecular mechanisms and improving the predictability of plasticity for fitness-related traits.
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Affiliation(s)
- Hao Tong
- Bioinformatics and Mathematical Modeling, Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany
| | - Roosa A E Laitinen
- Organismal and Evolutionary Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland
| | - Zoran Nikoloski
- Bioinformatics and Mathematical Modeling, Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany
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12
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Yong B, Zhu W, Wei S, Li B, Wang Y, Xu N, Lu J, Chen Q, He C. Parallel selection of loss-of-function alleles of Pdh1 orthologous genes in warm-season legumes for pod indehiscence and plasticity is related to precipitation. THE NEW PHYTOLOGIST 2023; 240:863-879. [PMID: 37501344 DOI: 10.1111/nph.19150] [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: 05/11/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023]
Abstract
Pod dehiscence facilitates seed dispersal in wild legumes but results in yield loss in cultivated legumes. The evolutionary genetics of the legume pod dehiscence trait remain largely elusive. We characterized the pod dehiscence of chromosome segment substitution lines of Glycine max crossed with Glycine soja and found that the gene underlying the predominant quantitative trait locus (QTL) of soybean pod-shattering trait was Pod dehiscence 1 (Pdh1). A few rare loss-of-function (LoF) Pdh1 alleles were identified in G. soja, while only an allele featuring a premature stop codon was selected for pod indehiscence in cultivated soybean and spread to low-precipitation regions with increased frequency. Moreover, correlated interactions among Pdh1's haplotype, gene expression, and environmental changes for the developmental plasticity of the pod dehiscence trait were revealed in G. max. We found that orthologous Pdh1 genes specifically originated in warm-season legumes and their LoF alleles were then parallel-selected during the domestication of legume crops. Our results provide insights into the convergent evolution of pod dehiscence in warm-season legumes, facilitate an understanding of the intricate interactions between genetic robustness and environmental adaptation for developmental plasticity, and guide the breeding of new legume varieties with pod indehiscence.
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Affiliation(s)
- Bin Yong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Weiwei Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Siming Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Bingbing Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Yan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Nan Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Jiangjie Lu
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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Meyer RC, Weigelt-Fischer K, Tschiersch H, Topali G, Altschmied L, Heuermann MC, Knoch D, Kuhlmann M, Zhao Y, Altmann T. Dynamic growth QTL action in diverse light environments: characterization of light regime-specific and stable QTL in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5341-5362. [PMID: 37306093 DOI: 10.1093/jxb/erad222] [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: 10/17/2022] [Accepted: 06/10/2023] [Indexed: 06/13/2023]
Abstract
Plant growth is a complex process affected by a multitude of genetic and environmental factors and their interactions. To identify genetic factors influencing plant performance under different environmental conditions, vegetative growth was assessed in Arabidopsis thaliana cultivated under constant or fluctuating light intensities, using high-throughput phenotyping and genome-wide association studies. Daily automated non-invasive phenotyping of a collection of 382 Arabidopsis accessions provided growth data during developmental progression under different light regimes at high temporal resolution. Quantitative trait loci (QTL) for projected leaf area, relative growth rate, and PSII operating efficiency detected under the two light regimes were predominantly condition-specific and displayed distinct temporal activity patterns, with active phases ranging from 2 d to 9 d. Eighteen protein-coding genes and one miRNA gene were identified as potential candidate genes at 10 QTL regions consistently found under both light regimes. Expression patterns of three candidate genes affecting projected leaf area were analysed in time-series experiments in accessions with contrasting vegetative leaf growth. These observations highlight the importance of considering both environmental and temporal patterns of QTL/allele actions and emphasize the need for detailed time-resolved analyses under diverse well-defined environmental conditions to effectively unravel the complex and stage-specific contributions of genes affecting plant growth processes.
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Affiliation(s)
- Rhonda C Meyer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Kathleen Weigelt-Fischer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Henning Tschiersch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Georgia Topali
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Marc C Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Dominic Knoch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Breeding Research, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
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14
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Alseekh S, Karakas E, Zhu F, Wijesingha Ahchige M, Fernie AR. Plant biochemical genetics in the multiomics era. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4293-4307. [PMID: 37170864 PMCID: PMC10433942 DOI: 10.1093/jxb/erad177] [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: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Esra Karakas
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070 Wuhan, China
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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15
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Veenstra RL, Hefley TJ, Berning D, Messina CD, Haag LA, Prasad PV, Ciampitti IA. Predicting corn tiller development in restrictive environments can be achieved to enhance defensive management decision tools for producers. FRONTIERS IN PLANT SCIENCE 2023; 14:1223961. [PMID: 37600203 PMCID: PMC10436094 DOI: 10.3389/fpls.2023.1223961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023]
Abstract
Introduction While globally appreciated for reliable, intensification-friendly phenotypes, modern corn (Zea mays L.) genotypes retain crop plasticity potential. For example, weather and heterogeneous field conditions can overcome phenotype uniformity and facilitate tiller expression. Such plasticity may be of interest in restrictive or otherwise variable environments around the world, where corn production is steadily expanding. No substantial effort has been made in available literature to predict tiller development in field scenarios, which could provide insight on corn plasticity capabilities and drivers. Therefore, the objectives of this investigation are as follows: 1) identify environment, management, or combinations of these factors key to accurately predict tiller density dynamics in corn; and 2) test outof-season prediction accuracy for identified factors. Methods Replicated field trials were conducted in 17 diverse site-years in Kansas (United States) during the 2019, 2020, and 2021 seasons. Two modern corn genotypes were evaluated with target plant densities of 25000, 42000, and 60000 plants ha -1. Environmental, phenological, and morphological data were recorded and evaluated with generalized additive models. Results Plant density interactions with cumulative growing degree days, photothermal quotient, mean minimum and maximum daily temperatures, cumulative vapor pressure deficit, soil nitrate, and soil phosphorus were identified as important predictive factors of tiller density. Many of these factors had stark non-limiting thresholds. Factors impacting growth rates and photosynthesis (specifically vapor pressure deficit and maximum temperatures) were most sensitive to changes in plant density. Out-of-season prediction errors were seasonally variable, highlighting model limitations due to training datasets. Discussion This study demonstrates that tillering is a predictable plasticity mechanism in corn, and therefore could be incorporated into decision tools for restrictive growing regions. While useful for diagnostics, these models are limited in forecast utility and should be coupled with appropriate decision theory and risk assessments for producers in climatically and socioeconomically vulnerable environments.
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Affiliation(s)
- Rachel L. Veenstra
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Trevor J. Hefley
- Department of Statistics, Kansas State University, Manhattan, KS, United States
| | - Dan Berning
- Corteva Agriscience Agronomy Sciences, Johnston, IA, United States
| | - Carlos D. Messina
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Lucas A. Haag
- Northwest Research-Extension Center, Kansas State University, Colby, KS, United States
| | - P.V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
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16
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Tetrault E, Swenson J, Aaronson B, Marcho C, Albertson RC. The transcriptional state and chromatin landscape of cichlid jaw shape variation across species and environments. Mol Ecol 2023; 32:3922-3941. [PMID: 37160741 PMCID: PMC10524807 DOI: 10.1111/mec.16975] [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: 11/30/2022] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/11/2023]
Abstract
Adaptive phenotypes are shaped by a combination of genetic and environmental forces, but how they interact remains poorly understood. Here, we utilize the cichlid oral jaw apparatus to better understand these gene-by-environment effects. First, we employed RNA-seq in bony and ligamentous tissues important for jaw opening to identify differentially expressed genes between species and across foraging environments. We used two Lake Malawi species adapted to different foraging habitats along the pelagic-benthic ecomorphological axis. Our foraging treatments were designed to force animals to employ either suction or biting/scraping, which broadly mimic pelagic or benthic modes of feeding. We found a large number of differentially expressed genes between species, and while we identified relatively few differences between environments, species differences were far more pronounced when they were challenged with a pelagic versus benthic foraging mode. Expression data carried the signature of genetic assimilation, and implicated cell cycle regulation in shaping the jaw across species and environments. Next, we repeated the foraging experiment and performed ATAC-seq procedures on nuclei harvested from the same tissues. Cross-referencing results from both analyses revealed subsets of genes that were both differentially expressed and differentially accessible. This reduced dataset implicated notable candidate genes including the Hedgehog effector, KIAA0586 and the ETS transcription factor, etv4, which connects environmental stress and craniofacial morphogenesis. Taken together, these data provide novel insights into the epigenetic, genetic and cellular bases of species- and environment-specific bone shapes.
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Affiliation(s)
- Emily Tetrault
- Graduate Program in Molecular and Cell Biology, University of Massachusetts, Amherst MA, 01003, U.S.A
| | - John Swenson
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst MA, 01003, U.S.A
| | - Ben Aaronson
- Biology Department, University of Massachusetts, Amherst MA, 01003, U.S.A
| | - Chelsea Marcho
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst MA, 01003, U.S.A
| | - R. Craig Albertson
- Biology Department, University of Massachusetts, Amherst MA, 01003, U.S.A
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17
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Zhu Z, Esche F, Babben S, Trenner J, Serfling A, Pillen K, Maurer A, Quint M. An exotic allele of barley EARLY FLOWERING 3 contributes to developmental plasticity at elevated temperatures. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2912-2931. [PMID: 36449391 DOI: 10.1093/jxb/erac470] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/28/2022] [Indexed: 06/06/2023]
Abstract
Increase in ambient temperatures caused by climate change affects various morphological and developmental traits of plants, threatening crop yield stability. In the model plant Arabidopsis thaliana, EARLY FLOWERING 3 (ELF3) plays prominent roles in temperature sensing and thermomorphogenesis signal transduction. However, how crop species respond to elevated temperatures is poorly understood. Here, we show that the barley ortholog of AtELF3 interacts with high temperature to control growth and development. We used heterogeneous inbred family (HIF) pairs generated from a segregating mapping population and systematically studied the role of exotic ELF3 variants in barley temperature responses. An exotic ELF3 allele of Syrian origin promoted elongation growth in barley at elevated temperatures, whereas plant area and estimated biomass were drastically reduced, resulting in an open canopy architecture. The same allele accelerated inflorescence development at high temperature, which correlated with early transcriptional induction of MADS-box floral identity genes BM3 and BM8. Consequently, barley plants carrying the exotic ELF3 allele displayed stable total grain number at elevated temperatures. Our findings therefore demonstrate that exotic ELF3 variants can contribute to phenotypic and developmental acclimation to elevated temperatures, providing a stimulus for breeding of climate-resilient crops.
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Affiliation(s)
- Zihao Zhu
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Finn Esche
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Steve Babben
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Jana Trenner
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin-Baur-Str. 27, D-06484, Quedlinburg, Germany
| | - Klaus Pillen
- Chair of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
| | - Andreas Maurer
- Chair of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research, Halle-Jena-Leipzig, Puschstrasse 4, D-04103, Leipzig, Germany
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18
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Palmquist EC, Ogle K, Whitham TG, Allan GJ, Shafroth PB, Butterfield BJ. Provenance, genotype, and flooding influence growth and resource acquisition characteristics in a clonal, riparian shrub. AMERICAN JOURNAL OF BOTANY 2023; 110:e16115. [PMID: 36462152 DOI: 10.1002/ajb2.16115] [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: 07/01/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
PREMISE Riparian plants can exhibit intraspecific phenotypic variability across the landscape related to temperature and flooding gradients. Phenotypes that vary across a climate gradient are often partly genetically determined and may differ in their response to inundation. Changes to inundation patterns across a climate gradient could thus result in site-specific inundation responses. Phenotypic variability is more often studied in riparian trees, yet riparian shrubs are key elements of riparian systems and may differ from trees in phenotypic variability and environmental responses. METHODS We tested whether individuals of a clonal, riparian shrub, Pluchea sericea, collected from provenances spanning a temperature gradient differed in their phenotypes and responses to inundation and to what degree any differences were related to genotype. Plants were subjected to different inundation depths and a subset genotyped. Variables related to growth and resource acquisition were measured and analyzed using hierarchical, multivariate Bayesian linear regressions. RESULTS Individuals from different provenances differed in their phenotypes, but not in their response to inundation. Phenotypes were not related to provenance temperature but were partially governed by genotype. Growth was more strongly influenced by inundation, while resource acquisition was more strongly controlled by genotype. CONCLUSIONS Growth and resource acquisition responses in a clonal, riparian shrub are affected by changes to inundation and plant demographics in unique ways. Shrubs appear to differ from trees in their responses to environmental change. Understanding environmental effects on shrubs separately from those of trees will be a key part of evaluating impacts of environmental change on riparian ecosystems.
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Affiliation(s)
- Emily C Palmquist
- U.S. Geological Survey, Southwest Biological Science Center, Grand Canyon Monitoring and Research Center, 2255 N Gemini Dr, Flagstaff, AZ, 86001, USA
- Department of Biological Sciences, Northern Arizona University, Box 5640, Flagstaff, AZ, 86011, USA
| | - Kiona Ogle
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Box 5693, Flagstaff, AZ, 86011, USA
| | - Thomas G Whitham
- Department of Biological Sciences, Northern Arizona University, Box 5640, Flagstaff, AZ, 86011, USA
- Center for Adaptable Western Landscapes (CAWL), Northern Arizona University, Box 5640, Flagstaff, AZ, 86011, USA
| | - Gerard J Allan
- Department of Biological Sciences, Northern Arizona University, Box 5640, Flagstaff, AZ, 86011, USA
- Center for Adaptable Western Landscapes (CAWL), Northern Arizona University, Box 5640, Flagstaff, AZ, 86011, USA
| | - Patrick B Shafroth
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Ave., Bldg C, Fort Collins, CO, 80526, USA
| | - Bradley J Butterfield
- Department of Biological Sciences, Northern Arizona University, Box 5640, Flagstaff, AZ, 86011, USA
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19
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Veenstra RL, Messina CD, Berning D, Haag LA, Carter P, Hefley TJ, Prasad PVV, Ciampitti IA. Corn yield components can be stabilized via tillering in sub-optimal plant densities. FRONTIERS IN PLANT SCIENCE 2023; 13:1047268. [PMID: 36684726 PMCID: PMC9853411 DOI: 10.3389/fpls.2022.1047268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Crop plasticity is fundamental to sustainability discussions in production agriculture. Modern corn (Zea mays L.) genetics can compensate yield determinants to a small degree, but plasticity mechanisms have been masked by breeder selection and plant density management preferences. While tillers are a well-known source of plasticity in cereal crops, the functional trade-offs of tiller expression to the hierarchical yield formation process in corn are unknown. This investigation aimed to further dissect the consequences of tiller expression on corn yield component determination and plasticity in a range of environments from two plant fraction perspectives - i) main stalks only, considering potential functional trade-offs due to tiller expression; and ii) comprehensive (main stalk plus tillers). METHODS This multi-seasonal study considered a dataset of 17 site-years across Kansas, United States. Replicated field trials evaluated tiller presence (removed or intact) in two hybrids (P0657AM and P0805AM) at three target plant densities (25000, 42000, and 60000 plants ha-1). Record of ears and kernels per unit area and kernel weight were collected separately for both main stalks and tillers in each plot. RESULTS Indicated tiller contributions impacted the plasticity of yield components in evaluated genotypes. Ear number and kernel number per area were less dependent on plant density, but kernel number remained key to yield stability. Although ear number was less related to yield stability, ear source and type were significant yield predictors, with tiller axillary ears as stronger contributors than main stalk secondary ears in high-yielding environments. DISCUSSIONS Certainly, managing for the most main stalk primary ears possible - that is, optimizing the plant density (which consequently reduces tiller expression), is desirable to maximize yields. However, the demonstrated escape from the deterministic hierarchy of corn yield formation may offer avenues to reduce corn management dependence on a seasonally variable optimum plant density, which cannot be remediated mid-season.
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Affiliation(s)
- Rachel L. Veenstra
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Carlos D. Messina
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Dan Berning
- Corteva Agriscience Agronomy Sciences, Johnston, IA, United States
| | - Lucas A. Haag
- Northwest Research-Extension Center, Kansas State University, Colby, KS, United States
| | - Paul Carter
- Formerly Corteva Agriscience, Independent Agronomist, Clive, IA, United States
| | - Trevor J. Hefley
- Department of Statistics, Kansas State University, Manhattan, KS, United States
| | - P. V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
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20
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Andreou GM, Messer M, Tong H, Nikoloski Z, Laitinen RAE. Heritability of temperature-mediated flower size plasticity in Arabidopsis thaliana. QUANTITATIVE PLANT BIOLOGY 2023; 4:e4. [PMID: 37077703 PMCID: PMC10095859 DOI: 10.1017/qpb.2023.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 05/03/2023]
Abstract
Phenotypic plasticity is a heritable trait that provides sessile organisms a strategy to rapidly mitigate negative effects of environmental change. Yet, we have little understanding of the mode of inheritance and genetic architecture of plasticity in different focal traits relevant to agricultural applications. This study builds on our recent discovery of genes controlling temperature-mediated flower size plasticity in Arabidopsis thaliana and focuses on dissecting the mode of inheritance and combining ability of plasticity in the context of plant breeding. We created a full diallel cross using 12 A. thaliana accessions displaying different temperature-mediated flower size plasticities, scored as the fold change between two temperatures. Griffing's analysis of variance in flower size plasticity indicated that non-additive genetic action shapes this trait and pointed at challenges and opportunities when breeding for reduced plasticity. Our findings provide an outlook of flower size plasticity that is important for developing resilient crops for future climates.
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Affiliation(s)
- Gregory M. Andreou
- Organismal and Evolutionary Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Michaela Messer
- Molecular Mechanisms of Plant Adaptation Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Hao Tong
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Zoran Nikoloski
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Roosa A. E. Laitinen
- Organismal and Evolutionary Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Molecular Mechanisms of Plant Adaptation Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Author for correspondence: Roosa A. E. Laitinen, E-mail:
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21
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Temperature-mediated flower size plasticity in Arabidopsis. iScience 2022; 25:105411. [PMID: 36388994 PMCID: PMC9646949 DOI: 10.1016/j.isci.2022.105411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/10/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Organisms can rapidly mitigate the effects of environmental changes by changing their phenotypes, known as phenotypic plasticity. Yet, little is known about the temperature-mediated plasticity of traits that are directly linked to plant fitness such as flower size. We discovered substantial genetic variation in flower size plasticity to temperature both among selfing Arabidopsis thaliana and outcrossing A. arenosa individuals collected from a natural growth habitat. Genetic analysis using a panel of 290 A. thaliana accession and mutant lines revealed that MADS AFFECTING FLOWERING (MAF) 2-5 gene cluster, previously shown to regulate temperature-mediated flowering time, was associated to the flower size plasticity to temperature. Furthermore, our findings pointed that the control of plasticity differs from control of the trait itself. Altogether, our study advances the understanding of genetic and molecular factors underlying plasticity on fundamental fitness traits, such as flower size, in response to future climate scenarios.
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22
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Li G, Zhao Y, Liu F, Shi M, Guan Y, Zhang T, Zhao F, Qiao Q, Geng Y. Transcriptional memory of gene expression across generations participates in transgenerational plasticity of field pennycress in response to cadmium stress. FRONTIERS IN PLANT SCIENCE 2022; 13:953794. [PMID: 36247570 PMCID: PMC9561902 DOI: 10.3389/fpls.2022.953794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Transgenerational plasticity (TGP) occurs when maternal environments influence the expression of traits in offspring, and in some cases may increase fitness of offspring and have evolutionary significance. However, little is known about the extent of maternal environment influence on gene expression of offspring, and its relationship with trait variations across generations. In this study, we examined TGP in the traits and gene expression of field pennycress (Thlaspi arvense) in response to cadmium (Cd) stress. In the first generation, along with the increase of soil Cd concentration, the total biomass, individual height, and number of seeds significantly decreased, whereas time to flowering, superoxide dismutase (SOD) activity, and content of reduced glutathione significantly increased. Among these traits, only SOD activity showed a significant effect of TGP; the offspring of Cd-treated individuals maintained high SOD activity in the absence of Cd stress. According to the results of RNA sequencing and bioinformatic analysis, 10,028 transcripts were identified as Cd-responsive genes. Among them, only 401 were identified as transcriptional memory genes (TMGs) that maintained the same expression pattern under normal conditions in the second generation as in Cd-treated parents in the first generation. These genes mainly participated in Cd tolerance-related processes such as response to oxidative stress, cell wall biogenesis, and the abscisic acid signaling pathways. The results of weighted correlation network analysis showed that modules correlated with SOD activity recruited more TMGs than modules correlated with other traits. The SOD-coding gene CSD2 was found in one of the modules correlated with SOD activity. Furthermore, several TMGs co-expressed with CSD2 were hub genes that were highly connected to other nodes and critical to the network's topology; therefore, recruitment of TMGs in offspring was potentially related to TGP. These findings indicated that, across generations, transcriptional memory of gene expression played an important role in TGP. Moreover, these results provided new insights into the trait evolution processes mediated by phenotypic plasticity.
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Affiliation(s)
- Gengyun Li
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Yuewan Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Fei Liu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Minnuo Shi
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Yabin Guan
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Fangqing Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Beijing Institute of Life Sciences, Chinese Academy of Sciences, Beijing, China
| | - Qin Qiao
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Yupeng Geng
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
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Type of Stress Induces Differential Responses in Acer rubrum (Red Maple), but Induced Responses Have No Effect on Herbivorous Pests. INTERNATIONAL JOURNAL OF PLANT BIOLOGY 2022. [DOI: 10.3390/ijpb13040033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Plants thrive in dynamic environments requiring adaptive strategies in response to environmental stressors. Furthermore, insect herbivores may be attracted or deterred by the expression of these traits. This study examines growth, physiological, and phytochemical adaptations of maple trees in response to stressors and how these stressors effect herbivore feeding behavior within an agricultural production system. Agricultural systems are unique because plants experience environmental stressors unique to production such as herbicide sprays and girdling. Using four environmental stressors commonly observed in agricultural production (control, mechanical defoliation, chemical defoliation, and girdling), applied to two cultivars of red maple (Acer rubrum, ‘Brandywine’ and ‘Franksred’), this study analyzed differentiation of expressed traits in a production system. Responses varied depending on cultivar and stress treatment but had no effect on insect herbivore behavior. Understanding the ecological interactions within these systems will provide information for better plant production and pest management recommendations.
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Schneider HM. Characterization, costs, cues and future perspectives of phenotypic plasticity. ANNALS OF BOTANY 2022; 130:131-148. [PMID: 35771883 PMCID: PMC9445595 DOI: 10.1093/aob/mcac087] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/28/2022] [Indexed: 06/09/2023]
Abstract
BACKGROUND Plastic responses of plants to the environment are ubiquitous. Phenotypic plasticity occurs in many forms and at many biological scales, and its adaptive value depends on the specific environment and interactions with other plant traits and organisms. Even though plasticity is the norm rather than the exception, its complex nature has been a challenge in characterizing the expression of plasticity, its adaptive value for fitness and the environmental cues that regulate its expression. SCOPE This review discusses the characterization and costs of plasticity and approaches, considerations, and promising research directions in studying plasticity. Phenotypic plasticity is genetically controlled and heritable; however, little is known about how organisms perceive, interpret and respond to environmental cues, and the genes and pathways associated with plasticity. Not every genotype is plastic for every trait, and plasticity is not infinite, suggesting trade-offs, costs and limits to expression of plasticity. The timing, specificity and duration of plasticity are critical to their adaptive value for plant fitness. CONCLUSIONS There are many research opportunities to advance our understanding of plant phenotypic plasticity. New methodology and technological breakthroughs enable the study of phenotypic responses across biological scales and in multiple environments. Understanding the mechanisms of plasticity and how the expression of specific phenotypes influences fitness in many environmental ranges would benefit many areas of plant science ranging from basic research to applied breeding for crop improvement.
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25
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Jacquiod S, Raynaud T, Pimet E, Ducourtieux C, Casieri L, Wipf D, Blouin M. Wheat Rhizosphere Microbiota Respond to Changes in Plant Genotype, Chemical Inputs, and Plant Phenotypic Plasticity. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.903008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Modern wheat varieties that were selected since the Green Revolution are generally grown with synthetic chemical inputs, and ancient varieties released before1960 without. Thus, when changes occur in rhizosphere microbiota structure, it is not possible to distinguish if they are due to (i) changes in wheat genotypes by breeding, (ii) modifications of the environment via synthetic chemical inputs, or (iii) phenotypic plasticity, the interaction between wheat genotype and the environment. Using a crossed factorial design in the field, we evaluated the effects of either modern or ancient wheat varieties grown with or without chemical inputs (a N fertilizer, a fungicide, and an herbicide) on “microbiome as a phenotype.” We analyzed the rhizosphere microbiota by bacterial and fungal amplicon sequencing, coupled with microscope observations of mycorrhizal associations. We found that plant genotype and phenotypic plasticity had the most influence on rhizosphere microbiota, whereas inputs had only marginal effects. Phenotypic plasticity was particularly important in explaining diversity variations in bacteria and fungi but had no impact on the mycorrhizal association. Our results show an interest in considering the interaction between wheat genotype and the environment in breeding programs, by focusing on genes involved in the phenotypic plasticity of plant-microbe interactions.
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26
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Feng L, Dong T, Jiang P, Yang Z, Dong A, Xie SQ, Griffin CH, Wu R. An eco-evo-devo genetic network model of stress response. HORTICULTURE RESEARCH 2022; 9:uhac135. [PMID: 36061617 PMCID: PMC9433980 DOI: 10.1093/hr/uhac135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/04/2022] [Indexed: 05/23/2023]
Abstract
The capacity of plants to resist abiotic stresses is of great importance to agricultural, ecological and environmental sustainability, but little is known about its genetic underpinnings. Existing genetic tools can identify individual genetic variants mediating biochemical, physiological, and cellular defenses, but fail to chart an overall genetic atlas behind stress resistance. We view stress response as an eco-evo-devo process by which plants adaptively respond to stress through complex interactions of developmental canalization, phenotypic plasticity, and phenotypic integration. As such, we define and quantify stress response as the developmental change of adaptive traits from stress-free to stress-exposed environments. We integrate composite functional mapping and evolutionary game theory to reconstruct omnigenic, information-flow interaction networks for stress response. Using desert-adapted Euphrates poplar as an example, we infer salt resistance-related genome-wide interactome networks and trace the roadmap of how each SNP acts and interacts with any other possible SNPs to mediate salt resistance. We characterize the previously unknown regulatory mechanisms driving trait variation; i.e. the significance of a SNP may be due to the promotion of positive regulators, whereas the insignificance of a SNP may result from the inhibition of negative regulators. The regulator-regulatee interactions detected are not only experimentally validated by two complementary experiments, but also biologically interpreted by their encoded protein-protein interactions. Our eco-evo-devo model of genetic interactome networks provides an approach to interrogate the genetic architecture of stress response and informs precise gene editing for improving plants' capacity to live in stress environments.
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Affiliation(s)
| | | | | | - Zhenyu Yang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Ang Dong
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shang-Qian Xie
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou 570228, China
| | - Christopher H Griffin
- Applied Research Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
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27
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Fournier-Level A, Taylor MA, Paril JF, Martínez-Berdeja A, Stitzer MC, Cooper MD, Roe JL, Wilczek AM, Schmitt J. Adaptive significance of flowering time variation across natural seasonal environments in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 234:719-734. [PMID: 35090191 DOI: 10.1111/nph.17999] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
The relevance of flowering time variation and plasticity to climate adaptation requires a comprehensive empirical assessment. We investigated natural selection and the genetic architecture of flowering time in Arabidopsis through field experiments in Europe across multiple sites and seasons. We estimated selection for flowering time, plasticity and canalization. Loci associated with flowering time, plasticity and canalization by genome-wide association studies were tested for a geographic signature of climate adaptation. Selection favored early flowering and increased canalization, except at the northernmost site, but was rarely detected for plasticity. Genome-wide association studies revealed significant associations with flowering traits and supported a substantial polygenic inheritance. Alleles associated with late flowering, including functional FRIGIDA variants, were more common in regions experiencing high annual temperature variation. Flowering time plasticity to fall vs spring and summer environments was associated with GIGANTEA SUPPRESSOR 5, which promotes early flowering under decreasing day length and temperature. The finding that late flowering genotypes and alleles are associated with climate is evidence for past adaptation. Real-time phenotypic selection analysis, however, reveals pervasive contemporary selection for rapid flowering in agricultural settings across most of the species range. The response to this selection may involve genetic shifts in environmental cuing compared to the ancestral state.
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Affiliation(s)
| | - Mark A Taylor
- Department of Evolution and Ecology, University of California at Davis, Davis, CA, 95616, USA
| | - Jefferson F Paril
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | | | - Michelle C Stitzer
- Department of Evolution and Ecology, University of California at Davis, Davis, CA, 95616, USA
| | - Martha D Cooper
- Department of Ecology and Evolution, Brown University, Providence, RI, 02912, USA
| | - Judith L Roe
- College of Arts and Sciences, Biology, Agricultural Science & Agribusiness, University of Maine at Presque Isle, Presque Isle, ME, 04769, USA
| | | | - Johanna Schmitt
- Department of Evolution and Ecology, University of California at Davis, Davis, CA, 95616, USA
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28
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de Rosas I, Deis L, Baldo Y, Cavagnaro JB, Cavagnaro PF. High Temperature Alters Anthocyanin Concentration and Composition in Grape Berries of Malbec, Merlot, and Pinot Noir in a Cultivar-Dependent Manner. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11070926. [PMID: 35406906 PMCID: PMC9003205 DOI: 10.3390/plants11070926] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 05/27/2023]
Abstract
Climate is determinant for grapevine geographical distribution, berry attributes, and wine quality. Due to climate change, a 2−4 °C increase in mean diurnal temperature is predicted by the end of the century for the most important Argentine viticulture region. We hypothesize that such temperature increase will affect color intensity and other quality attributes of red grapes and wines. The present study investigated the effect of high temperature (HT) on anthocyanin concentration and composition, pH, and resveratrol and solids content in berries of three major wine-producing varieties during fruit ripening in two seasons. To this end, a structure that increased mean diurnal temperature by 1.5−2.0 °C at berry sites, compared to Control (C) plants grown without such structure, was implemented in field grown vineyards of Malbec, Merlot, and Pinot Noir. Results revealed a cultivar-dependent response to HT conditions, with Malbec and Pinot Noir berries exhibiting significant decreases in total anthocyanin concentration (TAC) at veraison and harvest, respectively, while Merlot maintained an unaffected pigment content under HT. The decrease in TAC was associated with reduced levels of delphinidin, cyanidin, petunidin, peonidin, and malvidin glycosides, and increased ratios of acylated (AA)/non-acylated anthocyanins (NAA), suggesting pigment acylation as a possible stress-response mechanism for attenuating HT negative effects. Under HT, Pinot Noir, which does not produce AA, was the only cultivar with lower TAC at harvest (p < 0.05). pH, resveratrol, and solids content were not affected by HT. Our results predict high, medium, and low plasticity with regard to color quality attributes for Malbec, Merlot, and Pinot Noir, respectively, in the context of climate change.
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Affiliation(s)
- Inés de Rosas
- Plant Physiology Laboratory, Faculty of Agricultural Sciences, National University of Cuyo, Almirante Brown 500, Mendoza M5528 AHB, Argentina; (I.d.R.); (L.D.); (J.B.C.)
| | - Leonor Deis
- Plant Physiology Laboratory, Faculty of Agricultural Sciences, National University of Cuyo, Almirante Brown 500, Mendoza M5528 AHB, Argentina; (I.d.R.); (L.D.); (J.B.C.)
- Plant Physiology Laboratory, Institution of Agricultural Biology of Mendoza, Faculty of Agricultural Sciences, National University of Cuyo and Conicet, Almirante Brown 500, Chacras de Coria M5505 AHB, Argentina
| | - Yésica Baldo
- National Viticulture Institute (INV), Av. San Martín 430, Mendoza M5528 AHB, Argentina;
| | - Juan B. Cavagnaro
- Plant Physiology Laboratory, Faculty of Agricultural Sciences, National University of Cuyo, Almirante Brown 500, Mendoza M5528 AHB, Argentina; (I.d.R.); (L.D.); (J.B.C.)
- Plant Physiology Laboratory, Institution of Agricultural Biology of Mendoza, Faculty of Agricultural Sciences, National University of Cuyo and Conicet, Almirante Brown 500, Chacras de Coria M5505 AHB, Argentina
| | - Pablo F. Cavagnaro
- National Scientific and Technical Research Council (CONICET), Faculty of Agricultural Sciences, National Agricultural Technology Institute (INTA) E.E.A. La Consulta, National University of Cuyo and Conicet, Ex Ruta 40 s/n, San Carlos, La Consulta 5567, Mendoza M5528 AHB, Argentina
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29
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Curtin S, Qi Y, Peres LEP, Fernie AR, Zsögön A. Pathways to de novo domestication of crop wild relatives. PLANT PHYSIOLOGY 2022; 188:1746-1756. [PMID: 34850221 PMCID: PMC8968405 DOI: 10.1093/plphys/kiab554] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/03/2021] [Indexed: 05/24/2023]
Abstract
Growing knowledge about crop domestication, combined with increasingly powerful gene-editing toolkits, sets the stage for the continual domestication of crop wild relatives and other lesser-known plant species.
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Affiliation(s)
- Shaun Curtin
- United States Department of Agriculture, Plant Science Research Unit, St. Paul, Minnesota 55108, USA
- Center for Plant Precision Genomics, University of Minnesota, St. Paul, Minnesota 55108, USA
- Center for Genome Engineering, University of Minnesota, St. Paul, Minnesota 55108, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Lázaro E P Peres
- Laboratory of Hormonal Control of Plant Development. Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, CP 09, 13418-900, Piracicaba, São Paulo, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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30
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Sayed MA, Bakry BA, El-Samad M A, M. Eldemer S. Phenotypic Stability and Genotypic Responses of Bread Wheat Genotypes Across Multiple Environments in Egypt. ASIAN JOURNAL OF PLANT SCIENCES 2022; 21:243-256. [DOI: 10.3923/ajps.2022.243.256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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31
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Mu Q, Guo T, Li X, Yu J. Phenotypic plasticity in plant height shaped by interaction between genetic loci and diurnal temperature range. THE NEW PHYTOLOGIST 2022; 233:1768-1779. [PMID: 34870847 DOI: 10.1111/nph.17904] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
Phenotypic plasticity is observed widely in plants and often studied with reaction norms for adult plant or end-of-season traits. Uncovering genetic, environmental and developmental patterns behind the observed phenotypic variation under natural field conditions is needed. Using a sorghum (Sorghum bicolor) genetic population evaluated for plant height in seven natural field conditions, we investigated the major pattern that differentiated these environments. We then examined the physiological relevance of the identified environmental index by investigating the developmental trajectory of the population with multistage height measurements in four additional environments and conducting crop growth modelling. We found that diurnal temperature range (DTR) during the rapid growth period of sorghum development was an effective environmental index. Three genetic loci (Dw1, Dw3 and qHT7.1) were consistently detected for individual environments, reaction-norm parameters across environments and growth-curve parameters through the season. Their genetic effects changed dynamically along the environmental gradient and the developmental stage. A conceptual model with three-dimensional reaction norms was proposed to showcase the interconnecting components: genotype, environment and development. Beyond genomic and environmental analyses, further integration of development and physiology at the whole-plant and molecular levels into complex trait dissection would enhance our understanding of mechanisms underlying phenotypic variation.
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Affiliation(s)
- Qi Mu
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Tingting Guo
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Xianran Li
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
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32
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Relative flux trade-offs and optimization of metabolic network functionalities. Comput Struct Biotechnol J 2022; 20:3963-3971. [PMID: 35950188 PMCID: PMC9340536 DOI: 10.1016/j.csbj.2022.07.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 11/21/2022] Open
Abstract
Trade-offs between traits are present across different levels of biological systems and ultimately reflect constraints imposed by physicochemical laws and the structure of underlying biochemical networks. Yet, mechanistic explanation of how trade-offs between molecular traits arise and how they relate to optimization of fitness-related traits remains elusive. Here, we introduce the concept of relative flux trade-offs and propose a constraint-based approach, termed FluTOr, to identify metabolic reactions whose fluxes are in relative trade-off with respect to an optimized fitness-related cellular task, like growth. We then employed FluTOr to identify relative flux trade-offs in the genome-scale metabolic networks of Escherichia coli, Saccharomyces cerevisiae, and Arabidopsis thaliana. For the metabolic models of E. coli and S. cerevisiae we showed that: (i) the identified relative flux trade-offs depend on the carbon source used and that (ii) reactions that participated in relative trade-offs in both species were implicated in cofactor biosynthesis. In contrast to the two microorganisms, the relative flux trade-offs for the metabolic model of A. thaliana did not depend on the available nitrogen sources, reflecting the differences in the underlying metabolic network as well as the considered environments. Lastly, the established connection between relative flux trade-offs allowed us to identify overexpression targets that can be used to optimize fitness-related traits. Altogether, our computational approach and findings demonstrate how relative flux trade-offs can shape optimization of metabolic tasks, important in biotechnological applications.
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33
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Duarte GT, Pandey PK, Vaid N, Alseekh S, Fernie AR, Nikoloski Z, Laitinen RAE. Plasticity of rosette size in response to nitrogen availability is controlled by an RCC1-family protein. PLANT, CELL & ENVIRONMENT 2021; 44:3398-3411. [PMID: 34228823 DOI: 10.1111/pce.14146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 05/12/2023]
Abstract
Nitrogen (N) is fundamental to plant growth, development and yield. Genes underlying N utilization and assimilation are well-characterized, but mechanisms underpinning plasticity of different phenotypes in response to N remain elusive. Here, using Arabidopsis thaliana accessions, we dissected the genetic architecture of plasticity in early and late rosette diameter, flowering time and yield, in response to three levels of N in the soil. Furthermore, we found that the plasticity in levels of primary metabolites were related with the plasticities of the studied traits. Genome-wide association analysis identified three significant associations for phenotypic plasticity, one for early rosette diameter and two for flowering time. We confirmed that the gene At1g19880, hereafter named as PLASTICITY OF ROSETTE TO NITROGEN 1 (PROTON1), encoding for a regulator of chromatin condensation 1 (RCC1) family protein, conferred plasticity of rosette diameter in response to N. Treatment of PROTON1 T-DNA line with salt implied that the reduced plasticity of early rosette diameter was not a general growth response to stress. We further showed that plasticities of growth and flowering-related traits differed between environmental cues, indicating decoupled genetic programs regulating these traits. Our findings provide a prospective to identify genes that stabilize performance under fluctuating environments.
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Affiliation(s)
- Gustavo Turqueto Duarte
- Molecular Mechanisms of Plant Adaptation - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Prashant K Pandey
- Molecular Mechanisms of Plant Adaptation - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- National Research Council Canada (NRC-CNRC), Aquatic and Crop Resource Development (ACRD), Saskatoon, Saskatchewan, Canada
| | - Neha Vaid
- Molecular Mechanisms of Plant Adaptation - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Saleh Alseekh
- Central Metabolism - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Department of Plant Metabolomics, Center of Plant Systems Biology, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Central Metabolism - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Department of Plant Metabolomics, Center of Plant Systems Biology, Plovdiv, Bulgaria
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Department of Bioinformatics and Mathematical Modeling, Center of Plant Systems Biology, Plovdiv, Bulgaria
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Roosa A E Laitinen
- Molecular Mechanisms of Plant Adaptation - group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Organismal and Evolutionary Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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34
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Neinavaie F, Ibrahim-Hashim A, Kramer AM, Brown JS, Richards CL. The Genomic Processes of Biological Invasions: From Invasive Species to Cancer Metastases and Back Again. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.681100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The concept of invasion is useful across a broad range of contexts, spanning from the fine scale landscape of cancer tumors up to the broader landscape of ecosystems. Invasion biology provides extraordinary opportunities for studying the mechanistic basis of contemporary evolution at the molecular level. Although the field of invasion genetics was established in ecology and evolution more than 50 years ago, there is still a limited understanding of how genomic level processes translate into invasive phenotypes across different taxa in response to complex environmental conditions. This is largely because the study of most invasive species is limited by information about complex genome level processes. We lack good reference genomes for most species. Rigorous studies to examine genomic processes are generally too costly. On the contrary, cancer studies are fortified with extensive resources for studying genome level dynamics and the interactions among genetic and non-genetic mechanisms. Extensive analysis of primary tumors and metastatic samples have revealed the importance of several genomic mechanisms including higher mutation rates, specific types of mutations, aneuploidy or whole genome doubling and non-genetic effects. Metastatic sites can be directly compared to primary tumor cell counterparts. At the same time, clonal dynamics shape the genomics and evolution of metastatic cancers. Clonal diversity varies by cancer type, and the tumors’ donor and recipient tissues. Still, the cancer research community has been unable to identify any common events that provide a universal predictor of “metastatic potential” which parallels findings in evolutionary ecology. Instead, invasion in cancer studies depends strongly on context, including order of events and clonal composition. The detailed studies of the behavior of a variety of human cancers promises to inform our understanding of genome level dynamics in the diversity of invasive species and provide novel insights for management.
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35
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Inferring multilayer interactome networks shaping phenotypic plasticity and evolution. Nat Commun 2021; 12:5304. [PMID: 34489412 PMCID: PMC8421358 DOI: 10.1038/s41467-021-25086-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023] Open
Abstract
Phenotypic plasticity represents a capacity by which the organism changes its phenotypes in response to environmental stimuli. Despite its pivotal role in adaptive evolution, how phenotypic plasticity is genetically controlled remains elusive. Here, we develop a unified framework for coalescing all single nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) into a quantitative graph. This framework integrates functional genetic mapping, evolutionary game theory, and predator-prey theory to decompose the net genetic effect of each SNP into its independent and dependent components. The independent effect arises from the intrinsic capacity of a SNP, only expressed when it is in isolation, whereas the dependent effect results from the extrinsic influence of other SNPs. The dependent effect is conceptually beyond the traditional definition of epistasis by not only characterizing the strength of epistasis but also capturing the bi-causality of epistasis and the sign of the causality. We implement functional clustering and variable selection to infer multilayer, sparse, and multiplex interactome networks from any dimension of genetic data. We design and conduct two GWAS experiments using Staphylococcus aureus, aimed to test the genetic mechanisms underlying the phenotypic plasticity of this species to vancomycin exposure and Escherichia coli coexistence. We reconstruct the two most comprehensive genetic networks for abiotic and biotic phenotypic plasticity. Pathway analysis shows that SNP-SNP epistasis for phenotypic plasticity can be annotated to protein-protein interactions through coding genes. Our model can unveil the regulatory mechanisms of significant loci and excavate missing heritability from some insignificant loci. Our multilayer genetic networks provide a systems tool for dissecting environment-induced evolution.
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Wang X, Liu S, Zuo H, Zheng W, Zhang S, Huang Y, Pingcuo G, Ying H, Zhao F, Li Y, Liu J, Yi TS, Zan Y, Larkin RM, Deng X, Zeng X, Xu Q. Genomic basis of high-altitude adaptation in Tibetan Prunus fruit trees. Curr Biol 2021; 31:3848-3860.e8. [PMID: 34314676 DOI: 10.1016/j.cub.2021.06.062] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/25/2021] [Accepted: 06/22/2021] [Indexed: 01/03/2023]
Abstract
The Great Himalayan Mountains and their foothills are believed to be the place of origin and development of many plant species. The genetic basis of adaptation to high plateaus is a fascinating topic that is poorly understood at the population level. We comprehensively collected and sequenced 377 accessions of Prunus germplasm along altitude gradients ranging from 2,067 to 4,492 m in the Himalayas. We de novo assembled three high-quality genomes of Tibetan Prunus species. A comparative analysis of Prunus genomes indicated a remarkable expansion of the SINE retrotransposons occurred in the genomes of Tibetan species. We observed genetic differentiation between Tibetan peaches from high and low altitudes and that genes associated with light stress signaling, especially UV stress signaling, were enriched in the differentiated regions. By profiling the metabolomes of Tibetan peach fruit, we determined 379 metabolites had significant genetic correlations with altitudes and that in particular phenylpropanoids were positively correlated with altitudes. We identified 62 Tibetan peach-specific SINEs that colocalized with metabolites differentially accumualted in Tibetan relative to cultivated peach. We demonstrated that two SINEs were inserted in a locus controlling the accumulation of 3-O-feruloyl quinic acid. SINE1 was specific to Tibetan peach. SINE2 was predominant in high altitudes and associated with the accumulation of 3-O-feruloyl quinic acid. These genomic and metabolic data for Prunus populations native to the Himalayan region indicate that the expansion of SINE retrotransposons helped Tibetan Prunus species adapt to the harsh environment of the Himalayan plateau by promoting the accumulation of beneficial metabolites.
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Affiliation(s)
- Xia Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Shengjun Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Zuo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Weikang Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Shanshan Zhang
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Yue Huang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Gesang Pingcuo
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Hong Ying
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Fan Zhao
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Yuanrong Li
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Junwei Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yanjun Zan
- Department of Forestry Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå 90736, Sweden
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Zeng
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China.
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China.
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Liu N, Du Y, Warburton ML, Xiao Y, Yan J. Phenotypic Plasticity Contributes to Maize Adaptation and Heterosis. Mol Biol Evol 2021; 38:1262-1275. [PMID: 33212480 PMCID: PMC8480182 DOI: 10.1093/molbev/msaa283] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plant phenotypic plasticity describes altered phenotypic performance of an individual when grown in different environments. Exploring genetic architecture underlying plant plasticity variation may help mitigate the detrimental effects of a rapidly changing climate on agriculture, but little research has been done in this area to date. In the present study, we established a population of 976 maize F1 hybrids by crossing 488 diverse inbred lines with two elite testers. Genome-wide association study identified hundreds of quantitative trait loci associated with phenotypic plasticity variation across diverse F1 hybrids, the majority of which contributed very little variance, in accordance with the polygenic nature of these traits. We identified several quantitative trait locus regions that may have been selected during the tropical-temperate adaptation process. We also observed heterosis in terms of phenotypic plasticity, in addition to the traditional genetic value differences measured between hybrid and inbred lines, and the pattern of which was affected by genetic background. Our results demonstrate a landscape of phenotypic plasticity in maize, which will aid in the understanding of its genetic architecture, its contribution to adaptation and heterosis, and how it may be exploited for future maize breeding in a rapidly changing environment.
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Affiliation(s)
- Nannan Liu
- Horticulture Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuanhao Du
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Marilyn L Warburton
- United States Department of Agriculture-Agricultural Research Service: Corn Host Plant Resistance Research Unit, Mississippi State, MS
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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38
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Xie X, Quintana MR, Sandhu N, Subedi SR, Zou Y, Rutkoski JE, Henry A. Establishment method affects rice root plasticity in response to drought and its relationship with grain yield stability. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5208-5220. [PMID: 33989419 DOI: 10.1093/jxb/erab214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/12/2021] [Indexed: 06/12/2023]
Abstract
By responding to the variable soil environments in which they are grown, the roots of rice crops are likely to contribute to yield stability across a range of soil moistures, nutrient levels, and establishment methods. In this study, we explored different approaches to quantification of root plasticity and characterization of its relationship with yield stability. Using four different statistical approaches (plasticity index, slope, AMMI, and factor analytic) on a set of 17 genotypes including several recently-developed breeding lines targeted to dry direct-seeding, we identified only very few direct relationships between root plasticity and yield stability. However, genotypes identified as having combined yield stability and root plasticity showed higher grain yields across trials. Furthermore, root plasticity was expressed to a greater degree in puddled transplanted trials rather than under dry direct-seeding. Significant interactions between nitrogen and water resulted in contrasting relationships between nitrogen-use efficiency and biomass stability between puddled-transplanted and direct-seeded conditions. These results reflect the complex interaction between nitrogen, drought, and even different types of drought (as a result of the establishment method) on rice root growth, and suggest that although rice root plasticity may confer stable yield across a range of environments, it might be necessary to more narrowly define the targeted environments to which it will be most beneficial.
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Affiliation(s)
- Xiaobing Xie
- International Rice Research Institute, Los Baños, Laguna, Philippines
- Hunan Agricultural University, Changsha, China
| | | | - Nitika Sandhu
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Sushil R Subedi
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Yingbin Zou
- Hunan Agricultural University, Changsha, China
| | | | - Amelia Henry
- International Rice Research Institute, Los Baños, Laguna, Philippines
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39
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Zilio G, Nørgaard LS, Petrucci G, Zeballos N, Gougat-Barbera C, Fronhofer EA, Kaltz O. Parasitism and host dispersal plasticity in an aquatic model system. J Evol Biol 2021; 34:1316-1325. [PMID: 34157176 DOI: 10.1111/jeb.13893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/19/2021] [Accepted: 06/16/2021] [Indexed: 11/28/2022]
Abstract
Dispersal is a central determinant of spatial dynamics in communities and ecosystems, and various ecological factors can shape the evolution of constitutive and plastic dispersal behaviours. One important driver of dispersal plasticity is the biotic environment. Parasites, for example, influence the internal condition of infected hosts and define external patch quality. Thus, state-dependent dispersal may be determined by infection status and context-dependent dispersal by the abundance of infected hosts in the population. A prerequisite for such dispersal plasticity to evolve is a genetic basis on which natural selection can act. Using interconnected microcosms, we investigated dispersal in experimental populations of the freshwater protist Paramecium caudatum in response to the bacterial parasite Holospora undulata. For a collection of 20 natural host strains, we found substantial variation in constitutive dispersal and to a lesser degree in dispersal plasticity. First, infection tended to increase or decrease dispersal relative to uninfected controls, depending on strain identity, indicative of state-dependent dispersal plasticity. Infection additionally decreased host swimming speed compared to the uninfected counterparts. Second, for certain strains, there was a weak negative association between dispersal and infection prevalence, such that uninfected hosts dispersed less when infection was more frequent in the population, indicating context-dependent dispersal plasticity. Future experiments may test whether the observed differences in dispersal plasticity are sufficiently strong to be picked up by natural selection. The evolution of dispersal plasticity as a strategy to mitigate parasite effects spatially may have important implications for epidemiological dynamics.
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Affiliation(s)
- Giacomo Zilio
- ISEM, CNRS, EPHE, IRD, University of Montpellier, Montpellier, France
| | - Louise S Nørgaard
- ISEM, CNRS, EPHE, IRD, University of Montpellier, Montpellier, France.,School of Biological Sciences, Monash University, Melbourne, Vic., Australia
| | - Giovanni Petrucci
- ISEM, CNRS, EPHE, IRD, University of Montpellier, Montpellier, France
| | - Nathalie Zeballos
- ISEM, CNRS, EPHE, IRD, University of Montpellier, Montpellier, France.,CEFE, CNRS, EPHE, IRD, University of Montpellier, Montpellier, France
| | | | | | - Oliver Kaltz
- ISEM, CNRS, EPHE, IRD, University of Montpellier, Montpellier, France
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40
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Mounger J, Ainouche ML, Bossdorf O, Cavé-Radet A, Li B, Parepa M, Salmon A, Yang J, Richards CL. Epigenetics and the success of invasive plants. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200117. [PMID: 33866809 PMCID: PMC8059582 DOI: 10.1098/rstb.2020.0117] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
Biological invasions impose ecological and economic problems on a global scale, but also provide extraordinary opportunities for studying contemporary evolution. It is critical to understand the evolutionary processes that underly invasion success in order to successfully manage existing invaders, and to prevent future invasions. As successful invasive species sometimes are suspected to rapidly adjust to their new environments in spite of very low genetic diversity, we are obliged to re-evaluate genomic-level processes that translate into phenotypic diversity. In this paper, we review work that supports the idea that trait variation, within and among invasive populations, can be created through epigenetic or other non-genetic processes, particularly in clonal invaders where somatic changes can persist indefinitely. We consider several processes that have been implicated as adaptive in invasion success, focusing on various forms of 'genomic shock' resulting from exposure to environmental stress, hybridization and whole-genome duplication (polyploidy), and leading to various patterns of gene expression re-programming and epigenetic changes that contribute to phenotypic variation or even novelty. These mechanisms can contribute to transgressive phenotypes, including hybrid vigour and novel traits, and may thus help to understand the huge successes of some plant invaders, especially those that are genetically impoverished. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Jeannie Mounger
- Department of Integrative Biology, University of South Florida, 4202 E Fowler Avenue, Tampa, FL 33617, USA
| | - Malika L. Ainouche
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
| | - Armand Cavé-Radet
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
| | - Bo Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Madalin Parepa
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
| | - Armel Salmon
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
| | - Ji Yang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Christina L. Richards
- Department of Integrative Biology, University of South Florida, 4202 E Fowler Avenue, Tampa, FL 33617, USA
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
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Sobral M, Neylan IP, Narbona E, Dirzo R. Transgenerational Plasticity in Flower Color Induced by Caterpillars. FRONTIERS IN PLANT SCIENCE 2021; 12:617815. [PMID: 33790921 PMCID: PMC8006444 DOI: 10.3389/fpls.2021.617815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/19/2021] [Indexed: 05/03/2023]
Abstract
Variation in flower color due to transgenerational plasticity could stem directly from abiotic or biotic environmental conditions. Finding a link between biotic ecological interactions across generations and plasticity in flower color would indicate that transgenerational effects of ecological interactions, such as herbivory, might be involved in flower color evolution. We conducted controlled experiments across four generations of wild radish (Raphanus sativus, Brassicaceae) plants to explore whether flower color is influenced by herbivory, and to determine whether flower color is associated with transgenerational chromatin modifications. We found transgenerational effects of herbivory on flower color, partly related to chromatin modifications. Given the presence of herbivory in plant populations worldwide, our results are of broad significance and contribute to our understanding of flower color evolution.
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Affiliation(s)
- Mar Sobral
- Departamento de Biología Funcional, Universidade de Santiago de Compostela, USC, Santiago de Compostela, Spain
- Department of Biology, Stanford University, Stanford, CA, United States
| | - Isabelle P. Neylan
- Department of Biology, Stanford University, Stanford, CA, United States
- Department of Evolution and Ecology, Center for Population Biology, University of California, Davis, Davis, CA, United States
| | - Eduardo Narbona
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
| | - Rodolfo Dirzo
- Department of Biology, Stanford University, Stanford, CA, United States
- Woods Institute for the Environment, Stanford University, Stanford, CA, United States
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42
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Crespi M. Plant transcription links environmental cues and phenotypic plasticity. Transcription 2020; 11:97-99. [PMID: 33252015 DOI: 10.1080/21541264.2020.1837498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- M Crespi
- Institute of Plant Sciences Paris-Saclay IPS2, Universities of Paris-Saclay and Evry, CNRS, INRAE , Gif sur Yvette, France.,Institute of Plant Sciences Paris-Saclay IPS2, University of Paris, CNRS, INRAE , Gif sur Yvette, France
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43
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Diouf I, Derivot L, Koussevitzky S, Carretero Y, Bitton F, Moreau L, Causse M. Genetic basis of phenotypic plasticity and genotype × environment interactions in a multi-parental tomato population. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5365-5376. [PMID: 32474596 PMCID: PMC7501811 DOI: 10.1093/jxb/eraa265] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/25/2020] [Indexed: 05/25/2023]
Abstract
Deciphering the genetic basis of phenotypic plasticity and genotype × environment interactions (G×E) is of primary importance for plant breeding in the context of global climate change. Tomato (Solanum lycopersicum) is a widely cultivated crop that can grow in different geographical habitats and that displays a great capacity for expressing phenotypic plasticity. We used a multi-parental advanced generation intercross (MAGIC) tomato population to explore G×E and plasticity for multiple traits measured in a multi-environment trial (MET) comprising optimal cultural conditions together with water deficit, salinity, and heat stress over 12 environments. Substantial G×E was observed for all the traits measured. Different plasticity parameters were estimated by employing Finlay-Wilkinson and factorial regression models and these were used together with genotypic means for quantitative trait loci (QTL) mapping analyses. In addition, mixed linear models were also used to investigate the presence of QTL × environment interactions. The results highlighted a complex genetic architecture of tomato plasticity and G×E. Candidate genes that might be involved in the occurrence of G×E are proposed, paving the way for functional characterization of stress response genes in tomato and for breeding climate-adapted cultivars.
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Affiliation(s)
| | | | | | | | | | - Laurence Moreau
- UMR GQE-Le Moulon, INRA, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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Abstract
The importance of tree genetic variability in the ability of forests to respond and adapt to environmental changes is crucial in forest management and conservation. Along with genetics, recent advances have highlighted “epigenetics” as an emerging and promising field of research for the understanding of tree phenotypic plasticity and adaptive responses. In this paper, we review recent advances in this emerging field and their potential applications for tree researchers and breeders, as well as for forest managers. First, we present the basics of epigenetics in plants before discussing its potential for trees. We then propose a bibliometric and overview of the literature on epigenetics in trees, including recent advances on tree priming. Lastly, we outline the promises of epigenetics for forest research and management, along with current gaps and future challenges. Research in epigenetics could use highly diverse paths to help forests adapt to global change by eliciting different innovative silvicultural approaches for natural- and artificial-based forest management.
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45
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Borghi M, Fernie AR. Outstanding questions in flower metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1275-1288. [PMID: 32410253 DOI: 10.1111/tpj.14814] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/29/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
The great diversity of flowers, their color, odor, taste, and shape, is mostly a result of the metabolic processes that occur in this reproductive organ when the flower and its tissues develop, grow, and finally die. Some of these metabolites serve to advertise flowers to animal pollinators, other confer protection towards abiotic stresses, and a large proportion of the molecules of the central metabolic pathways have bioenergetic and signaling functions that support growth and the transition to fruits and seeds. Although recent studies have advanced our general understanding of flower metabolism, several questions still await an answer. Here, we have compiled a list of open questions on flower metabolism encompassing molecular aspects, as well as topics of relevance for agriculture and the ecosystem. These questions include the study of flower metabolism through development, the biochemistry of nectar and its relevance to promoting plant-pollinator interaction, recycling of metabolic resources after flowers whiter and die, as well as the manipulation of flower metabolism by pathogens. We hope with this review to stimulate discussion on the topic of flower metabolism and set a reference point to return to in the future when assessing progress in the field.
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Affiliation(s)
- Monica Borghi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam, 14476, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam, 14476, Germany
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46
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Asao S, Hayes L, Aspinwall MJ, Rymer PD, Blackman C, Bryant CJ, Cullerne D, Egerton JJG, Fan Y, Innes P, Millar AH, Tucker J, Shah S, Wright IJ, Yvon-Durocher G, Tissue D, Atkin OK. Leaf trait variation is similar among genotypes of Eucalyptus camaldulensis from differing climates and arises in plastic responses to the seasons rather than water availability. THE NEW PHYTOLOGIST 2020; 227:780-793. [PMID: 32255508 DOI: 10.1111/nph.16579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
We used a widely distributed tree Eucalyptus camaldulensis subsp. camaldulensis to partition intraspecific variation in leaf functional traits to genotypic variation and phenotypic plasticity. We examined if genotypic variation is related to the climate of genotype provenance and whether phenotypic plasticity maintains performance in a changing environment. Ten genotypes from different climates were grown in a common garden under watering treatments reproducing the wettest and driest edges of the subspecies' distribution. We measured functional traits reflecting leaf metabolism and associated with growth (respiration rate, nitrogen and phosphorus concentrations, and leaf mass per area) and performance proxies (aboveground biomass and growth rate) each season over a year. Genotypic variation contributed substantially to the variation in aboveground biomass but much less in growth rate and leaf traits. Phenotypic plasticity was a large source of the variation in leaf traits and performance proxies and was greater among sampling dates than between watering treatments. The variation in leaf traits was weakly correlated to performance proxies, and both were unrelated to the climate of genotype provenance. Intraspecific variation in leaf traits arises similarly among genotypes in response to seasonal environmental variation, instead of long-term water availability or climate of genotype provenance.
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Affiliation(s)
- Shinichi Asao
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
| | - Lucy Hayes
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
| | - Michael J Aspinwall
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
- Department of Biology, University of North Florida, 1 UNF Drive, Jacksonville, FL, 32224, USA
| | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Chris Blackman
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Callum J Bryant
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
| | - Darren Cullerne
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
| | - John J G Egerton
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
| | - Yuzhen Fan
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
| | - Peter Innes
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
| | - A Harvey Millar
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Josephine Tucker
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
| | - Shahen Shah
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
- The University of Agriculture Peshawar, Khyber Pakhtunkhwa, 25130, Pakistan
| | - Ian J Wright
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Gabriel Yvon-Durocher
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9EZ, UK
| | - David Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Owen K Atkin
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Building 134, Canberra, ACT, 2601, Australia
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Zhang Y, Li Z, Chen N, Huang Y, Huang S. Phase separation of Arabidopsis EMB1579 controls transcription, mRNA splicing, and development. PLoS Biol 2020; 18:e3000782. [PMID: 32692742 PMCID: PMC7413564 DOI: 10.1371/journal.pbio.3000782] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 08/07/2020] [Accepted: 07/06/2020] [Indexed: 11/19/2022] Open
Abstract
Tight regulation of gene transcription and mRNA splicing is essential for plant growth and development. Here we demonstrate that a plant-specific protein, EMBRYO DEFECTIVE 1579 (EMB1579), controls multiple growth and developmental processes in Arabidopsis. We demonstrate that EMB1579 forms liquid-like condensates both in vitro and in vivo, and the formation of normal-sized EMB1579 condensates is crucial for its cellular functions. We found that some chromosomal and RNA-related proteins interact with EMB1579 compartments, and loss of function of EMB1579 affects global gene transcription and mRNA splicing. Using floral transition as a physiological process, we demonstrate that EMB1579 is involved in FLOWERING LOCUS C (FLC)-mediated repression of flowering. Interestingly, we found that EMB1579 physically interacts with a homologue of Drosophila nucleosome remodeling factor 55-kDa (p55) called MULTIPLE SUPPRESSOR OF IRA 4 (MSI4), which has been implicated in repressing the expression of FLC by forming a complex with DNA Damage Binding Protein 1 (DDB1) and Cullin 4 (CUL4). This complex, named CUL4-DDB1MSI4, physically associates with a CURLY LEAF (CLF)-containing Polycomb Repressive Complex 2 (CLF-PRC2). We further demonstrate that EMB1579 interacts with CUL4 and DDB1, and EMB1579 condensates can recruit and condense MSI4 and DDB1. Furthermore, emb1579 phenocopies msi4 in terms of the level of H3K27 trimethylation on FLC. This allows us to propose that EMB1579 condensates recruit and condense CUL4-DDB1MSI4 complex, which facilitates the interaction of CUL4-DDB1MSI4 with CLF-PRC2 and promotes the role of CLF-PRC2 in establishing and/or maintaining the level of H3K27 trimethylation on FLC. Thus, we report a new mechanism for regulating plant gene transcription, mRNA splicing, and growth and development. This study reveals that a plant-specific protein, EMB1579, controls multiple growth and developmental processes in Arabidopsis thaliana by regulating gene transcription and mRNA splicing through the formation of liquid-like droplets via liquid-liquid phase separation.
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Affiliation(s)
- Yiling Zhang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhankun Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Naizhi Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yao Huang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shanjin Huang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- * E-mail:
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Dwivedi SL, Stoddard FL, Ortiz R. Genomic-based root plasticity to enhance abiotic stress adaptation and edible yield in grain crops. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 295:110365. [PMID: 32534611 DOI: 10.1016/j.plantsci.2019.110365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/15/2019] [Accepted: 12/01/2019] [Indexed: 06/11/2023]
Abstract
Phenotypic plasticity refers to changes expressed by a genotype across different environments and is one of the major means by which plants cope with environmental variability. Multi-fold differences in phenotypic plasticity have been noted across crops, with wild ancestors and landraces being more plastic than crops when under stress. Plasticity in response to abiotic stress adaptation, plant architecture, physio-reproductive and quality traits are multi-genic (QTL). Plasticity QTL (pQTL) were either collocated with main effect QTL and QEI (QTL × environment interaction) or located independently from the main effect QTL. For example, variations in root plasticity have been successfully introgressed to enhance abiotic stress adaptation in rice. The independence of genetic control of a trait and of its plasticity suggests that breeders may select for high or low plasticity in combination with high or low performance of economically important traits. Trait plasticity in stressful environments may be harnessed through breeding stress-tolerant crops. There exists a genetic cost associated with plasticity, so a better understanding of the trade-offs between plasticity and productivity is warranted prior to undertaking breeding for plasticity traits together with productivity in stress environments.
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Affiliation(s)
| | | | - Rodomiro Ortiz
- Swedish University of Agricultural Sciences, Department of Plant Breeding, Sundsvagen, 14 Box 101, SE 23053, Alnarp, Sweden.
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Calvo P, Gagliano M, Souza GM, Trewavas A. Plants are intelligent, here's how. ANNALS OF BOTANY 2020; 125:11-28. [PMID: 31563953 PMCID: PMC6948212 DOI: 10.1093/aob/mcz155] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/01/2019] [Accepted: 09/26/2019] [Indexed: 05/07/2023]
Abstract
HYPOTHESES The drive to survive is a biological universal. Intelligent behaviour is usually recognized when individual organisms including plants, in the face of fiercely competitive or adverse, real-world circumstances, change their behaviour to improve their probability of survival. SCOPE This article explains the potential relationship of intelligence to adaptability and emphasizes the need to recognize individual variation in intelligence showing it to be goal directed and thus being purposeful. Intelligent behaviour in single cells and microbes is frequently reported. Individual variation might be underpinned by a novel learning mechanism, described here in detail. The requirements for real-world circumstances are outlined, and the relationship to organic selection is indicated together with niche construction as a good example of intentional behaviour that should improve survival. Adaptability is important in crop development but the term may be complex incorporating numerous behavioural traits some of which are indicated. CONCLUSION There is real biological benefit to regarding plants as intelligent both from the fundamental issue of understanding plant life but also from providing a direction for fundamental future research and in crop breeding.
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Affiliation(s)
- Paco Calvo
- Minimal Intelligence Laboratory, Universidad de Murcia, Murcia, Spain
| | - Monica Gagliano
- Biological Intelligence Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Gustavo M Souza
- Laboratory of Plant Cognition and Electrophysiology, Federal University of Pelotas, Pelotas - RS, Brazil
| | - Anthony Trewavas
- Institute of Molecular Plant Science, Kings Buildings, University of Edinburgh, Edinburgh, UK
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Singh J, Fabrizio J, Desnoues E, Silva JP, Busch W, Khan A. Root system traits impact early fire blight susceptibility in apple (Malus × domestica). BMC PLANT BIOLOGY 2019; 19:579. [PMID: 31870310 PMCID: PMC6929320 DOI: 10.1186/s12870-019-2202-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 12/12/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND Although it is known that resistant rootstocks facilitate management of fire blight disease, incited by Erwinia amylovora, the role of rootstock root traits in providing systemic defense against E. amylovora is unclear. In this study, the hypothesis that rootstocks of higher root vigor provide higher tolerance to fire blight infection in apples is tested. Several apple scion genotypes grafted onto a single rootstock genotype and non-grafted 'M.7' rootstocks of varying root vigor are used to assess phenotypic and molecular relationships between root traits of rootstocks and fire blight susceptibility of apple scion cultivars. RESULTS It is observed that different root traits display significant (p < 0.05) negative correlations with fire blight susceptibility. In fact, root surface area partially dictates differential levels of fire blight susceptibility of 'M.7' rootstocks. Furthermore, contrasting changes in gene expression patterns of diverse molecular pathways accompany observed differences in levels of root-driven fire blight susceptibility. It is noted that a singular co-expression gene network consisting of genes from defense, carbohydrate metabolism, protein kinase activity, oxidation-reduction, and stress response pathways modulates root-dependent fire blight susceptibility in apple. In particular, WRKY75 and UDP-glycotransferase are singled-out as hub genes deserving of further detailed analysis. CONCLUSIONS It is proposed that low root mass may incite resource-limiting conditions to activate carbohydrate metabolic pathways, which reciprocally interact with plant immune system genes to elicit differential levels of fire blight susceptibility.
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Affiliation(s)
- Jugpreet Singh
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA
| | - Jack Fabrizio
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA
| | - Elsa Desnoues
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA
| | - Julliany Pereira Silva
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA
| | - Wolfgang Busch
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, and Integrative Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA.
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