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Kimutai JJC, Makumbi D, Burgueño J, Pérez-Rodríguez P, Crossa J, Gowda M, Menkir A, Pacheco A, Ifie BE, Tongoona P, Danquah EY, Prasanna BM. Genomic prediction of the performance of tropical doubled haploid maize lines under artificial Striga hermonthica (Del.) Benth. infestation. G3 (BETHESDA, MD.) 2024; 14:jkae186. [PMID: 39129203 PMCID: PMC11457060 DOI: 10.1093/g3journal/jkae186] [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: 05/31/2024] [Revised: 07/23/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024]
Abstract
Striga hermonthica (Del.) Benth., a parasitic weed, causes substantial yield losses in maize production in sub-Saharan Africa. Breeding for Striga resistance in maize is constrained by limited genetic diversity for Striga resistance within the elite germplasm and phenotyping capacity under artificial Striga infestation. Genomics-enabled approaches have the potential to accelerate identification of Striga resistant lines for hybrid development. The objectives of this study were to evaluate the accuracy of genomic selection for traits associated with Striga resistance and grain yield (GY) and to predict genetic values of tested and untested doubled haploid maize lines. We genotyped 606 doubled haploid lines with 8,439 rAmpSeq markers. A training set of 116 doubled haploid lines crossed to 2 testers was phenotyped under artificial Striga infestation at 3 locations in Kenya. Heritability for Striga resistance parameters ranged from 0.38-0.65 while that for GY was 0.54. The prediction accuracies for Striga resistance-associated traits across locations, as determined by cross-validation (CV) were 0.24-0.53 for CV0 and from 0.20 to 0.37 for CV2. For GY, the prediction accuracies were 0.59 and 0.56 for CV0 and CV2, respectively. The results revealed 300 doubled haploid lines with desirable genomic estimated breeding values for reduced number of emerged Striga plants (STR) at 8, 10, and 12 weeks after planting. The genomic estimated breeding values of doubled haploid lines for Striga resistance-associated traits in the training and testing sets were similar in magnitude. These results highlight the potential application of genomic selection in breeding for Striga resistance in maize. The integration of genomic-assisted strategies and doubled haploid technology for line development coupled with forward breeding for major adaptive traits will enhance genetic gains in breeding for Striga resistance in maize.
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Affiliation(s)
- Joan J C Kimutai
- Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041-00621, Nairobi, Kenya
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, PMB 30 Legon, Accra, Ghana
| | - Dan Makumbi
- Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041-00621, Nairobi, Kenya
| | - Juan Burgueño
- Biometrics and Statistics Unit, CIMMYT, Apdo. Postal 6-641, 06600 Mexico DF, Mexico
| | - Paulino Pérez-Rodríguez
- Socioeconomía, Estadística e Informática, Colegio de Postgraduados, Edo. de México 56230, Montecillos, Mexico
| | - Jose Crossa
- Biometrics and Statistics Unit, CIMMYT, Apdo. Postal 6-641, 06600 Mexico DF, Mexico
- Socioeconomía, Estadística e Informática, Colegio de Postgraduados, Edo. de México 56230, Montecillos, Mexico
| | - Manje Gowda
- Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041-00621, Nairobi, Kenya
| | - Abebe Menkir
- International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, 200001, Nigeria
| | - Angela Pacheco
- Biometrics and Statistics Unit, CIMMYT, Apdo. Postal 6-641, 06600 Mexico DF, Mexico
| | - Beatrice E Ifie
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, PMB 30 Legon, Accra, Ghana
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3EE Wales, UK
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, PMB 30 Legon, Accra, Ghana
| | - Eric Y Danquah
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, PMB 30 Legon, Accra, Ghana
| | - Boddupalli M Prasanna
- Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041-00621, Nairobi, Kenya
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Géron C, Lembrechts JJ, Fameree M, Taddei V, Nijs I, Monty A. Phenotypic plasticity as the main driver of alien plant trait variation in urban versus rural microclimate for the model species Veronica persica. Oecologia 2024; 205:643-654. [PMID: 39073568 DOI: 10.1007/s00442-024-05597-w] [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: 05/18/2023] [Accepted: 07/13/2024] [Indexed: 07/30/2024]
Abstract
Urban environments are warmer than the rural surroundings, impacting plant phenotypic traits. When plants are present over areas with contrasted conditions such as along urbanization gradients, their phenotypes may differ, and these differences depend on different processes, including phenotypic plasticity, maternal environmental effects and genetic differentiation (local adaptation and/or genetic drift). Successful establishment of alien species along environmental gradients has been linked to high phenotypic plasticity and rapid evolutionary responses, which are easier to track for species with a known residence time. The mechanisms explaining trait variation in plants in urban versus rural microclimatic conditions have received little attention. Using the alien Veronica persica as model species, we measured leaf traits in urban and rural populations and performed a reciprocal common-garden experiment to study how germination, leaf, growth, and flowering traits varied in response to experimental microclimate (rural or urban) and population origin environment (rural or urban). Veronica persica displayed phenotypic plasticity in all measured traits, with reduced germination, development, and flowering under urban microclimate which suggests more stressful growing conditions in the urban than in the rural microclimate. No significant effect of the rural or urban origin environment was detected, providing no evidence for local adaptation to urban or rural environments. Additionally, we found limited signs of maternal environmental effects. We noted the importance of the mother plant and the population identities suggesting genetically based differences. Our results indicate that urban environments are more hostile than rural ones, and that V. persica does not show any adaptation to urban environments despite genetic differences between populations.
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Affiliation(s)
- Charly Géron
- UMR 6553, University of Rennes, CNRS, ECOBIO (Écosystèmes, Biodiversité, Évolution), 263, Avenue du Général Leclerc, 35042, Rennes, France.
- Biodiversity and Landscape, TERRA Research Centre, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030, Gembloux, Belgium.
- PLEACO (Plants and Ecosystems), University of Antwerp, Universiteitsplein, 1, 2610, Wilrijk, Belgium.
| | - Jonas J Lembrechts
- PLEACO (Plants and Ecosystems), University of Antwerp, Universiteitsplein, 1, 2610, Wilrijk, Belgium
| | - Mathilde Fameree
- Biodiversity and Landscape, TERRA Research Centre, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030, Gembloux, Belgium
| | - Vanille Taddei
- Biodiversity and Landscape, TERRA Research Centre, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030, Gembloux, Belgium
- Faculté des Sciences et Technologies, Université de Lorraine et AgroParisTech de Nancy, Boulevard des Aiguillettes, 54506, Vandoeuvre Les Nancy, France
| | - Ivan Nijs
- PLEACO (Plants and Ecosystems), University of Antwerp, Universiteitsplein, 1, 2610, Wilrijk, Belgium
| | - Arnaud Monty
- Biodiversity and Landscape, TERRA Research Centre, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030, Gembloux, Belgium
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Resende RT, Xavier A, Silva PIT, Resende MPM, Jarquin D, Marcatti GE. GIS-based G × E modeling of maize hybrids through enviromic markers engineering. THE NEW PHYTOLOGIST 2024. [PMID: 39014516 DOI: 10.1111/nph.19951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/22/2024] [Indexed: 07/18/2024]
Abstract
Through enviromics, precision breeding leverages innovative geotechnologies to customize crop varieties to specific environments, potentially improving both crop yield and genetic selection gains. In Brazil's four southernmost states, data from 183 distinct geographic field trials (also accounting for 2017-2021) covered information on 164 genotypes: 79 phenotyped maize hybrid genotypes for grain yield and their 85 nonphenotyped parents. Additionally, 1342 envirotypic covariates from weather, soil, sensor-based, and satellite sources were collected to engineer 10 K synthetic enviromic markers via machine learning. Soil, radiation light, and surface temperature variations remarkably affect differential genotype yield, hinting at ecophysiological adjustments including evapotranspiration and photosynthesis. The enviromic ensemble-based random regression model showcases superior predictive performance and efficiency compared to the baseline and kernel models, matching the best genotypes to specific geographic coordinates. Clustering analysis has identified regions that minimize genotype-environment (G × E) interactions. These findings underscore the potential of enviromics in crafting specific parental combinations to breed new, higher-yielding hybrid crops. The adequate use of envirotypic information can enhance the precision and efficiency of maize breeding by providing important inputs about the environmental factors that affect the average crop performance. Generating enviromic markers associated with grain yield can enable a better selection of hybrids for specific environments.
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Affiliation(s)
- Rafael T Resende
- Plant Breeding Sector, School of Agronomy (EA), Federal University of Goiás (UFG), Av. Esperança, s/n, Samambaia Campus, Goiânia, GO, 74690-900, Brazil
- TheCROP, A Precision Breeding Project, Av. Esperança, n° 1533, FUNAPE, Samambaia Technological Park, Samambaia Campus - UFG, Goiânia, GO, 74690-612, Brazil
| | - Alencar Xavier
- Corteva Agriscience, 8305 NW 62ndAve, Johnston, IA, 50131, USA
- Purdue University, 915 Mitch Daniels Blvd, West Lafayette, IN, 47907, USA
| | | | - Marcela P M Resende
- Plant Breeding Sector, School of Agronomy (EA), Federal University of Goiás (UFG), Av. Esperança, s/n, Samambaia Campus, Goiânia, GO, 74690-900, Brazil
| | - Diego Jarquin
- University of Florida, 1604 McCarty Drive G052B McCarty Hall D, Gainesville, FL, 32611, USA
| | - Gustavo E Marcatti
- TheCROP, A Precision Breeding Project, Av. Esperança, n° 1533, FUNAPE, Samambaia Technological Park, Samambaia Campus - UFG, Goiânia, GO, 74690-612, Brazil
- Forest Engineering Department, Federal University of São João del Rei (UFSJ), Sete Lagoas Campus, MG-424 Highway, Km 47, Sete Lagoas, MG, 35701-970, Brazil
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Wang D, Candry P, Hunt KA, Flinkstrom Z, Shi Z, Liu Y, Wofford NQ, McInerney MJ, Tanner RS, De Leόn KB, Zhou J, Winkler MKH, Stahl DA, Pan C. Metaproteomics-informed stoichiometric modeling reveals the responses of wetland microbial communities to oxygen and sulfate exposure. NPJ Biofilms Microbiomes 2024; 10:55. [PMID: 38961111 PMCID: PMC11222425 DOI: 10.1038/s41522-024-00525-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 06/07/2024] [Indexed: 07/05/2024] Open
Abstract
Climate changes significantly impact greenhouse gas emissions from wetland soil. Specifically, wetland soil may be exposed to oxygen (O2) during droughts, or to sulfate (SO42-) as a result of sea level rise. How these stressors - separately and together - impact microbial food webs driving carbon cycling in the wetlands is still not understood. To investigate this, we integrated geochemical analysis, proteogenomics, and stoichiometric modeling to characterize the impact of elevated SO42- and O2 levels on microbial methane (CH4) and carbon dioxide (CO2) emissions. The results uncovered the adaptive responses of this community to changes in SO42- and O2 availability and identified altered microbial guilds and metabolic processes driving CH4 and CO2 emissions. Elevated SO42- reduced CH4 emissions, with hydrogenotrophic methanogenesis more suppressed than acetoclastic. Elevated O2 shifted the greenhouse gas emissions from CH4 to CO2. The metabolic effects of combined SO42- and O2 exposures on CH4 and CO2 emissions were similar to those of O2 exposure alone. The reduction in CH4 emission by increased SO42- and O2 was much greater than the concomitant increase in CO2 emission. Thus, greater SO42- and O2 exposure in wetlands is expected to reduce the aggregate warming effect of CH4 and CO2. Metaproteomics and stoichiometric modeling revealed a unique subnetwork involving carbon metabolism that converts lactate and SO42- to produce acetate, H2S, and CO2 when SO42- is elevated under oxic conditions. This study provides greater quantitative resolution of key metabolic processes necessary for the prediction of CH4 and CO2 emissions from wetlands under future climate scenarios.
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Affiliation(s)
- Dongyu Wang
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Pieter Candry
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Zachary Flinkstrom
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Zheng Shi
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Yunlong Liu
- School of Computer Science, University of Oklahoma, Norman, OK, USA
| | - Neil Q Wofford
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | | | - Ralph S Tanner
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Kara B De Leόn
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Computer Science, University of Oklahoma, Norman, OK, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Chongle Pan
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA.
- School of Computer Science, University of Oklahoma, Norman, OK, USA.
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Weine E, Smith SP, Knowlton RK, Harpak A. Tradeoffs in Modeling Context Dependency in Complex Trait Genetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.21.545998. [PMID: 38370664 PMCID: PMC10871201 DOI: 10.1101/2023.06.21.545998] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Genetic effects on complex traits may depend on context, such as age, sex, environmental exposures or social settings. However, it is often unclear if the extent of context dependency, or Gene-by-Environment interaction (GxE), merits more involved models than the additive model typically used to analyze data from genome-wide association studies (GWAS). Here, we suggest considering the utility of GxE models in GWAS as a tradeoff between bias and variance parameters. In particular, We derive a decision rule for choosing between competing models for the estimation of allelic effects. The rule weighs the increased estimation noise when context is considered against the potential bias when context dependency is ignored. In the empirical example of GxSex in human physiology, the increased noise of context-specific estimation often outweighs the bias reduction, rendering GxE models less useful when variants are considered independently. However, we argue that for complex traits, the joint consideration of context dependency across many variants mitigates both noise and bias. As a result, polygenic GxE models can improve both estimation and trait prediction. Finally, we exemplify (using GxDiet effects on longevity in fruit flies) how analyses based on independently ascertained "top hits" alone can be misleading, and that considering polygenic patterns of GxE can improve interpretation.
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6
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Hinz A, Amado A, Kassen R, Bank C, Wong A. Unpredictability of the Fitness Effects of Antimicrobial Resistance Mutations Across Environments in Escherichia coli. Mol Biol Evol 2024; 41:msae086. [PMID: 38709811 PMCID: PMC11110942 DOI: 10.1093/molbev/msae086] [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: 11/08/2023] [Revised: 04/11/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024] Open
Abstract
The evolution of antimicrobial resistance (AMR) in bacteria is a major public health concern, and antibiotic restriction is often implemented to reduce the spread of resistance. These measures rely on the existence of deleterious fitness effects (i.e. costs) imposed by AMR mutations during growth in the absence of antibiotics. According to this assumption, resistant strains will be outcompeted by susceptible strains that do not pay the cost during the period of restriction. The fitness effects of AMR mutations are generally studied in laboratory reference strains grown in standard growth environments; however, the genetic and environmental context can influence the magnitude and direction of a mutation's fitness effects. In this study, we measure how three sources of variation impact the fitness effects of Escherichia coli AMR mutations: the type of resistance mutation, the genetic background of the host, and the growth environment. We demonstrate that while AMR mutations are generally costly in antibiotic-free environments, their fitness effects vary widely and depend on complex interactions between the mutation, genetic background, and environment. We test the ability of the Rough Mount Fuji fitness landscape model to reproduce the empirical data in simulation. We identify model parameters that reasonably capture the variation in fitness effects due to genetic variation. However, the model fails to accommodate the observed variation when considering multiple growth environments. Overall, this study reveals a wealth of variation in the fitness effects of resistance mutations owing to genetic background and environmental conditions, which will ultimately impact their persistence in natural populations.
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Affiliation(s)
- Aaron Hinz
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - André Amado
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Division of Theoretical Ecology and Evolution, Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Evolutionary Dynamics Group, Gulbenkian Science Institute, Oeiras, Portugal
| | - Rees Kassen
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - Claudia Bank
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Division of Theoretical Ecology and Evolution, Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Evolutionary Dynamics Group, Gulbenkian Science Institute, Oeiras, Portugal
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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Garin V, Diallo C, Tékété ML, Théra K, Guitton B, Dagno K, Diallo AG, Kouressy M, Leiser W, Rattunde F, Sissoko I, Touré A, Nébié B, Samaké M, Kholovà J, Berger A, Frouin J, Pot D, Vaksmann M, Weltzien E, Témé N, Rami JF. Characterization of adaptation mechanisms in sorghum using a multireference back-cross nested association mapping design and envirotyping. Genetics 2024; 226:iyae003. [PMID: 38381593 PMCID: PMC10990433 DOI: 10.1093/genetics/iyae003] [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: 10/19/2023] [Accepted: 12/20/2023] [Indexed: 02/23/2024] Open
Abstract
Identifying the genetic factors impacting the adaptation of crops to environmental conditions is of key interest for conservation and selection purposes. It can be achieved using population genomics, and evolutionary or quantitative genetics. Here we present a sorghum multireference back-cross nested association mapping population composed of 3,901 lines produced by crossing 24 diverse parents to 3 elite parents from West and Central Africa-back-cross nested association mapping. The population was phenotyped in environments characterized by differences in photoperiod, rainfall pattern, temperature levels, and soil fertility. To integrate the multiparental and multi-environmental dimension of our data we proposed a new approach for quantitative trait loci (QTL) detection and parental effect estimation. We extended our model to estimate QTL effect sensitivity to environmental covariates, which facilitated the integration of envirotyping data. Our models allowed spatial projections of the QTL effects in agro-ecologies of interest. We utilized this strategy to analyze the genetic architecture of flowering time and plant height, which represents key adaptation mechanisms in environments like West Africa. Our results allowed a better characterization of well-known genomic regions influencing flowering time concerning their response to photoperiod with Ma6 and Ma1 being photoperiod-sensitive and the region of possible candidate gene Elf3 being photoperiod-insensitive. We also accessed a better understanding of plant height genetic determinism with the combined effects of phenology-dependent (Ma6) and independent (qHT7.1 and Dw3) genomic regions. Therefore, we argue that the West and Central Africa-back-cross nested association mapping and the presented analytical approach constitute unique resources to better understand adaptation in sorghum with direct application to develop climate-smart varieties.
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Affiliation(s)
- Vincent Garin
- Crop Physiology Laboratory, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502 324, India
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Chiaka Diallo
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
- Département d’Enseignement et de Recherche des Sciences et Techniques Agricoles, Institut polytechnique rural de formation et de recherche appliquée de Katibougou, Koulikoro, BP 06, Mali
| | - Mohamed Lamine Tékété
- Institut d’Economie Rurale, Bamako, BP 262, Mali
- Faculté des Sciences et Techniques, Université des Sciences des Techniques et des Technologies de Bamako, Bamako, BP E 3206, Mali
| | | | - Baptiste Guitton
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Karim Dagno
- Institut d’Economie Rurale, Bamako, BP 262, Mali
| | | | | | - Willmar Leiser
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
| | - Fred Rattunde
- Agronomy Department, University of Wisconsin, Madison, WI 53705, WI, USA
| | - Ibrahima Sissoko
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
| | - Aboubacar Touré
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
| | - Baloua Nébié
- Dryland Crops Program, International Maize and Wheat Improvement Center (CIMMYT-Senegal) U/C CERAAS, Thiès, Po Box 3320, Senegal
| | - Moussa Samaké
- Faculté des Sciences et Techniques, Université des Sciences des Techniques et des Technologies de Bamako, Bamako, BP E 3206, Mali
| | - Jana Kholovà
- Crop Physiology Laboratory, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502 324, India
- Department of Information Technologies, Faculty of Economics and Management, Czech University of Life Sciences, Prague, 165 00, Czech Republic
| | - Angélique Berger
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Julien Frouin
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - David Pot
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Michel Vaksmann
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Eva Weltzien
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
- Agronomy Department, University of Wisconsin, Madison, WI 53705, WI, USA
| | - Niaba Témé
- Institut d’Economie Rurale, Bamako, BP 262, Mali
| | - Jean-François Rami
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
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8
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Blumstein M. The drivers of intraspecific trait variation and their implications for future tree productivity and survival. AMERICAN JOURNAL OF BOTANY 2024; 111:e16312. [PMID: 38576091 DOI: 10.1002/ajb2.16312] [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: 09/30/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024]
Abstract
Forests are facing unprecedented levels of stress from pest and disease outbreaks, disturbance, fragmentation, development, and a changing climate. These selective agents act to alter forest composition from regional to cellular levels. Thus, a central challenge for understanding how forests will be impacted by future change is how to integrate across scales of biology. Phenotype, or an observable trait, is the product of an individual's genes (G) and the environment in which an organism lives (E). To date, researchers have detailed how environment drives variation in tree phenotypes over long time periods (e.g., long-term ecological research sites [LTERs]) and across large spatial scales (e.g., flux network). In parallel, researchers have discovered the genes and pathways that govern phenotypes, finding high degrees of genetic control and signatures of local adaptation in many plant traits. However, the research in these two areas remain largely independent of each other, hindering our ability to generate accurate predictions of plant response to environment, an increasingly urgent need given threats to forest systems. I present the importance of both genes and environment in determining tree responses to climate stress. I highlight why the difference between G versus E in driving variation is critical for our understanding of climate responses, then propose means of accelerating research that examines G and E simultaneously by leveraging existing long-term, large-scale phenotypic data sets from ecological networks and adding newly affordable sequence (-omics) data to both drill down to find the genes and alleles influencing phenotypes and scale up to find how patterns of demography and local adaptation may influence future response to change.
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Affiliation(s)
- Meghan Blumstein
- Harvard Forest, Harvard University, Petersham, 01366, MA, USA
- Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar St, Cambridge, 02139, MA, USA
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9
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Zou H, Wang W, Huang J, Li X, Ma M, Wu S, Zhao C. Soil Nitrogen and Flooding Intensity Determine the Trade-Off between Leaf and Root Traits of Riparian Plant Species. PLANTS (BASEL, SWITZERLAND) 2024; 13:978. [PMID: 38611507 PMCID: PMC11013260 DOI: 10.3390/plants13070978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
The investigation into trade-offs among plant functional traits sheds light on how plants strategically balance growth and survival when facing environmental stress. This study sought to evaluate whether trade-offs observed at both community and individual species levels could indicate adaptive fitness across an intensity of flooding intensity. The study was conducted at 25 sampling sites spanning approximately 600 km along the riparian zone in the Three Gorges Reservoir area, China. The findings revealed that, along the flooding gradient, the overall riparian community did not exhibit significant trade-offs between leaf and root traits. Examining three broadly distributed dominant species (Cynodon dactylon, Xanthium strumarium, and Abutilon theophrasti), perennial plants showed pronounced trade-offs under low flooding intensity, while annuals exhibited trade-offs under moderate and low flooding intensity. The trade-offs were evident in traits related to nitrogen-carbon resources, such as specific leaf area, root tissue density, and photosynthetic rate. However, under strong flooding intensity, the relationship between leaf and root traits of the species studied was decoupled. Furthermore, the study identified a significant correlation between soil nitrogen and the trade-off traits under moderate and low flooding intensity. Integrating results from the CSR (Competitors, Stress-tolerators, Ruderals) strategy model, species niche breath analysis, and nitrogen-regulated trade-off, the study revealed that, in the face of high flooding intensity, perennial species (C. dactylon) adopts an S-strategy, demonstrating tolerance through a conservative resource allocation that decouples leaf-root coordination. Annual species (X. strumarium and A. theophrasti), on the other hand, exhibit niche specialization along the flooding gradient, employing distinct strategies (R- and C-strategy). As flooding stress diminishes and soil nitrogen level decreases, plant strategies tend to shift towards an R-strategy with a competition for reduced N resources. In conclusion, the study highlighted the pivotal roles of soil nitrogen and flooding intensity acting as the dual determinants of species growth and tolerance. These dynamics of growth-tolerance balance were evident in the diverse trade-offs between leaf and root traits of individual plant species with different life histories, underscoring the array of adaptive strategies employed by riparian plants across the flooding intensity gradient.
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Affiliation(s)
- Hang Zou
- The College of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China
- Chongqing Institute of Green Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing College, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Wanyu Wang
- Chongqing Institute of Green Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing College, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Jinxia Huang
- The College of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China
- Chongqing Institute of Green Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing College, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Xiaohong Li
- Chongqing Institute of Green Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing College, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Maohua Ma
- Chongqing Institute of Green Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing College, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Shengjun Wu
- Chongqing Institute of Green Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing College, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Cunfeng Zhao
- Chongqing Institute of Green Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing College, University of Chinese Academy of Sciences, Chongqing 400714, China
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10
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McLaughlin CM, Li M, Perryman M, Heymans A, Schneider H, Lasky JR, Sawers RJH. Evidence that variation in root anatomy contributes to local adaptation in Mexican native maize. Evol Appl 2024; 17:e13673. [PMID: 38468714 PMCID: PMC10925829 DOI: 10.1111/eva.13673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Mexican native maize (Zea mays ssp. mays) is adapted to a wide range of climatic and edaphic conditions. Here, we focus specifically on the potential role of root anatomical variation in this adaptation. Given the investment required to characterize root anatomy, we present a machine-learning approach using environmental descriptors to project trait variation from a relatively small training panel onto a larger panel of genotyped and georeferenced Mexican maize accessions. The resulting models defined potential biologically relevant clines across a complex environment that we used subsequently for genotype-environment association. We found evidence of systematic variation in maize root anatomy across Mexico, notably a prevalence of trait combinations favoring a reduction in axial hydraulic conductance in varieties sourced from cooler, drier highland areas. We discuss our results in the context of previously described water-banking strategies and present candidate genes that are associated with both root anatomical and environmental variation. Our strategy is a refinement of standard environmental genome-wide association analysis that is applicable whenever a training set of georeferenced phenotypic data is available.
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Affiliation(s)
- Chloee M. McLaughlin
- Intercollege Graduate Degree Program in Plant BiologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Meng Li
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Melanie Perryman
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Adrien Heymans
- Umeå Plant Science Centre, Department of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeåSweden
- Earth and Life InstituteUC LouvainLouvain‐la‐NeuveBelgium
| | - Hannah Schneider
- Department of Physiology and Cell BiologyLeibniz Institute for Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Jesse R. Lasky
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Ruairidh J. H. Sawers
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
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11
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Lee G, Sanderson BJ, Ellis TJ, Dilkes BP, McKay JK, Ågren J, Oakley CG. A large-effect fitness trade-off across environments is explained by a single mutation affecting cold acclimation. Proc Natl Acad Sci U S A 2024; 121:e2317461121. [PMID: 38289961 PMCID: PMC10861903 DOI: 10.1073/pnas.2317461121] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/26/2023] [Indexed: 02/01/2024] Open
Abstract
Identifying the genetic basis of local adaptation and fitness trade-offs across environments is a central goal of evolutionary biology. Cold acclimation is an adaptive plastic response for surviving seasonal freezing, and costs of acclimation may be a general mechanism for fitness trade-offs across environments in temperate zone species. Starting with locally adapted ecotypes of Arabidopsis thaliana from Italy and Sweden, we examined the fitness consequences of a naturally occurring functional polymorphism in CBF2. This gene encodes a transcription factor that is a major regulator of cold-acclimated freezing tolerance and resides within a locus responsible for a genetic trade-off for long-term mean fitness. We estimated the consequences of alternate genotypes of CBF2 on 5-y mean fitness and fitness components at the native field sites by comparing near-isogenic lines with alternate genotypes of CBF2 to their genetic background ecotypes. The effects of CBF2 were validated at the nucleotide level using gene-edited lines in the native genetic backgrounds grown in simulated parental environments. The foreign CBF2 genotype in the local genetic background reduced long-term mean fitness in Sweden by more than 10%, primarily via effects on survival. In Italy, fitness was reduced by more than 20%, primarily via effects on fecundity. At both sites, the effects were temporally variable and much stronger in some years. The gene-edited lines confirmed that CBF2 encodes the causal variant underlying this genetic trade-off. Additionally, we demonstrated a substantial fitness cost of cold acclimation, which has broad implications for potential maladaptive responses to climate change.
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Affiliation(s)
- Gwonjin Lee
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
| | - Brian J. Sanderson
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
| | - Thomas J. Ellis
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, UppsalaSE-752 36, Sweden
| | - Brian P. Dilkes
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
- Department of Biochemistry, Purdue University, West Lafayette, IN47907
| | - John K. McKay
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO80523
| | - Jon Ågren
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, UppsalaSE-752 36, Sweden
| | - Christopher G. Oakley
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
- Center for Plant Biology, Purdue University, West Lafayette, IN47907
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12
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Blumstein M, Oseguera M, Caso-McHugh T, Des Marais DL. Nonstructural carbohydrate dynamics' relationship to leaf development under varying environments. THE NEW PHYTOLOGIST 2024; 241:102-113. [PMID: 37882355 DOI: 10.1111/nph.19333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023]
Abstract
Leaf-out in temperate forests is a critical transition point each spring and advancing with global change. The mechanism linking phenological variation to external cues is poorly understood. Nonstructural carbohydrate (NSC) availability may be key. Here, we use branch cuttings from northern red oak (Quercus rubra) and measure NSCs throughout bud development in branch tissue. Given genes and environment influence phenology, we placed branches in an arrayed factorial experiment (three temperatures × two photoperiods, eight genotypes) to examine their impact on variation in leaf-out timing and corresponding NSCs. Despite significant differences in leaf-out timing between treatments, NSC patterns were much more consistent, with all treatments and genotypes displaying similar NSC concentrations across phenophases. Notably, the moderate and hot temperature treatments reached the same NSC concentrations and phenophases at the same growing degree days (GDD), but 20 calendar days apart, while the cold treatment achieved only half the GDD of the other two. Our results suggest that NSCs are coordinated with leaf-out and could act as a molecular clock, signaling to cells the passage of time and triggering leaf development to begin. This link between NSCs and budburst is critical for improving predictions of phenological timing.
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Affiliation(s)
- Meghan Blumstein
- Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar St., Cambridge, MA, 02139, USA
| | - Miranda Oseguera
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Philadelphia, PA, 19131, USA
| | - Theresa Caso-McHugh
- Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar St., Cambridge, MA, 02139, USA
| | - David L Des Marais
- Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar St., Cambridge, MA, 02139, USA
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13
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Chen R, Li D, Fu J, Fu C, Qin P, Zhang X, Sun Z, He K, Li L, Zhou W, Wang Y, Wang K, Liu X, Yang Y. Exploration of quality variation and stability of hybrid rice under multi-environments. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:4. [PMID: 38225950 PMCID: PMC10788329 DOI: 10.1007/s11032-024-01442-3] [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: 11/07/2023] [Accepted: 12/25/2023] [Indexed: 01/17/2024]
Abstract
Improving quality is an essential goal of rice breeding and production. However, rice quality is not solely determined by genotype, but is also influenced by the environment. Phenotype plasticity refers to the ability of a given genotype to produce different phenotypes under different environmental conditions, which can be a representation of the stability of traits. Seven quality traits of 141 hybrid combinations, deriving from the test-crossing of 7 thermosensitive genic male sterile (TGMS) and 25 restorer lines, were evaluated at 5 trial sites with intermittent sowing of three to five in Southern China. In the Yangtze River Basin, it was observed that delaying the sowing time of hybrid rice combinations leads to an improvement in their overall quality. Twelve parents were identified to have lower plasticity general combing ability (GCA) values with increased ability to produce hybrids with a more stable quality. The parents with superior quality tend to exhibit lower GCA values for plasticity. The genome-wide association study (GWAS) identified 13 and 15 quantitative trait loci (QTLs) associated with phenotype plasticity and BLUP measurement, respectively. Notably, seven QTLs simultaneously affected both phenotype plasticity and BLUP measurement. Two cloned rice quality genes, ALK and GL7, may be involved in controlling the plasticity of quality traits in hybrid rice. The direction of the genetic effect of the QTL6 (ALK) on alkali spreading value (ASV) plasticity varies in different cropping environments. This study provides novel insights into the dynamic genetic basis of quality traits in response to different cropping regions, cultivation practices, and changing climates. These findings establish a foundation for precise breeding and production of stable and high-quality rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01442-3.
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Affiliation(s)
- Rirong Chen
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha, 410082 Hunan China
- State Key Laboratory of Hybrid Rice, Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128 China
| | - Dongxu Li
- State Key Laboratory of Hybrid Rice, Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128 China
- Software Engineering Institute, East China Normal University, Shanghai, 200062 China
| | - Jun Fu
- State Key Laboratory of Hybrid Rice, Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128 China
| | - Chenjian Fu
- State Key Laboratory of Hybrid Rice, Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128 China
| | - Peng Qin
- State Key Laboratory of Hybrid Rice, Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128 China
| | - Xuanwen Zhang
- State Key Laboratory of Hybrid Rice, Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128 China
| | - Zhenbiao Sun
- State Key Laboratory of Hybrid Rice, Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128 China
| | - Kui He
- State Key Laboratory of Hybrid Rice, Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128 China
| | - Liang Li
- State Key Laboratory of Hybrid Rice, Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128 China
| | - Wei Zhou
- State Key Laboratory of Hybrid Rice, Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128 China
| | - Yingjie Wang
- State Key Laboratory of Hybrid Rice, Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128 China
- College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan China
| | - Kai Wang
- State Key Laboratory of Hybrid Rice, Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128 China
- College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan China
| | - Xuanming Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha, 410082 Hunan China
| | - Yuanzhu Yang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha, 410082 Hunan China
- State Key Laboratory of Hybrid Rice, Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha, 410128 China
- College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan China
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14
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Saieed MAU, Zhao Y, Chen K, Rahman S, Zhang J, Islam S, Ma W. Phenotypic Plasticity of Yield and Yield-Related Traits Contributing to the Wheat Yield in a Doubled Haploid Population. PLANTS (BASEL, SWITZERLAND) 2023; 13:17. [PMID: 38202324 PMCID: PMC10780773 DOI: 10.3390/plants13010017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 01/12/2024]
Abstract
Phenotypic plasticity is the ability of an individual genotype to express phenotype variably in different environments. This study investigated the plasticity of yield-related traits of bread wheat by utilising 225 doubled haploid (DH) lines developed from cv. Westonia and cv. Kauz, through two field trials in Western Australia. Plasticity was quantified via two previously published methods: responsiveness to varying ecological conditions and slopes of reaction norms. The spikelets/spike was the most plastic trait, with an overall plasticity of 1.62. The least plastic trait was grain protein content, with an overall plasticity of 0.79. The trait hierarchy based on phenotypic plasticity was spikelets/spike > thousand kernel weight > seed number > seed length > grain yield > grain protein content. An increase in yield plasticity of 0.1 was associated with an increase in maximum yield of 4.45 kg ha-1. The plasticity of seed number and grain protein content were significantly associated with yield plasticity. The maximal yield was positively associated with spikelets/spike and grain yield, whereas it negatively associated with grain protein content. In contrast, the minimal yield was found to be negatively related to the plasticity of spikelets/spike and the plasticity of grain yield, whereas it was not related to grain protein content plasticity. Seed number and seed length exhibited plastic responses at the higher fertilisation state while remaining relatively stable at the lower fertilisation state for the wheat DH population. The finding of the current study will play a key role in wheat improvement under the changing climate. Seed length and seed number should be the breeding target for achieving stable yield in adverse environmental conditions.
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Affiliation(s)
- Md Atik Us Saieed
- Food Futures Institute, School of Health, Education & Environment, Murdoch University, Perth, WA 6150, Australia
- Department of Seed Science & Technology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Yun Zhao
- Food Futures Institute, School of Health, Education & Environment, Murdoch University, Perth, WA 6150, Australia
| | - Kefei Chen
- Curtin Biometry and Agriculture Data Analytics, Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Shanjida Rahman
- Food Futures Institute, School of Health, Education & Environment, Murdoch University, Perth, WA 6150, Australia
- Department of Genetics & Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Jingjuan Zhang
- Food Futures Institute, School of Health, Education & Environment, Murdoch University, Perth, WA 6150, Australia
| | - Shahidul Islam
- Food Futures Institute, School of Health, Education & Environment, Murdoch University, Perth, WA 6150, Australia
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Wujun Ma
- Food Futures Institute, School of Health, Education & Environment, Murdoch University, Perth, WA 6150, Australia
- College of Agronomy, Qingdao Agriculture University, Qingdao 266109, China
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15
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Huang Y, Qi Z, Li J, You J, Zhang X, Wang M. Genetic interrogation of phenotypic plasticity informs genome-enabled breeding in cotton. J Genet Genomics 2023; 50:971-982. [PMID: 37211312 DOI: 10.1016/j.jgg.2023.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/19/2023] [Accepted: 05/04/2023] [Indexed: 05/23/2023]
Abstract
Phenotypic plasticity, or the ability to adapt to and thrive in changing climates and variable environments, is essential for developmental programs in plants. Despite its importance, the genetic underpinnings of phenotypic plasticity for key agronomic traits remain poorly understood in many crops. In this study, we aim to fill this gap by using genome-wide association studies to identify genetic variations associated with phenotypic plasticity in upland cotton (Gossypium hirsutum L.). We identified 73 additive quantitative trait loci (QTLs), 32 dominant QTLs, and 6799 epistatic QTLs associated with 20 traits. We also identified 117 additive QTLs, 28 dominant QTLs, and 4691 epistatic QTLs associated with phenotypic plasticity in 19 traits. Our findings reveal new genetic factors, including additive, dominant, and epistatic QTLs, that are linked to phenotypic plasticity and agronomic traits. Meanwhile, we find that the genetic factors controlling the mean phenotype and phenotypic plasticity are largely independent in upland cotton, indicating the potential for simultaneous improvement. Additionally, we envision a genomic design strategy by utilizing the identified QTLs to facilitate cotton breeding. Taken together, our study provides new insights into the genetic basis of phenotypic plasticity in cotton, which should be valuable for future breeding.
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Affiliation(s)
- Yuefan Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhengyang Qi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jiaqi You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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16
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Swartz LG, Liu S, Dahlquist D, Kramer ST, Walter ES, McInturf SA, Bucksch A, Mendoza-Cózatl DG. OPEN leaf: an open-source cloud-based phenotyping system for tracking dynamic changes at leaf-specific resolution in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1600-1616. [PMID: 37733751 DOI: 10.1111/tpj.16449] [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: 12/24/2022] [Accepted: 08/16/2023] [Indexed: 09/23/2023]
Abstract
The first draft of the Arabidopsis genome was released more than 20 years ago and despite intensive molecular research, more than 30% of Arabidopsis genes remained uncharacterized or without an assigned function. This is in part due to gene redundancy within gene families or the essential nature of genes, where their deletion results in lethality (i.e., the dark genome). High-throughput plant phenotyping (HTPP) offers an automated and unbiased approach to characterize subtle or transient phenotypes resulting from gene redundancy or inducible gene silencing; however, access to commercial HTPP platforms remains limited. Here we describe the design and implementation of OPEN leaf, an open-source phenotyping system with cloud connectivity and remote bilateral communication to facilitate data collection, sharing and processing. OPEN leaf, coupled with our SMART imaging processing pipeline was able to consistently document and quantify dynamic changes at the whole rosette level and leaf-specific resolution when plants experienced changes in nutrient availability. Our data also demonstrate that VIS sensors remain underutilized and can be used in high-throughput screens to identify and characterize previously unidentified phenotypes in a leaf-specific time-dependent manner. Moreover, the modular and open-source design of OPEN leaf allows seamless integration of additional sensors based on users and experimental needs.
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Affiliation(s)
- Landon G Swartz
- Department of Electrical Engineering and Computer Science, University of Missouri, 411 S 6th St., Columbia, Missouri, 65201, USA
- Division of Plant Science and Technology, C.S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, Missouri, 65211, USA
| | - Suxing Liu
- School of Plant Sciences, University of Arizona, 1140 E South Campus, Tucson, Arizona, 85721, USA
| | - Drew Dahlquist
- Department of Electrical Engineering and Computer Science, University of Missouri, 411 S 6th St., Columbia, Missouri, 65201, USA
| | - Skyler T Kramer
- MU Institute of Data Science and Informatics, C.S. Bond Life Sciences Center, University of Missouri, 1201 Rollinst St., Columbia, Missouri, 65211, USA
| | - Emily S Walter
- Division of Plant Science and Technology, C.S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, Missouri, 65211, USA
| | - Samuel A McInturf
- Division of Plant Science and Technology, C.S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, Missouri, 65211, USA
| | - Alexander Bucksch
- School of Plant Sciences, University of Arizona, 1140 E South Campus, Tucson, Arizona, 85721, USA
| | - David G Mendoza-Cózatl
- Department of Electrical Engineering and Computer Science, University of Missouri, 411 S 6th St., Columbia, Missouri, 65201, USA
- Division of Plant Science and Technology, C.S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, Missouri, 65211, USA
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17
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Wade MJ, Sultan SE. Niche construction and the environmental term of the price equation: How natural selection changes when organisms alter their environments. Evol Dev 2023; 25:451-469. [PMID: 37530093 DOI: 10.1111/ede.12452] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/30/2023] [Accepted: 07/07/2023] [Indexed: 08/03/2023]
Abstract
Organisms construct their own environments and phenotypes through the adaptive processes of habitat choice, habitat construction, and phenotypic plasticity. We examine how these processes affect the dynamics of mean fitness change through the environmental change term of the Price Equation. This tends to be ignored in evolutionary theory, owing to the emphasis on the first term describing the effect of natural selection on mean fitness (the additive genetic variance for fitness of Fisher's Fundamental Theorem). Using population genetic models and the Price Equation, we show how adaptive niche constructing traits favorably alter the distribution of environments that organisms encounter and thereby increase population mean fitness. Because niche-constructing traits increase the frequency of higher-fitness environments, selection favors their evolution. Furthermore, their alteration of the actual or experienced environmental distribution creates selective feedback between niche constructing traits and other traits, especially those with genotype-by-environment interaction for fitness. By altering the distribution of experienced environments, niche constructing traits can increase the additive genetic variance for such traits. This effect accelerates the process of overall adaption to the niche-constructed environmental distribution and can contribute to the rapid refinement of alternative phenotypic adaptations to different environments. Our findings suggest that evolutionary biologists revisit and reevaluate the environmental term of the Price Equation: owing to adaptive niche construction, it contributes directly to positive change in mean fitness; its magnitude can be comparable to that of natural selection; and, when there is fitness G × E, it increases the additive genetic variance for fitness, the much-celebrated first term.
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Affiliation(s)
- Michael J Wade
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Sonia E Sultan
- Department of Biology, Wesleyan University, Middletown, Connecticut, USA
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18
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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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19
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Bhaskara GB, Haque T, Bonnette JE, Napier JD, Bauer D, Schmutz J, Juenger TE. Evolutionary Analyses of Gene Expression Divergence in Panicum hallii: Exploring Constitutive and Plastic Responses Using Reciprocal Transplants. Mol Biol Evol 2023; 40:msad210. [PMID: 37738160 PMCID: PMC10556983 DOI: 10.1093/molbev/msad210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/27/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
The evolution of gene expression is thought to be an important mechanism of local adaptation and ecological speciation. Gene expression divergence occurs through the evolution of cis- polymorphisms and through more widespread effects driven by trans-regulatory factors. Here, we explore expression and sequence divergence in a large sample of Panicum hallii accessions encompassing the species range using a reciprocal transplantation experiment. We observed widespread genotype and transplant site drivers of expression divergence, with a limited number of genes exhibiting genotype-by-site interactions. We used a modified FST-QST outlier approach (QPC analysis) to detect local adaptation. We identified 514 genes with constitutive expression divergence above and beyond the levels expected under neutral processes. However, no plastic expression responses met our multiple testing correction as QPC outliers. Constitutive QPC outlier genes were involved in a number of developmental processes and responses to abiotic environments. Leveraging earlier expression quantitative trait loci results, we found a strong enrichment of expression divergence, including for QPC outliers, in genes previously identified with cis and cis-environment interactions but found no patterns related to trans-factors. Population genetic analyses detected elevated sequence divergence of promoters and coding sequence of constitutive expression outliers but little evidence for positive selection on these proteins. Our results are consistent with a hypothesis of cis-regulatory divergence as a primary driver of expression divergence in P. hallii.
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Affiliation(s)
| | - Taslima Haque
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Jason E Bonnette
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Joseph D Napier
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Diane Bauer
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Schmutz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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20
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Gao L, Kantar MB, Moxley D, Ortiz-Barrientos D, Rieseberg LH. Crop adaptation to climate change: An evolutionary perspective. MOLECULAR PLANT 2023; 16:1518-1546. [PMID: 37515323 DOI: 10.1016/j.molp.2023.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
The disciplines of evolutionary biology and plant and animal breeding have been intertwined throughout their development, with responses to artificial selection yielding insights into the action of natural selection and evolutionary biology providing statistical and conceptual guidance for modern breeding. Here we offer an evolutionary perspective on a grand challenge of the 21st century: feeding humanity in the face of climate change. We first highlight promising strategies currently under way to adapt crops to current and future climate change. These include methods to match crop varieties with current and predicted environments and to optimize breeding goals, management practices, and crop microbiomes to enhance yield and sustainable production. We also describe the promise of crop wild relatives and recent technological innovations such as speed breeding, genomic selection, and genome editing for improving environmental resilience of existing crop varieties or for developing new crops. Next, we discuss how methods and theory from evolutionary biology can enhance these existing strategies and suggest novel approaches. We focus initially on methods for reconstructing the evolutionary history of crops and their pests and symbionts, because such historical information provides an overall framework for crop-improvement efforts. We then describe how evolutionary approaches can be used to detect and mitigate the accumulation of deleterious mutations in crop genomes, identify alleles and mutations that underlie adaptation (and maladaptation) to agricultural environments, mitigate evolutionary trade-offs, and improve critical proteins. Continuing feedback between the evolution and crop biology communities will ensure optimal design of strategies for adapting crops to climate change.
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Affiliation(s)
- Lexuan Gao
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Michael B Kantar
- Department of Tropical Plant & Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Dylan Moxley
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences and Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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21
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Miller CL, Sun D, Thornton LH, McGuigan K. The Contribution of Mutation to Variation in Temperature-Dependent Sprint Speed in Zebrafish, Danio rerio. Am Nat 2023; 202:519-533. [PMID: 37792923 DOI: 10.1086/726011] [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] [Indexed: 10/06/2023]
Abstract
AbstractThe contribution of new mutations to phenotypic variation and the consequences of this variation for individual fitness are fundamental concepts for understanding genetic variation and adaptation. Here, we investigated how mutation influenced variation in a complex trait in zebrafish, Danio rerio. Typical of many ecologically relevant traits in ectotherms, swimming speed in fish is temperature dependent, with evidence of adaptive evolution of thermal performance. We chemically induced novel germline point mutations in males and measured sprint speed in their sons at six temperatures (between 16°C and 34°C). Heterozygous mutational effects on speed were strongly positively correlated among temperatures, resulting in statistical support for only a single axis of mutational variation, reflecting temperature-independent variation in speed (faster-slower mode). These results suggest pleiotropic effects on speed across different temperatures; however, spurious correlations arise via linkage or heterogeneity in mutation number when mutations have consistent directional effects on each trait. Here, mutation did not change mean speed, indicating no directional bias in mutational effects. The results contribute to emerging evidence that mutations may predominantly have synergistic cross-environment effects, in contrast to conditionally neutral or antagonistic effects that underpin thermal adaptation. We discuss several aspects of experimental design that may affect resolution of mutations with nonsynergistic effects.
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22
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Earley TS, Feiner N, Alvarez MF, Coolon JD, Sultan SE. The relative impact of parental and current environment on plant transcriptomes depends on type of stress and genotype. Proc Biol Sci 2023; 290:20230824. [PMID: 37752834 PMCID: PMC10523085 DOI: 10.1098/rspb.2023.0824] [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: 04/06/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023] Open
Abstract
Through developmental plasticity, an individual organism integrates influences from its immediate environment with those due to the environment of its parents. While both effects on phenotypes are well documented, their relative impact has been little studied in natural systems, especially at the level of gene expression. We examined this issue in four genotypes of the annual plant Persicaria maculosa by varying two key resources-light and soil moisture-in both generations. Transcriptomic analyses showed that the relative effects of parent and offspring environment on gene expression (i.e. the number of differentially expressed transcripts, DETs) varied both for the two types of resource stress and among genotypes. For light, immediate environment induced more DETs than parental environment for all genotypes, although the precise proportion of parental versus immediate DETs varied among genotypes. By contrast, the relative effect of soil moisture varied dramatically among genotypes, from 8-fold more DETs due to parental than immediate conditions to 10-fold fewer. These findings provide evidence at the transcriptomic level that the relative impacts of parental and immediate environment on the developing organism may depend on the environmental factor and vary strongly among genotypes, providing potential for the interplay of these developmental influences to evolve.
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Affiliation(s)
- Timothy S. Earley
- Biology Department, Wesleyan University, 52 Lawn Avenue, Middletown, CT 06459, USA
| | | | - Mariano F. Alvarez
- Biology Department, Wesleyan University, 52 Lawn Avenue, Middletown, CT 06459, USA
| | - Joseph D. Coolon
- Biology Department, Wesleyan University, 52 Lawn Avenue, Middletown, CT 06459, USA
| | - Sonia E. Sultan
- Biology Department, Wesleyan University, 52 Lawn Avenue, Middletown, CT 06459, USA
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23
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Gururani MA. Photobiotechnology for abiotic stress resilient crops: Recent advances and prospects. Heliyon 2023; 9:e20158. [PMID: 37810087 PMCID: PMC10559926 DOI: 10.1016/j.heliyon.2023.e20158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Massive crop failures worldwide are caused by abiotic stress. In plants, adverse environmental conditions cause extensive damage to the overall physiology and agronomic yield at various levels. Phytochromes are photosensory phosphoproteins that absorb red (R)/far red (FR) light and play critical roles in different physiological and biochemical responses to light. Considering the role of phytochrome in essential plant developmental processes, genetically manipulating its expression offers a promising approach to crop improvement. Through modulated phytochrome-mediated signalling pathways, plants can become more resistant to environmental stresses by increasing photosynthetic efficiency, antioxidant activity, and expression of genes associated with stress resistance. Plant growth and development in adverse environments can be improved by understanding the roles of phytochromes in stress tolerance characteristics. A comprehensive overview of recent findings regarding the role of phytochromes in modulating abiotic stress by discussing biochemical and molecular aspects of these mechanisms of photoreceptors is offered in this review.
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Affiliation(s)
- Mayank Anand Gururani
- Biology Department, College of Science, UAE University, Al Ain, United Arab Emirates
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24
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Della Coletta R, Liese SE, Fernandes SB, Mikel MA, Bohn MO, Lipka AE, Hirsch CN. Linking genetic and environmental factors through marker effect networks to understand trait plasticity. Genetics 2023; 224:iyad103. [PMID: 37246567 DOI: 10.1093/genetics/iyad103] [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: 04/17/2023] [Revised: 05/19/2023] [Accepted: 05/24/2023] [Indexed: 05/30/2023] Open
Abstract
Understanding how plants adapt to specific environmental changes and identifying genetic markers associated with phenotypic plasticity can help breeders develop plant varieties adapted to a rapidly changing climate. Here, we propose the use of marker effect networks as a novel method to identify markers associated with environmental adaptability. These marker effect networks are built by adapting commonly used software for building gene coexpression networks with marker effects across growth environments as the input data into the networks. To demonstrate the utility of these networks, we built networks from the marker effects of ∼2,000 nonredundant markers from 400 maize hybrids across 9 environments. We demonstrate that networks can be generated using this approach, and that the markers that are covarying are rarely in linkage disequilibrium, thus representing higher biological relevance. Multiple covarying marker modules associated with different weather factors throughout the growing season were identified within the marker effect networks. Finally, a factorial test of analysis parameters demonstrated that marker effect networks are relatively robust to these options, with high overlap in modules associated with the same weather factors across analysis parameters. This novel application of network analysis provides unique insights into phenotypic plasticity and specific environmental factors that modulate the genome.
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Affiliation(s)
- Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Sharon E Liese
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Samuel B Fernandes
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Mark A Mikel
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Martin O Bohn
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
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25
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FitzPatrick JA, Doucet BI, Holt SD, Patterson CM, Kooyers NJ. Unique drought resistance strategies occur among monkeyflower populations spanning an aridity gradient. AMERICAN JOURNAL OF BOTANY 2023; 110:e16207. [PMID: 37347451 DOI: 10.1002/ajb2.16207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/30/2023] [Accepted: 05/01/2023] [Indexed: 06/23/2023]
Abstract
PREMISE Annual plants often exhibit drought-escape and avoidance strategies to cope with limited water availability. Determining the extent of variation and factors underlying the evolution of divergent strategies is necessary for determining population responses to more frequent and severe droughts. METHODS We leveraged five Mimulus guttatus populations collected across an aridity gradient within manipulative drought and quantitative genetics experiments to examine constitutive and terminal-drought induced responses in drought resistance traits. RESULTS Populations varied considerably in drought-escape- and drought-avoidance-associated traits. The most mesic population demonstrated a unique resource conservative strategy. Xeric populations exhibited extreme plasticity when exposed to terminal drought that included flowering earlier at shorter heights, increasing water-use efficiency, and shifting C:N ratios. However, plasticity responses also differed between populations, with two populations slowing growth rates and flowering at earlier nodes and another population increasing growth rate. While nearly all traits were heritable, phenotypic correlations differed substantially between treatments and often, populations. CONCLUSIONS Our results suggest drought resistance strategies of populations may be finely adapted to local patterns of water availability. Substantial plastic responses suggest that xeric populations can already acclimate to drought through plasticity, but populations not frequently exposed to drought may be more vulnerable.
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Affiliation(s)
| | - Braden I Doucet
- Department of Biology, University of Louisiana, Lafayette, LA, 70503, USA
| | - Stacy D Holt
- Department of Biology, University of Louisiana, Lafayette, LA, 70503, USA
| | | | - Nicholas J Kooyers
- Department of Biology, University of Louisiana, Lafayette, LA, 70503, USA
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26
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Mefleh M, Motzo R, Boukid F, Giunta F. Clipping Effect on the Grain Nitrogen and Protein Fractions of Ancient and Old Wheats Grown in a Mediterranean Environment. Foods 2023; 12:2582. [PMID: 37444319 DOI: 10.3390/foods12132582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/23/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
This study is the first to assess the effects of clipping, cultivar, season, and their interactions on the protein composition of six old and ancient wheat cultivars (n = 6). For this, nitrogen content, the proportion of wheat protein fractions, and the molecular weight distribution of the extractable and unextractable glutenin polymers were investigated as a function of cultivar and clipping in two consecutive seasons. The relationships between genotypic variation in grain nitrogen and protein fraction content under clipping and non-clipping conditions were also assessed. Clipping delayed and shortened the grain filling period of all of the cultivars. The protein composition of some cultivars behaved differently to clipping due to differences in the environmental conditions of S1 (exceptional dry season) and S2 (rainy season). In S1, clipping decreased the ratio of gliadins over glutenins (GLI/GLU) (<1) of Cappelli and Giovanni Paolo, while in S2, clipping improved the GLI/GLU of Giovanni Paolo, Monlis, and Norberto. The unextractable polymeric proteins were not affected by clipping. Khorasan was shown to be indifferent to clipping in S1 and S2. These results suggest that it is possible to have ancient/old wheats suitable for a dual-purpose system, in different climatic conditions, while maintaining good grain quality traits. The increased market demand for ancient and old wheats presents an economic opportunity for farmers who adopt the dual-purpose technique to cultivate these resilient crops again and increase their profit margins and revenues.
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Affiliation(s)
- Marina Mefleh
- Department of Agricultural Sciences, University of Sassari, Viale Italia 39/a, 07100 Sassari, Italy
| | - Rosella Motzo
- Department of Agricultural Sciences, University of Sassari, Viale Italia 39/a, 07100 Sassari, Italy
| | - Fatma Boukid
- ClonBio Group Ltd., 6 Fitzwilliam Pl, D02 XE61 Dublin, Ireland
| | - Francesco Giunta
- Department of Agricultural Sciences, University of Sassari, Viale Italia 39/a, 07100 Sassari, Italy
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27
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Eckert S, Eilers EJ, Jakobs R, Anaia RA, Aragam KS, Bloss T, Popp M, Sasidharan R, Schnitzler JP, Stein F, Steppuhn A, Unsicker SB, van Dam NM, Yepes S, Ziaja D, Müller C. Inter-laboratory comparison of plant volatile analyses in the light of intra-specific chemodiversity. Metabolomics 2023; 19:62. [PMID: 37351733 DOI: 10.1007/s11306-023-02026-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/09/2023] [Indexed: 06/24/2023]
Abstract
INTRODUCTION Assessing intraspecific variation in plant volatile organic compounds (VOCs) involves pitfalls that may bias biological interpretation, particularly when several laboratories collaborate on joint projects. Comparative, inter-laboratory ring trials can inform on the reproducibility of such analyses. OBJECTIVES In a ring trial involving five laboratories, we investigated the reproducibility of VOC collections with polydimethylsiloxane (PDMS) and analyses by thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS). As model plant we used Tanacetum vulgare, which shows a remarkable diversity in terpenoids, forming so-called chemotypes. We performed our ring-trial with two chemotypes to examine the sources of technical variation in plant VOC measurements during pre-analytical, analytical, and post-analytical steps. METHODS Monoclonal root cuttings were generated in one laboratory and distributed to five laboratories, in which plants were grown under laboratory-specific conditions. VOCs were collected on PDMS tubes from all plants before and after a jasmonic acid (JA) treatment. Thereafter, each laboratory (donors) sent a subset of tubes to four of the other laboratories (recipients), which performed TD-GC-MS with their own established procedures. RESULTS Chemotype-specific differences in VOC profiles were detected but with an overall high variation both across donor and recipient laboratories. JA-induced changes in VOC profiles were not reproducible. Laboratory-specific growth conditions led to phenotypic variation that affected the resulting VOC profiles. CONCLUSION Our ring trial shows that despite large efforts to standardise each VOC measurement step, the outcomes differed both qualitatively and quantitatively. Our results reveal sources of variation in plant VOC research and may help to avoid systematic errors in similar experiments.
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Affiliation(s)
- Silvia Eckert
- Department of Chemical Ecology, Bielefeld University, Bielefeld, Germany
| | - Elisabeth J Eilers
- Department of Chemical Ecology, Bielefeld University, Bielefeld, Germany
| | - Ruth Jakobs
- Department of Chemical Ecology, Bielefeld University, Bielefeld, Germany
| | - Redouan Adam Anaia
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
- Molecular Interaction Ecology, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | - Tanja Bloss
- Department of Chemical Ecology, Bielefeld University, Bielefeld, Germany
| | - Moritz Popp
- Research Unit Environmental Simulation, Helmholtz Zentrum München, Munich, Germany
| | - Rohit Sasidharan
- Department of Chemical Ecology, Bielefeld University, Bielefeld, Germany
| | | | - Florian Stein
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Anke Steppuhn
- Department of Molecular Botany, Hohenheim University, Stuttgart, Germany
| | - Sybille B Unsicker
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Nicole M van Dam
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
- Molecular Interaction Ecology, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Sol Yepes
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Dominik Ziaja
- Department of Chemical Ecology, Bielefeld University, Bielefeld, Germany
| | - Caroline Müller
- Department of Chemical Ecology, Bielefeld University, Bielefeld, Germany.
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28
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Fu R, Wang X. Modeling the influence of phenotypic plasticity on maize hybrid performance. PLANT COMMUNICATIONS 2023; 4:100548. [PMID: 36635964 DOI: 10.1016/j.xplc.2023.100548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/31/2022] [Accepted: 01/10/2023] [Indexed: 05/11/2023]
Abstract
Phenotypic plasticity, the ability of an individual to alter its phenotype in response to changes in the environment, has been proposed as a target for breeding crop varieties with high environmental fitness. Here, we used phenotypic and genotypic data from multiple maize (Zea mays L.) populations to mathematically model phenotypic plasticity in response to the environment (PPRE) in inbred and hybrid lines. PPRE can be simply described by a linear model in which the two main parameters, intercept a and slope b, reflect two classes of genes responsive to endogenous (class A) and exogenous (class B) signals that coordinate plant development. Together, class A and class B genes contribute to the phenotypic plasticity of an individual in response to the environment. We also made connections between phenotypic plasticity and hybrid performance or general combining ability (GCA) of yield using 30 F1 hybrid populations generated by crossing the same maternal line with 30 paternal lines from different maize heterotic groups. We show that the parameters a and b from two given parental lines must be concordant to reach an ideal GCA of F1 yield. We hypothesize that coordinated regulation of the two classes of genes in the F1 hybrid genome is the basis for high GCA. Based on this theory, we built a series of predictive models to evaluate GCA in silico between parental lines of different heterotic groups.
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Affiliation(s)
- Ran Fu
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China; Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
| | - Xiangfeng Wang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China; Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China.
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29
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Jin M, Liu H, Liu X, Guo T, Guo J, Yin Y, Ji Y, Li Z, Zhang J, Wang X, Qiao F, Xiao Y, Zan Y, Yan J. Complex genetic architecture underlying the plasticity of maize agronomic traits. PLANT COMMUNICATIONS 2023; 4:100473. [PMID: 36642074 DOI: 10.1016/j.xplc.2022.100473] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/21/2022] [Accepted: 11/07/2022] [Indexed: 05/11/2023]
Abstract
Phenotypic plasticity is the ability of a given genotype to produce multiple phenotypes in response to changing environmental conditions. Understanding the genetic basis of phenotypic plasticity and establishing a predictive model is highly relevant to future agriculture under a changing climate. Here we report findings on the genetic basis of phenotypic plasticity for 23 complex traits using a diverse maize population planted at five sites with distinct environmental conditions. We found that latitude-related environmental factors were the main drivers of across-site variation in flowering time traits but not in plant architecture or yield traits. For the 23 traits, we detected 109 quantitative trait loci (QTLs), 29 for mean values, 66 for plasticity, and 14 for both parameters, and 80% of the QTLs interacted with latitude. The effects of several QTLs changed in magnitude or sign, driving variation in phenotypic plasticity. We experimentally validated one plastic gene, ZmTPS14.1, whose effect was likely mediated by the compensation effect of ZmSPL6 from a downstream pathway. By integrating genetic diversity, environmental variation, and their interaction into a joint model, we could provide site-specific predictions with increased accuracy by as much as 9.9%, 2.2%, and 2.6% for days to tassel, plant height, and ear weight, respectively. This study revealed a complex genetic architecture involving multiple alleles, pleiotropy, and genotype-by-environment interaction that underlies variation in the mean and plasticity of maize complex traits. It provides novel insights into the dynamic genetic architecture of agronomic traits in response to changing environments, paving a practical way toward precision agriculture.
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Affiliation(s)
- Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Haijun Liu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, 1030 Vienna, Austria
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Tingting Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jia Guo
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Yuejia Yin
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Yan Ji
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266000, China
| | - Zhenxian Li
- Institute of Agricultural Sciences of Xishuangbanna Prefecture of Yunnan Province, Jinghong 666100, China
| | - Jinhong Zhang
- Institute of Agricultural Sciences of Xishuangbanna Prefecture of Yunnan Province, Jinghong 666100, China
| | - Xiaqing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Feng Qiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yanjun Zan
- Umeå Plant Science Center, Department of Forestry Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90736 Umeå, Sweden; Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266000, China.
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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Hu Y, Schmidhalter U. Opportunity and challenges of phenotyping plant salt tolerance. TRENDS IN PLANT SCIENCE 2023; 28:552-566. [PMID: 36628656 DOI: 10.1016/j.tplants.2022.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 12/03/2022] [Accepted: 12/15/2022] [Indexed: 05/22/2023]
Abstract
Salinity is a key factor limiting agricultural production worldwide. Recent advances in field phenotyping have enabled the recording of the environmental history and dynamic response of plants by considering both genotype × environment (G×E) interactions and envirotyping. However, only a few studies have focused on plant salt tolerance phenotyping. Therefore, we analyzed the potential opportunities and major challenges in improving plant salt tolerance using advanced field phenotyping technologies. RGB imaging and spectral and thermal sensors are the most useful and important sensing techniques for assessing key morphological and physiological traits of plant salt tolerance. However, field phenotyping faces challenges owing to its practical applications and high costs, limiting its use in early generation breeding and in developing countries.
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Affiliation(s)
- Yuncai Hu
- Chair of Plant Nutrition, School of Life Sciences, Technical University of Munich, D-85354 Freising, Germany.
| | - Urs Schmidhalter
- Chair of Plant Nutrition, School of Life Sciences, Technical University of Munich, D-85354 Freising, Germany
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Liu M, Zhang S, Li W, Zhao X, Wang XQ. Identifying yield-related genes in maize based on ear trait plasticity. Genome Biol 2023; 24:94. [PMID: 37098597 PMCID: PMC10127483 DOI: 10.1186/s13059-023-02937-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 04/13/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Phenotypic plasticity is defined as the phenotypic variation of a trait when an organism is exposed to different environments, and it is closely related to genotype. Exploring the genetic basis behind the phenotypic plasticity of ear traits in maize is critical to achieve climate-stable yields, particularly given the unpredictable effects of climate change. Performing genetic field studies in maize requires development of a fast, reliable, and automated system for phenotyping large numbers of samples. RESULTS Here, we develop MAIZTRO as an automated maize ear phenotyping platform for high-throughput measurements in the field. Using this platform, we analyze 15 common ear phenotypes and their phenotypic plasticity variation in 3819 transgenic maize inbred lines targeting 717 genes, along with the wild type lines of the same genetic background, in multiple field environments in two consecutive years. Kernel number is chosen as the primary target phenotype because it is a key trait for improving the grain yield and ensuring yield stability. We analyze the phenotypic plasticity of the transgenic lines in different environments and identify 34 candidate genes that may regulate the phenotypic plasticity of kernel number. CONCLUSIONS Our results suggest that as an integrated and efficient phenotyping platform for measuring maize ear traits, MAIZTRO can help to explore new traits that are important for improving and stabilizing the yield. This study indicates that genes and alleles related with ear trait plasticity can be identified using transgenic maize inbred populations.
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Affiliation(s)
- Minguo Liu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Frontier Technology Research Institute of China Agricultural University in Shenzhen, Shenzhen, 518000, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Shuaisong Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Wei Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiaoming Zhao
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Xi-Qing Wang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- Frontier Technology Research Institute of China Agricultural University in Shenzhen, Shenzhen, 518000, China.
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China.
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Cai H, Des Marais DL. Revisiting regulatory coherence: accounting for temporal bias in plant gene co-expression analyses. THE NEW PHYTOLOGIST 2023; 238:16-24. [PMID: 36617750 DOI: 10.1111/nph.18720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Haoran Cai
- Department of Civil and Environmental Engineering, MIT, 15 Vassar St., Cambridge, MA, 02139, USA
| | - David L Des Marais
- Department of Civil and Environmental Engineering, MIT, 15 Vassar St., Cambridge, MA, 02139, USA
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Méndez-Cea B, García-García I, Gazol A, Camarero JJ, de Andrés EG, Colangelo M, Valeriano C, Gallego FJ, Linares JC. Weak genetic differentiation but strong climate-induced selective pressure toward the rear edge of mountain pine in north-eastern Spain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159778. [PMID: 36309267 DOI: 10.1016/j.scitotenv.2022.159778] [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: 07/26/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Local differentiation at distribution limits may influence species' adaptive capacity to environmental changes. However, drivers, such gene flow and local selection, are still poorly understood. We focus on the role played by range limits in mountain forests to test the hypothesis that relict tree populations are subjected to genetic differentiation and local adaptation. Two alpine treelines of mountain pine (Pinus uncinata Ram. ex DC) were investigated in the Spanish Pyrenees. Further, an isolated relict population forming the species' southernmost distribution limit in north-eastern Spain was also investigated. Using genotyping by sequencing, a genetic matrix conformed by single nucleotide polymorphisms (SNPs) was obtained. This matrix was used to perform genotype-environment and genotype-phenotype associations, as well as to model risk of non-adaptedness. Increasing climate seasonality appears as an essential element in the interpretation of SNPs subjected to selective pressures. Genetic differentiations were overall weak. The differences in leaf mass area and radial growth rate, as well as the identification of several SNPs subjected to selective pressures, exceeded neutral predictions of differentiation among populations. Despite genetic drift might prevail in the isolated population, the Fst values (0.060 and 0.066) showed a moderate genetic drift and Nm values (3.939 and 3.555) indicate the presence of gene flow between the relict population and both treelines. Nonetheless, the SNPs subjected to selection pressures provide evidences of possible selection in treeline ecotones. Persistence in range boundaries seems to involve several selective pressures in species' traits, which were significantly related to enhanced drought seasonality at the limit of P. uncinata distribution range. We conclude that gene flow is unlikely to constrain adaptation in the P. uncinata rear edge, although this species shows vulnerability to future climate change scenarios involving warmer and drier conditions.
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Affiliation(s)
- Belén Méndez-Cea
- Dpto. Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, 28040, Spain.
| | - Isabel García-García
- Dpto. Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, 28040, Spain.
| | - Antonio Gazol
- Pyrenean Institute of Ecology (IPE-CSIC), Zaragoza E-50059, Spain.
| | - J Julio Camarero
- Pyrenean Institute of Ecology (IPE-CSIC), Zaragoza E-50059, Spain.
| | | | - Michele Colangelo
- Pyrenean Institute of Ecology (IPE-CSIC), Zaragoza E-50059, Spain; School of Agricultural, Forest, Food and Environmental Sciences (SAFE), University of Basilicata, Potenza 85100, Italy
| | | | - Francisco Javier Gallego
- Dpto. Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, 28040, Spain.
| | - Juan Carlos Linares
- Dpto. Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain.
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Khasanova A, Edwards J, Bonnette J, Singer E, Haque T, Juenger TE. Quantitative genetic-by-soil microbiome interactions in a perennial grass affect functional traits. Proc Biol Sci 2023; 290:20221350. [PMID: 36651054 PMCID: PMC9845970 DOI: 10.1098/rspb.2022.1350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Plants interact with diverse microbiomes that can impact plant growth and performance. Recent studies highlight the potential beneficial aspects of plant microbiomes, including the possibility that microbes facilitate the process of local adaptation in their host plants. Microbially mediated local adaptation in plants occurs when local host genotypes have higher fitness than foreign genotypes because of their affiliation with locally beneficial microbes. Here, plant adaptation results from genetic interactions of the host with locally beneficial microbes (e.g. host genotype-by-microbiome interactions). We used a recombinant inbred line (RIL) mapping population derived from upland and lowland ecotypes of the diploid C4 perennial bunch grass Panicum hallii to explore quantitative genetic responses to soil microbiomes focusing on functional root and shoot traits involved in ecotypic divergence. We show that the growth and development of ecotypes and their trait divergence depends on soil microbiomes. Moreover, we find that the genetic architecture is modified by soil microbiomes, revealing important plant genotype-by-microbiome interactions for quantitative traits. We detected a number of quantitative trait loci (QTL) that interact with the soil microbiome. Our results highlight the importance of microbial interactions in ecotypic divergence and trait genetic architecture in C4 perennial grasses.
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Affiliation(s)
- Albina Khasanova
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78712, USA,Lawrence Berkeley National Laboratory, 717 Potter Street, Berkeley, CA 94710, USA
| | - Joseph Edwards
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78712, USA
| | - Jason Bonnette
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78712, USA
| | - Esther Singer
- Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA,Lawrence Berkeley National Laboratory, 717 Potter Street, Berkeley, CA 94710, USA
| | - Taslima Haque
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78712, USA
| | - Thomas E. Juenger
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78712, USA
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35
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Napier JD, Heckman RW, Juenger TE. Gene-by-environment interactions in plants: Molecular mechanisms, environmental drivers, and adaptive plasticity. THE PLANT CELL 2023; 35:109-124. [PMID: 36342220 PMCID: PMC9806611 DOI: 10.1093/plcell/koac322] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/03/2022] [Indexed: 05/13/2023]
Abstract
Plants demonstrate a broad range of responses to environmental shifts. One of the most remarkable responses is plasticity, which is the ability of a single plant genotype to produce different phenotypes in response to environmental stimuli. As with all traits, the ability of plasticity to evolve depends on the presence of underlying genetic diversity within a population. A common approach for evaluating the role of genetic variation in driving differences in plasticity has been to study genotype-by-environment interactions (G × E). G × E occurs when genotypes produce different phenotypic trait values in response to different environments. In this review, we highlight progress and promising methods for identifying the key environmental and genetic drivers of G × E. Specifically, methodological advances in using algorithmic and multivariate approaches to understand key environmental drivers combined with new genomic innovations can greatly increase our understanding about molecular responses to environmental stimuli. These developing approaches can be applied to proliferating common garden networks that capture broad natural environmental gradients to unravel the underlying mechanisms of G × E. An increased understanding of G × E can be used to enhance the resilience and productivity of agronomic systems.
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Affiliation(s)
- Joseph D Napier
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Robert W Heckman
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
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36
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Genome-Wide Association Studies across Environmental and Genetic Contexts Reveal Complex Genetic Architecture of Symbiotic Extended Phenotypes. mBio 2022; 13:e0182322. [PMID: 36286519 PMCID: PMC9765617 DOI: 10.1128/mbio.01823-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host's own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here, we use naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti paired with two genotypes of the host Medicago truncatula in four genome-wide association studies (GWAS) to determine the genomic architecture of a key symbiotic extended phenotype-partner quality, or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, (i) loci whose identities depend on the environment, (ii) those that depend on the host genotype with which rhizobia interact, and (iii) universal loci that are likely important in all or most environments. IMPORTANCE Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.
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Liang Z, Myers ZA, Petrella D, Engelhorn J, Hartwig T, Springer NM. Mapping responsive genomic elements to heat stress in a maize diversity panel. Genome Biol 2022; 23:234. [PMID: 36345007 PMCID: PMC9639295 DOI: 10.1186/s13059-022-02807-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Many plant species exhibit genetic variation for coping with environmental stress. However, there are still limited approaches to effectively uncover the genomic region that regulates distinct responsive patterns of the gene across multiple varieties within the same species under abiotic stress. RESULTS By analyzing the transcriptomes of more than 100 maize inbreds, we reveal many cis- and trans-acting eQTLs that influence the expression response to heat stress. The cis-acting eQTLs in response to heat stress are identified in genes with differential responses to heat stress between genotypes as well as genes that are only expressed under heat stress. The cis-acting variants for heat stress-responsive expression likely result from distinct promoter activities, and the differential heat responses of the alleles are confirmed for selected genes using transient expression assays. Global footprinting of transcription factor binding is performed in control and heat stress conditions to document regions with heat-enriched transcription factor binding occupancies. CONCLUSIONS Footprints enriched near proximal regions of characterized heat-responsive genes in a large association panel can be utilized for prioritizing functional genomic regions that regulate genotype-specific responses under heat stress.
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Affiliation(s)
- Zhikai Liang
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA.
| | - Zachary A Myers
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Dominic Petrella
- Department of Horticulture, University of Minnesota, Saint Paul, MN, 55108, USA
- Present address: Agricultural Technical Institute, The Ohio State University, Wooster, OH, 44691, USA
| | - Julia Engelhorn
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Heinrich-Heine University, 40225, Dusseldorf, Germany
| | - Thomas Hartwig
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Heinrich-Heine University, 40225, Dusseldorf, Germany
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA.
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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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Giridhar M, Meier B, Imani J, Kogel KH, Peiter E, Vothknecht UC, Chigri F. Comparative analysis of stress-induced calcium signals in the crop species barley and the model plant Arabidopsis thaliana. BMC PLANT BIOLOGY 2022; 22:447. [PMID: 36114461 PMCID: PMC9482192 DOI: 10.1186/s12870-022-03820-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Plants are continuously exposed to changing environmental conditions and biotic attacks that affect plant growth. In crops, the inability to respond appropriately to stress has strong detrimental effects on agricultural production and yield. Ca2+ signalling plays a fundamental role in the response of plants to most abiotic and biotic stresses. However, research on stimulus-specific Ca2+ signals has mostly been pursued in Arabidopsis thaliana, while in other species these events are little investigated . RESULTS In this study, we introduced the Ca2+ reporter-encoding gene APOAEQUORIN into the crop species barley (Hordeum vulgare). Measurements of the dynamic changes in [Ca2+]cyt in response to various stimuli such as NaCl, mannitol, H2O2, and flagellin 22 (flg22) revealed the occurrence of dose- as well as tissue-dependent [Ca2+]cyt transients. Moreover, the Ca2+ signatures were unique for each stimulus, suggesting the involvement of different Ca2+ signalling components in the corresponding stress response. Alongside, the barley Ca2+ signatures were compared to those produced by the phylogenetically distant model plant Arabidopsis. Notable differences in temporal kinetics and dose responses were observed, implying species-specific differences in stress response mechanisms. The plasma membrane Ca2+ channel blocker La3+ strongly inhibited the [Ca2+]cyt response to all tested stimuli, indicating a critical role of extracellular Ca2+ in the induction of stress-associated Ca2+ signatures in barley. Moreover, by analysing spatio-temporal dynamics of the [Ca2+]cyt transients along the developmental gradient of the barley leaf blade we demonstrate that different parts of the barley leaf show quantitative differences in [Ca2+]cyt transients in response to NaCl and H2O2. There were only marginal differences in the response to flg22, indicative of developmental stage-dependent Ca2+ responses specifically to NaCl and H2O2. CONCLUSION This study reveals tissue-specific Ca2+ signals with stimulus-specific kinetics in the crop species barley, as well as quantitative differences along the barley leaf blade. A number of notable differences to the model plants Arabidopsis may be linked to different stimulus sensitivity. These transgenic barley reporter lines thus present a valuable tool to further analyse mechanisms of Ca2+ signalling in this crop and to gain insights into the variation of Ca2+-dependent stress responses between stress-susceptible and -resistant species.
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Affiliation(s)
- Maya Giridhar
- Plant Cell Biology, IZMB, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Bastian Meier
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Betty Heimann Str. 3, D-06120, Halle (Saale), Germany
| | - Jafargholi Imani
- Research Centre for BioSystems, Land Use and Nutrition (IFZ), Institute for Phytopathology, Justus Liebig University Gießen, Heinrich-Buff-Ring 26-32, D-35392, Gießen, Germany
| | - Karl-Heinz Kogel
- Research Centre for BioSystems, Land Use and Nutrition (IFZ), Institute for Phytopathology, Justus Liebig University Gießen, Heinrich-Buff-Ring 26-32, D-35392, Gießen, Germany
| | - Edgar Peiter
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Betty Heimann Str. 3, D-06120, Halle (Saale), Germany.
| | - Ute C Vothknecht
- Plant Cell Biology, IZMB, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany.
| | - Fatima Chigri
- Plant Cell Biology, IZMB, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany
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40
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Abstract
Maize genes influence which species of bacteria are recruited from the soil, especially in the absence of nitrogen supplied by fertilizer.
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Affiliation(s)
- Maggie R Wagner
- Department of Ecology and Evolutionary Biology, Kansas Biological Survey and Center for Ecological Research, University of Kansas
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41
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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: 23] [Impact Index Per Article: 11.5] [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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42
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Le MK, Smith OS, Akbari A, Harpak A, Reich D, Narasimhan VM. 1,000 ancient genomes uncover 10,000 years of natural selection in Europe. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.24.505188. [PMID: 36052370 PMCID: PMC9435429 DOI: 10.1101/2022.08.24.505188] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Ancient DNA has revolutionized our understanding of human population history. However, its potential to examine how rapid cultural evolution to new lifestyles may have driven biological adaptation has not been met, largely due to limited sample sizes. We assembled genome-wide data from 1,291 individuals from Europe over 10,000 years, providing a dataset that is large enough to resolve the timing of selection into the Neolithic, Bronze Age, and Historical periods. We identified 25 genetic loci with rapid changes in frequency during these periods, a majority of which were previously undetected. Signals specific to the Neolithic transition are associated with body weight, diet, and lipid metabolism-related phenotypes. They also include immune phenotypes, most notably a locus that confers immunity to Salmonella infection at a time when ancient Salmonella genomes have been shown to adapt to human hosts, thus providing a possible example of human-pathogen co-evolution. In the Bronze Age, selection signals are enriched near genes involved in pigmentation and immune-related traits, including at a key human protein interactor of SARS-CoV-2. Only in the Historical period do the selection candidates we detect largely mirror previously-reported signals, highlighting how the statistical power of previous studies was limited to the last few millennia. The Historical period also has multiple signals associated with vitamin D binding, providing evidence that lactase persistence may have been part of an oligogenic adaptation for efficient calcium uptake and challenging the theory that its adaptive value lies only in facilitating caloric supplementation during times of scarcity. Finally, we detect selection on complex traits in all three periods, including selection favoring variants that reduce body weight in the Neolithic. In the Historical period, we detect selection favoring variants that increase risk for cardiovascular disease plausibly reflecting selection for a more active inflammatory response that would have been adaptive in the face of increased infectious disease exposure. Our results provide an evolutionary rationale for the high prevalence of these deadly diseases in modern societies today and highlight the unique power of ancient DNA in elucidating biological change that accompanied the profound cultural transformations of recent human history.
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Affiliation(s)
- Megan K Le
- Department of Computer Science, The University of Texas at Austin
| | - Olivia S Smith
- Department of Integrative Biology, The University of Texas at Austin
| | - Ali Akbari
- Department of Genetics, Harvard Medical School
- Department of Human Evolutionary Biology, Harvard University
- Broad Institute of MIT and Harvard
| | - Arbel Harpak
- Department of Integrative Biology, The University of Texas at Austin
- Department of Population Health, Dell Medical School
| | - David Reich
- Department of Genetics, Harvard Medical School
- Department of Human Evolutionary Biology, Harvard University
- Howard Hughes Medical Institute, Harvard Medical School
- Broad Institute of MIT and Harvard
| | - Vagheesh M Narasimhan
- Department of Integrative Biology, The University of Texas at Austin
- Department of Statistics and Data Science, The University of Texas at Austin
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43
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Liu H, Ye Q, Simpson KJ, Cui E, Xia J. Can evolutionary history predict plant plastic responses to climate change? THE NEW PHYTOLOGIST 2022; 235:1260-1271. [PMID: 35488493 DOI: 10.1111/nph.18194] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Plant plastic responses are critical to the adaptation and survival of species under climate change, but whether they are constrained by evolutionary history (phylogeny) is largely unclear. Plant leaf traits are key in determining plants' performance in different environments, and if these traits and their variation are phylogenetically dependent, predictions could be made to identify species vulnerable to climate change. We compiled data on three leaf traits (photosynthetic rate, specific leaf area, and leaf nitrogen content) and their variation under four environmental change scenarios (warming, drought, elevated CO2 , or nitrogen addition) for 434 species, from 210 manipulation experiments. We found phylogenetic signal in the three traits but not in their variation under the four scenarios. This indicates that closely related species show similar traits but that their plastic responses could not be predicted from species relatedness under environmental change. Meanwhile, phylogeny weakened the slopes but did not change the directions of conventional pairwise trait relationships, suggesting that co-evolved leaf trait pairs have consistent responses under contrasting environmental conditions. Phylogeny can identify lineages rich in species showing similar traits and predict their relationships under climate change, but the degree of plant phenotypic variation does not vary consistently across evolutionary clades.
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Affiliation(s)
- Hui Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Guangzhou, 510650, China
| | - Qing Ye
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Guangzhou, 510650, China
- College of Life Sciences, Gannan Normal University, Ganzhou, 341000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), no. 1119, Haibin Road, Nansha District, Guangzhou, 511458, China
| | - Kimberley J Simpson
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Erqian Cui
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, State Key Laboratory of Estuarine and Coastal Research, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
- Research Center for Global Change and Ecological Forecasting, East China Normal University, Shanghai, 200241, China
| | - Jianyang Xia
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, State Key Laboratory of Estuarine and Coastal Research, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
- Research Center for Global Change and Ecological Forecasting, East China Normal University, Shanghai, 200241, China
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44
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Zhang L, MacQueen A, Weng X, Behrman KD, Bonnette J, Reilley JL, Rouquette FM, Fay PA, Wu Y, Fritschi FB, Mitchell RB, Lowry DB, Boe AR, Juenger TE. The genetic basis for panicle trait variation in switchgrass (Panicum virgatum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2577-2592. [PMID: 35780149 PMCID: PMC9325832 DOI: 10.1007/s00122-022-04096-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
We investigate the genetic basis of panicle architecture in switchgrass in two mapping populations across a latitudinal gradient, and find many stable, repeatable genetic effects and limited genetic interactions with the environment. Grass species exhibit large diversity in panicle architecture influenced by genes, the environment, and their interaction. The genetic study of panicle architecture in perennial grasses is limited. In this study, we evaluate the genetic basis of panicle architecture including panicle length, primary branching number, and secondary branching number in an outcrossed switchgrass QTL population grown across ten field sites in the central USA through multi-environment mixed QTL analysis. We also evaluate genetic effects in a diversity panel of switchgrass grown at three of the ten field sites using genome-wide association (GWAS) and multivariate adaptive shrinkage. Furthermore, we search for candidate genes underlying panicle traits in both of these independent mapping populations. Overall, 18 QTL were detected in the QTL mapping population for the three panicle traits, and 146 unlinked genomic regions in the diversity panel affected one or more panicle trait. Twelve of the QTL exhibited consistent effects (i.e., no QTL by environment interactions or no QTL × E), and most (four of six) of the effects with QTL × E exhibited site-specific effects. Most (59.3%) significant partially linked diversity panel SNPs had significant effects in all panicle traits and all field sites and showed pervasive pleiotropy and limited environment interactions. Panicle QTL co-localized with significant SNPs found using GWAS, providing additional power to distinguish between true and false associations in the diversity panel.
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Affiliation(s)
- Li Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Alice MacQueen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Xiaoyu Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Kathrine D Behrman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - John L Reilley
- Kika de la Garza Plant Materials Center, National Resources Conservation Service, US Department of Agriculture, Kingsville, TX, 78363, USA
| | - Francis M Rouquette
- Texas A&M AgriLife Research and Extension Center, Texas A&M University, Overton, TX, 75684, USA
| | - Philip A Fay
- Grassland, Soil and Water Research Laboratory, Agricultural Research Service, US Department of Agriculture, Temple, TX, 76502, USA
| | - Yanqi Wu
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Felix B Fritschi
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Robert B Mitchell
- Wheat, Sorghum, and Forage Research Unit, Agricultural Research Service, US Department of Agriculture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - David B Lowry
- Department of Plant Biology and DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
| | - Arvid R Boe
- Departmentof Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA.
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45
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Fuller RC, McGhee KE, Sandkam B, Schrader M, Travis J. Polyphenisms and polymorphisms: Genetic variation in plasticity and color variation within and among bluefin killifish populations. Evolution 2022; 76:1590-1606. [PMID: 35598089 DOI: 10.1111/evo.14511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/28/2021] [Accepted: 01/26/2022] [Indexed: 01/22/2023]
Abstract
The presence of stable color polymorphisms within populations begs the question of how genetic variation is maintained. Consistent variation among populations in coloration, especially when correlated with environmental variation, raises questions about whether environmental conditions affect either the fulcrum of those balanced polymorphisms, the plastic expression of coloration, or both. Color patterns in male bluefin killifish provoke both types of questions. Red and yellow morphs are common in all populations. Blue males are more common in tannin-stained swamps relative to clear springs. Here, we combined crosses with a manipulation of light to explore how genetic variation and phenotypic plasticity shape these patterns. We found that the variation in coloration is attributable mainly to two axes of variation: (1) a red-yellow axis with yellow being dominant to red, and (2) a blue axis that can override red-yellow and is controlled by genetics, phenotypic plasticity, and genetic variation for phenotypic plasticity. The variation among populations in plasticity suggests it is adaptive in some populations but not others. The variation among sires in plasticity within the swamp population suggests balancing selection may be acting not only on the red-yellow polymorphism but also on plasticity for blue coloration.
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Affiliation(s)
- Rebecca C Fuller
- Department of Evolution, Ecology, and Behavior, University of Illinois, Champaign, Illinois, USA
| | - Katie E McGhee
- Department of Biology, University of the South, Sewanee, Tennessee, USA
| | - Benjamin Sandkam
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
| | - Matthew Schrader
- Department of Biology, University of the South, Sewanee, Tennessee, USA
| | - Joseph Travis
- Department of Biological Sciences, Florida State University, Tallahassee, Florida, USA
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46
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Mawass W, Mayer FM, Milot E. Genotype-by-environment interactions modulate the rate of microevolution in reproductive timing in humans. Evolution 2022; 76:1391-1405. [PMID: 35548908 DOI: 10.1111/evo.14504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 01/21/2023]
Abstract
Evidence from natural populations shows that changes in environmental conditions can cause rapid modifications in the evolutionary potential of phenotypes, partly through genotype-by-environment interactions (G×E). Therefore, the overall rate of microevolution should depend on fluctuations in environmental conditions, even when directional selection is sustained over several generations. We tested this hypothesis in a preindustrial human population that experienced a microevolutionary change in age at first reproduction (AFR) of mothers, using the annual infant mortality rate (IMR) as an indicator of environmental conditions during their early life. Using quantitative genetics analyses, we found that G×Es explained a nonnegligible fraction of the additive genetic variance in AFR and in relative fitness, as well as of the genetic covariance between AFR and fitness (i.e., the Robertson-Price covariance). The covariance was stronger for individuals exposed to unfavorable early-life environmental conditions. Our results unravel the presence of G×Es in an important life history trait and its impact on the rate of microevolution, which appears to have been sensitive to short-term fluctuations in local environmental conditions.
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Affiliation(s)
- Walid Mawass
- Department of Chemistry, Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivieres, QC, G9A 5H7, Canada
| | - Francine M Mayer
- Department of Biological Sciences, University of Québec at Montréal, Montréal, QC, H4A 2Y4, Canada
| | - Emmanuel Milot
- Department of Chemistry, Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivieres, QC, G9A 5H7, Canada
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47
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Manggabarani AM, Hashiguchi T, Hashiguchi M, Hayashi A, Kikuchi M, Mustamin Y, Bamba M, Kodama K, Tanabata T, Isobe S, Tanaka H, Akashi R, Nakaya A, Sato S. Construction of prediction models for growth traits of soybean cultivars based on phenotyping in diverse genotype and environment combinations. DNA Res 2022; 29:6653298. [PMID: 35916715 PMCID: PMC9358015 DOI: 10.1093/dnares/dsac024] [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: 08/30/2021] [Indexed: 11/14/2022] Open
Abstract
Abstract
As soybean cultivars are adapted to a relatively narrow range of latitude, the effects of climate changes are estimated to be severe. To address this issue, it is important to improve our understanding of the effects of climate change by applying the simulation model including both genetic and environmental factors with their interactions (G×E). To achieve this goal, we conducted the field experiments for soybean core collections using multiple sowing times in multi-latitudinal fields. Sowing time shifts altered the flowering time (FT) and growth phenotypes, and resulted in increasing the combinations of genotypes and environments. Genome-wide association studies for the obtained phenotypes revealed the effects of field and sowing time to the significance of detected alleles, indicating the presence of G×E. By using accumulated phenotypic and environmental data in 2018 and 2019, we constructed multiple regression models for FT and growth pattern. Applicability of the constructed models was evaluated by the field experiments in 2020 including a novel field, and high correlation between the predicted and measured values was observed, suggesting the robustness of the models. The models presented here would allow us to predict the phenotype of the core collections in a given environment.
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Affiliation(s)
| | - Takuyu Hashiguchi
- Faculty of Agriculture, University of Miyazaki , Miyazaki 889-2192, Japan
| | | | - Atsushi Hayashi
- Kazusa DNA Research Institute , Kisarazu, Chiba 292-0818, Japan
| | - Masataka Kikuchi
- Graduate School of Medicine, Osaka University , Suita, Osaka 565-0871, Japan
| | - Yusdar Mustamin
- Graduate School of Life Sciences, Tohoku University , Sendai, Miyagi 980-8577, Japan
| | - Masaru Bamba
- Graduate School of Life Sciences, Tohoku University , Sendai, Miyagi 980-8577, Japan
| | - Kunihiro Kodama
- Kazusa DNA Research Institute , Kisarazu, Chiba 292-0818, Japan
| | | | - Sachiko Isobe
- Kazusa DNA Research Institute , Kisarazu, Chiba 292-0818, Japan
| | - Hidenori Tanaka
- Faculty of Agriculture, University of Miyazaki , Miyazaki 889-2192, Japan
| | - Ryo Akashi
- Faculty of Agriculture, University of Miyazaki , Miyazaki 889-2192, Japan
| | - Akihiro Nakaya
- Graduate School of Medicine, Osaka University , Suita, Osaka 565-0871, Japan
- Graduate School of Frontier Sciences, The University of Tokyo , Kashiwa, Chiba 277-0882, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University , Sendai, Miyagi 980-8577, Japan
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48
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Mounger JM, van Riemsdijk I, Boquete MT, Wagemaker CAM, Fatma S, Robertson MH, Voors SA, Oberstaller J, Gawehns F, Hanley TC, Grosse I, Verhoeven KJF, Sotka EE, Gehring CA, Hughes AR, Lewis DB, Schmid MW, Richards CL. Genetic and Epigenetic Differentiation Across Intertidal Gradients in the Foundation Plant Spartina alterniflora. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.868826] [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
Ecological genomics approaches have informed us about the structure of genetic diversity in natural populations that might underlie patterns in trait variation. However, we still know surprisingly little about the mechanisms that permit organisms to adapt to variable environmental conditions. The salt marsh foundation plant Spartina alterniflora exhibits a dramatic range in phenotype that is associated with a pronounced intertidal environmental gradient across a narrow spatial scale. Both genetic and non-genetic molecular mechanisms might underlie this phenotypic variation. To investigate both, we used epigenotyping-by-sequencing (epiGBS) to evaluate the make-up of natural populations across the intertidal environmental gradient. Based on recent findings, we expected that both DNA sequence and DNA methylation diversity would be explained by source population and habitat within populations. However, we predicted that epigenetic variation might be more strongly associated with habitat since similar epigenetic modifications could be rapidly elicited across different genetic backgrounds by similar environmental conditions. Overall, with PERMANOVA we found that population of origin explained a significant amount of the genetic (8.6%) and epigenetic (3.2%) variance. In addition, we found that a small but significant amount of genetic and epigenetic variance (<1%) was explained by habitat within populations. The interaction of population and habitat explained an additional 2.9% of the genetic variance and 1.4% of the epigenetic variance. By examining genetic and epigenetic variation within the same fragments (variation in close-cis), we found that population explained epigenetic variation in 9.2% of 8,960 tested loci, even after accounting for differences in the DNA sequence of the fragment. Habitat alone explained very little (<0.1%) of the variation in these close-cis comparisons, but the interaction of population and habitat explained 2.1% of the epigenetic variation in these loci. Using multiple matrix regression with randomization (MMRR) we found that phenotypic differences in natural populations were correlated with epigenetic and environmental differences even when accounting for genetic differences. Our results support the contention that sequence variation explains most of the variation in DNA methylation, but we have provided evidence that DNA methylation distinctly contributes to plant responses in natural populations.
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49
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Ballinger MA, Nachman MW. The Contribution of Genetic and Environmental Effects to Bergmann's Rule and Allen's Rule in House Mice. Am Nat 2022; 199:691-704. [PMID: 35472023 DOI: 10.1086/719028] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
AbstractDistinguishing between genetic, environmental, and genotype × environment effects is central to understanding geographic variation in phenotypic clines. Two of the best-documented phenotypic clines are Bergmann's rule and Allen's rule, which describe larger body sizes and shortened extremities in colder climates, respectively. Although numerous studies have found inter- and intraspecific evidence for both ecogeographic patterns, we still have a poor understanding of the extent to which these patterns are driven by genetics, environment, or both. Here, we measured the genetic and environmental contributions to Bergmann's rule and Allen's rule across introduced populations of house mice (Mus musculus domesticus) in the Americas. First, we documented clines for body mass, tail length, and ear length in natural populations and found that these conform to both Bergmann's rule and Allen's rule. We then raised descendants of wild-caught mice in the lab and showed that these differences persisted in a common environment and are heritable, indicating that they have a genetic basis. Finally, using a full-sib design, we reared mice under warm and cold conditions. We found very little plasticity associated with body size, suggesting that Bergmann's rule has been shaped by strong directional selection in house mice. However, extremities showed considerable plasticity, as both tails and ears grew shorter in cold environments. These results indicate that adaptive phenotypic plasticity as well as genetic changes underlie major patterns of clinal variation in house mice and likely facilitated their rapid expansion into new environments across the Americas.
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50
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Archambeau J, Garzón MB, Barraquand F, Miguel MD, Plomion C, González-Martínez SC. Combining climatic and genomic data improves range-wide tree height growth prediction in a forest tree. Am Nat 2022; 200:E141-E159. [DOI: 10.1086/720619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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