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Kamal NM, Gorafi YSA, Tomemori H, Kim JS, Elhadi GMI, Tsujimoto H. Genetic variation for grain nutritional profile and yield potential in sorghum and the possibility of selection for drought tolerance under irrigated conditions. BMC Genomics 2023; 24:515. [PMID: 37660014 PMCID: PMC10474746 DOI: 10.1186/s12864-023-09613-w] [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: 03/28/2023] [Accepted: 08/22/2023] [Indexed: 09/04/2023] Open
Abstract
BACKGROUND Increasing grain nutritional value in sorghum (Sorghum bicolor) is a paramount breeding objective, as is increasing drought resistance (DR), because sorghum is grown mainly in drought-prone areas. The genetic basis of grain nutritional traits remains largely unknown. Marker-assisted selection using significant loci identified through genome-wide association study (GWAS) shows potential for selecting desirable traits in crops. This study assessed natural variation available in sorghum accessions from around the globe to identify novel genes or genomic regions with potential for improving grain nutritional value, and to study associations between DR traits and grain weight and nutritional composition. RESULTS We dissected the genetic architecture of grain nutritional composition, protein content, thousand-kernel weight (TKW), and plant height (PH) in sorghum through GWAS of 163 unique African and Asian accessions under irrigated and post-flowering drought conditions. Several QTLs were detected. Some were significantly associated with DR, TKW, PH, protein, and Zn, Mn, and Ca contents. Genomic regions on chromosomes 1, 2, 4, 8, 9, and 10 were associated with TKW, nutritional, and DR traits; colocalization patterns of these markers indicate potential for simultaneous improvement of these traits. In African accessions, markers associated with TKW were mapped to six regions also associated with protein, Zn, Ca, Mn, Na, and DR, suggesting the potential for simultaneous selection for higher grain nutrition and TKW. Our results indicate that it may be possible to select for increased DR on the basis of grain nutrition and weight potential. CONCLUSIONS This study provides a valuable resource for selecting landraces for use in plant breeding programs and for identifying loci that may contribute to grain nutrition and weight with the hope of producing cultivars that combine improved yield traits, nutrition, and DR.
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Affiliation(s)
- Nasrein Mohamed Kamal
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
- Agricultural Research Corporation, PO Box 126, Wad Medani, Sudan.
| | - Yasir Serag Alnor Gorafi
- Agricultural Research Corporation, PO Box 126, Wad Medani, Sudan
- International Platform for Dryland Research and Education, Tottori University, Tottori, Japan
| | - Hisashi Tomemori
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan
| | - June-Sik Kim
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | | | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
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Beegum S, Timlin D, Reddy KR, Reddy V, Sun W, Wang Z, Fleisher D, Ray C. Improving the cotton simulation model, GOSSYM, for soil, photosynthesis, and transpiration processes. Sci Rep 2023; 13:7314. [PMID: 37147386 PMCID: PMC10163017 DOI: 10.1038/s41598-023-34378-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/28/2023] [Indexed: 05/07/2023] Open
Abstract
GOSSYM, a mechanistic, process-level cotton crop simulation model, has a two-dimensional (2D) gridded soil model called Rhizos that simulates the below-ground processes daily. Water movement is based on gradients of water content and not hydraulic heads. In GOSSYM, photosynthesis is calculated using a daily empirical light response function that requires calibration for response to elevated carbon dioxide (CO2). This report discusses improvements made to the GOSSYM model for soil, photosynthesis, and transpiration processes. GOSSYM's predictions of below-ground processes using Rhizos are improved by replacing it with 2DSOIL, a mechanistic 2D finite element soil process model. The photosynthesis and transpiration model in GOSSYM is replaced with a Farquhar biochemical model and Ball-Berry leaf energy balance model. The newly developed model (modified GOSSYM) is evaluated using field-scale and experimental data from SPAR (soil-plant-atmosphere-research) chambers. Modified GOSSYM better predicted net photosynthesis (root mean square error (RMSE) 25.5 versus 45.2 g CO2 m-2 day-1; index of agreement (IA) 0.89 versus 0.76) and transpiration (RMSE 3.3 versus 13.7 L m-2 day-1; IA 0.92 versus 0.14) and improved the yield prediction by 6.0%. Modified GOSSYM improved the simulation of soil, photosynthesis, and transpiration processes, thereby improving the predictive ability of cotton crop growth and development.
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Affiliation(s)
- Sahila Beegum
- Adaptive Cropping System Laboratory, USDA-ARS, Beltsville, MD, 20705, USA.
- Nebraska Water Center, Robert B. Daugherty Water for Food Global Institute, 2021 Transformation Drive, University of Nebraska, Lincoln, NE, 68588, USA.
| | - Dennis Timlin
- Adaptive Cropping System Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | - Kambham Raja Reddy
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi, MS, 39762, USA
| | - Vangimalla Reddy
- Adaptive Cropping System Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | - Wenguang Sun
- Adaptive Cropping System Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
- Nebraska Water Center, Robert B. Daugherty Water for Food Global Institute, 2021 Transformation Drive, University of Nebraska, Lincoln, NE, 68588, USA
| | - Zhuangji Wang
- Adaptive Cropping System Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - David Fleisher
- Adaptive Cropping System Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | - Chittaranjan Ray
- Nebraska Water Center, Robert B. Daugherty Water for Food Global Institute, 2021 Transformation Drive, University of Nebraska, Lincoln, NE, 68588, USA
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3
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Reproductive Stage Drought Tolerance in Wheat: Importance of Stomatal Conductance and Plant Growth Regulators. Genes (Basel) 2021; 12:genes12111742. [PMID: 34828346 PMCID: PMC8623834 DOI: 10.3390/genes12111742] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
Drought stress requires plants to adjust their water balance to maintain tissue water levels. Isohydric plants (‘water-savers’) typically achieve this through stomatal closure, while anisohydric plants (‘water-wasters’) use osmotic adjustment and maintain stomatal conductance. Isohydry or anisohydry allows plant species to adapt to different environments. In this paper we show that both mechanisms occur in bread wheat (Triticum aestivum L.). Wheat lines with reproductive drought-tolerance delay stomatal closure and are temporarily anisohydric, before closing stomata and become isohydric at higher threshold levels of drought stress. Drought-sensitive wheat is isohydric from the start of the drought treatment. The capacity of the drought-tolerant line to maintain stomatal conductance correlates with repression of ABA synthesis in spikes and flag leaves. Gene expression profiling revealed major differences in the drought response in spikes and flag leaves of both wheat lines. While the isohydric drought-sensitive line enters a passive growth mode (arrest of photosynthesis, protein translation), the tolerant line mounts a stronger stress defence response (ROS protection, LEA proteins, cuticle synthesis). The drought response of the tolerant line is characterised by a strong response in the spike, displaying enrichment of genes involved in auxin, cytokinin and ethylene metabolism/signalling. While isohydry may offer advantages for longer term drought stress, anisohydry may be more beneficial when drought stress occurs during the critical stages of wheat spike development, ultimately improving grain yield.
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4
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Hilty J, Muller B, Pantin F, Leuzinger S. Plant growth: the What, the How, and the Why. THE NEW PHYTOLOGIST 2021; 232:25-41. [PMID: 34245021 DOI: 10.1111/nph.17610] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 06/19/2021] [Indexed: 05/28/2023]
Abstract
Growth is a widely used term in plant science and ecology, but it can have different meanings depending on the context and the spatiotemporal scale of analysis. At the meristem level, growth is associated with the production of cells and initiation of new organs. At the organ or plant scale and over short time periods, growth is often used synonymously with tissue expansion, while over longer time periods the increase in biomass is a common metric. At even larger temporal and spatial scales, growth is mostly described as net primary production. Here, we first address the question 'what is growth?'. We propose a general framework to distinguish between the different facets of growth, and the corresponding physiological processes, environmental drivers and mathematical formalisms. Based on these different definitions, we then review how plant growth can be measured and analysed at different organisational, spatial and temporal scales. We conclude by discussing why gaining a better understanding of the different facets of plant growth is essential to disentangle genetic and environmental effects on the phenotype, and to uncover the causalities around source or sink limitations of plant growth.
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Affiliation(s)
- Jonas Hilty
- School of Science, Auckland University of Technology, 46 Wakefield Street, Auckland, 1142, New Zealand
| | - Bertrand Muller
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, 34000, France
| | - Florent Pantin
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, 34000, France
| | - Sebastian Leuzinger
- School of Science, Auckland University of Technology, 46 Wakefield Street, Auckland, 1142, New Zealand
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5
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Leveau S, Parent B, Zaka S, Martre P. Sensitivities to temperature and evaporative demand in wheat relatives. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab431. [PMID: 34559211 DOI: 10.1093/jxb/erab431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Indexed: 06/13/2023]
Abstract
There is potential sources of alleles and genes currently locked into wheat-related species that could be introduced into wheat breeding programs for current and future hot and dry climates. However, neither the intra- nor the inter-specific diversity of the responses of leaf growth and transpiration to temperature and evaporative demand have been investigated in a large diversity of wheat-related species. By analysing 12 groups of wheat-related sub-species, we questioned the n-dimensional structure of the genetic diversity for traits linked to plant vegetative structures and development, leaf expansion and transpiration together with their responses to "non-stressing" range of temperature and evaporative demand. In addition to provide new insight on how genome type, ploidy level, phylogeny and breeding pressure together structure this genetic diversity, this study provides new mathematical formalisms and the associated parameters of trait responses in the large genetic diversity of wheat-related species. This potentially allow crop models predicting the impact of this diversity on yield, and indicate potential sources of varietal improvement for modern wheat germplasms, through interspecific crosses.
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Affiliation(s)
- Stéphane Leveau
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
- ITK, Clapiers, France
| | - Boris Parent
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | | | - Pierre Martre
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
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6
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Liu S, Baret F, Abichou M, Manceau L, Andrieu B, Weiss M, Martre P. Importance of the description of light interception in crop growth models. PLANT PHYSIOLOGY 2021; 186:977-997. [PMID: 33710303 PMCID: PMC8253170 DOI: 10.1093/plphys/kiab113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/11/2021] [Indexed: 05/22/2023]
Abstract
Canopy light interception determines the amount of energy captured by a crop, and is thus critical to modeling crop growth and yield, and may substantially contribute to the prediction uncertainty of crop growth models (CGMs). We thus analyzed the canopy light interception models of the 26 wheat (Triticum aestivum) CGMs used by the Agricultural Model Intercomparison and Improvement Project (AgMIP). Twenty-one CGMs assume that the light extinction coefficient (K) is constant, varying from 0.37 to 0.80 depending on the model. The other models take into account the illumination conditions and assume either that all green surfaces in the canopy have the same inclination angle (θ) or that θ distribution follows a spherical distribution. These assumptions have not yet been evaluated due to a lack of experimental data. Therefore, we conducted a field experiment with five cultivars with contrasting leaf stature sown at normal and double row spacing, and analyzed θ distribution in the canopies from three-dimensional canopy reconstructions. In all the canopies, θ distribution was well represented by an ellipsoidal distribution. We thus carried out an intercomparison between the light interception models of the AgMIP-Wheat CGMs ensemble and a physically based K model with ellipsoidal leaf angle distribution and canopy clumping (KellC). Results showed that the KellC model outperformed current approaches under most illumination conditions and that the uncertainty in simulated wheat growth and final grain yield due to light models could be as high as 45%. Therefore, our results call for an overhaul of light interception models in CGMs.
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Affiliation(s)
- Shouyang Liu
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
- CAPTE-EMMAH, Université d'Avignon et des Pays de Vaucluse, INRAE, Avignon, France
- PheniX, Plant Phenomics Research Centre, Nanjing Agricultural University, Nanjing, China
| | - Frédéric Baret
- CAPTE-EMMAH, Université d'Avignon et des Pays de Vaucluse, INRAE, Avignon, France
| | | | - Loïc Manceau
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
| | - Bruno Andrieu
- EcoSys, INRAE, AgroParisTech, Thiverval-Grignon, France
| | - Marie Weiss
- CAPTE-EMMAH, Université d'Avignon et des Pays de Vaucluse, INRAE, Avignon, France
| | - Pierre Martre
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
- Author for communication:
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7
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Wang DR, Venturas MD, Mackay DS, Hunsaker DJ, Thorp KR, Gore MA, Pauli D. Use of hydraulic traits for modeling genotype-specific acclimation in cotton under drought. THE NEW PHYTOLOGIST 2020; 228:898-909. [PMID: 32557592 PMCID: PMC7586954 DOI: 10.1111/nph.16751] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Abstract
Understanding the genetic and physiological basis of abiotic stress tolerance under field conditions is key to varietal crop improvement in the face of climate variability. Here, we investigate dynamic physiological responses to water stress in silico and their relationships to genotypic variation in hydraulic traits of cotton (Gossypium hirsutum), an economically important species for renewable textile fiber production. In conjunction with an ecophysiological process-based model, heterogeneous data (plant hydraulic traits, spatially-distributed soil texture, soil water content and canopy temperature) were used to examine hydraulic characteristics of cotton, evaluate their consequences on whole plant performance under drought, and explore potential genotype × environment effects. Cotton was found to have R-shaped hydraulic vulnerability curves (VCs), which were consistent under drought stress initiated at flowering. Stem VCs, expressed as percent loss of conductivity, differed across genotypes, whereas root VCs did not. Simulation results demonstrated how plant physiological stress can depend on the interaction between soil properties and irrigation management, which in turn affect genotypic rankings of transpiration in a time-dependent manner. Our study shows how a process-based modeling framework can be used to link genotypic variation in hydraulic traits to differential acclimating behaviors under drought.
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Affiliation(s)
- Diane R. Wang
- Department of GeographyUniversity at BuffaloBuffaloNY14261USA
- Present address:
Department of AgronomyPurdue UniversityWest LafayetteIN47907USA
| | | | - D. Scott Mackay
- Department of GeographyUniversity at BuffaloBuffaloNY14261USA
| | | | - Kelly R. Thorp
- US Arid‐Land Agricultural Research CenterMaricopaAZ37860USA
| | - Michael A. Gore
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Duke Pauli
- School of Plant SciencesUniversity of ArizonaTucsonAZ85721USA
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8
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Lacube S, Manceau L, Welcker C, Millet EJ, Gouesnard B, Palaffre C, Ribaut JM, Hammer G, Parent B, Tardieu F. Simulating the effect of flowering time on maize individual leaf area in contrasting environmental scenarios. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5577-5588. [PMID: 32526015 PMCID: PMC7501815 DOI: 10.1093/jxb/eraa278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
The quality of yield prediction is linked to that of leaf area. We first analysed the consequences of flowering time and environmental conditions on the area of individual leaves in 127 genotypes presenting contrasting flowering times in fields of Europe, Mexico, and Kenya. Flowering time was the strongest determinant of leaf area. Combined with a detailed field experiment, this experiment showed a large effect of flowering time on the final leaf number and on the distribution of leaf growth rate and growth duration along leaf ranks, in terms of both length and width. Equations with a limited number of genetic parameters predicted the beginning, end, and maximum growth rate (length and width) for each leaf rank. The genotype-specific environmental effects were analysed with datasets in phenotyping platforms that assessed the effects (i) of the amount of intercepted light on leaf width, and (ii) of temperature, evaporative demand, and soil water potential on leaf elongation rate. The resulting model was successfully tested for 31 hybrids in 15 European and Mexican fields. It potentially allows prediction of the vertical distribution of leaf area of a large number of genotypes in contrasting field conditions, based on phenomics and on sensor networks.
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Affiliation(s)
| | | | | | | | - Brigitte Gouesnard
- Univ. Montpellier, INRAE, CIRAD, Institut Agro, UMR AGAP, Montpellier, France
| | - Carine Palaffre
- INRAE, UE 0394, SMH Maïs, Centre de recherche de Bordeaux Aquitaine, Saint-Martin-De-Hinx, France
| | | | - Graeme Hammer
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Centre for Crop Science, Brisbane, QLD, Australia
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9
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Campbell MT, Grondin A, Walia H, Morota G. Leveraging genome-enabled growth models to study shoot growth responses to water deficit in rice. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5669-5679. [PMID: 32526013 PMCID: PMC7501813 DOI: 10.1093/jxb/eraa280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 06/09/2020] [Indexed: 05/06/2023]
Abstract
Elucidating genotype-by-environment interactions and partitioning its contribution to phenotypic variation remains a challenge for plant scientists. We propose a framework that utilizes genome-wide markers to model genotype-specific shoot growth trajectories as a function of time and soil water availability. A rice diversity panel was phenotyped daily for 21 d using an automated, high-throughput image-based, phenotyping platform that enabled estimation of daily shoot biomass and soil water content. Using these data, we modeled shoot growth as a function of time and soil water content, and were able to determine the time point where an inflection in the growth trajectory occurred. We found that larger, more vigorous plants exhibited an earlier repression in growth compared with smaller, slow-growing plants, indicating a trade-off between early vigor and tolerance to prolonged water deficits. Genomic inference for model parameters and time of inflection (TOI) identified several candidate genes. This study is the first to utilize a genome-enabled growth model to study drought responses in rice, and presents a new approach to jointly model dynamic morpho-physiological responses and environmental covariates.
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Affiliation(s)
- Malachy T Campbell
- Department of Animal and Poultry Sciences Virginia Polytechnic Institute and State University Blacksburg, VA, USA
- Department of Agronomy and Horticulture University of Nebraska-Lincoln, Lincoln, NE, USA
- Correspondence:
| | - Alexandre Grondin
- Department of Agronomy and Horticulture University of Nebraska-Lincoln, Lincoln, NE, USA
- UMR DIADE, Université de Montpellier Institut de Recherche pour le Développement (IRD) Montpellier, France
| | - Harkamal Walia
- Department of Agronomy and Horticulture University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Gota Morota
- Department of Animal and Poultry Sciences Virginia Polytechnic Institute and State University Blacksburg, VA, USA
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10
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Dingkuhn M, Luquet D, Fabre D, Muller B, Yin X, Paul MJ. The case for improving crop carbon sink strength or plasticity for a CO 2-rich future. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:259-272. [PMID: 32682621 DOI: 10.1016/j.pbi.2020.05.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/13/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Atmospheric CO2 concentration [CO2] has increased from 260 to 280μmolmol-1 (level during crop domestication up to the industrial revolution) to currently 400 and will reach 550μmolmol-1 by 2050. C3 crops are expected to benefit from elevated [CO2] (e-CO2) thanks to photosynthesis responsiveness to [CO2] but this may require greater sink capacity. We review recent literature on crop e-CO2 responses, related source-sink interactions, how abiotic stresses potentially interact, and prospects to improve e-CO2 response via breeding or genetic engineering. Several lines of evidence suggest that e-CO2 responsiveness is related either to sink intrinsic capacity or adaptive plasticity, for example, involving enhanced branching. Wild relatives and old cultivars mostly showed lower photosynthetic rates, less downward acclimation of photosynthesis to e-CO2 and responded strongly to e-CO2 due to greater phenotypic plasticity. While reverting to such archaic traits would be an inappropriate strategy for breeding, we argue that substantial enhancement of vegetative sink vigor, inflorescence size and/or number and root sinks will be necessary to fully benefit from e-CO2. Potential ideotype features based on enhanced sinks are discussed. The generic 'feast-famine' sugar signaling pathway may be suited to engineer sink strength tissue-specifically and stage-specifically and help validate ideotype concepts. Finally, we argue that models better accounting for acclimation to e-CO2 are needed to predict which trait combinations should be targeted by breeders for a CO2-rich world.
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Affiliation(s)
| | | | - Denis Fabre
- CIRAD, UMR 108 AGAP, F-34398 Montpellier, France
| | - Bertrand Muller
- INRAE, UMR 759 LEPSE, Institut de Biologie Intégrative des Plantes, F-34060 Montpellier, France
| | - Xinyou Yin
- Centre for Crop Systems Analysis, Dept. Plant Sciences, Wageningen University & Research, Wageningen, The Netherlands
| | - Matthew J Paul
- Plant Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom
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11
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Palit P, Kudapa H, Zougmore R, Kholova J, Whitbread A, Sharma M, Varshney RK. An integrated research framework combining genomics, systems biology, physiology, modelling and breeding for legume improvement in response to elevated CO 2 under climate change scenario. CURRENT PLANT BIOLOGY 2020; 22:100149. [PMID: 32494569 PMCID: PMC7233140 DOI: 10.1016/j.cpb.2020.100149] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 05/24/2023]
Abstract
How unprecedented changes in climatic conditions will impact yield and productivity of some crops and their response to existing stresses, abiotic and biotic interactions is a key global concern. Climate change can also alter natural species' abundance and distribution or favor invasive species, which in turn can modify ecosystem dynamics and the provisioning of ecosystem services. Basic anatomical differences in C3 and C4 plants lead to their varied responses to climate variations. In plants having a C3 pathway of photosynthesis, increased atmospheric carbon dioxide (CO2) positively regulates photosynthetic carbon (C) assimilation and depresses photorespiration. Legumes being C3 plants, they may be in a favorable position to increase biomass and yield through various strategies. This paper comprehensively presents recent progress made in the physiological and molecular attributes in plants with special emphasis on legumes under elevated CO2 conditions in a climate change scenario. A strategic research framework for future action integrating genomics, systems biology, physiology and crop modelling approaches to cope with changing climate is also discussed. Advances in sequencing and phenotyping methodologies make it possible to use vast genetic and genomic resources by deploying high resolution phenotyping coupled with high throughput multi-omics approaches for trait improvement. Integrated crop modelling studies focusing on farming systems design and management, prediction of climate impacts and disease forecasting may also help in planning adaptation. Hence, an integrated research framework combining genomics, plant molecular physiology, crop breeding, systems biology and integrated crop-soil-climate modelling will be very effective to cope with climate change.
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Affiliation(s)
- Paramita Palit
- Research Program- Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Himabindu Kudapa
- Research Program- Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Robert Zougmore
- CGIAR Research Program on Climate Change, Agriculture and Food Security program (CCAFS), Bamako, Mali
- Research Program- West & Central Africa, ICRISAT, Bamako, Mali
| | - Jana Kholova
- Research Program- Innovation System for Drylands, ICRISAT, Patancheru, India
| | - Anthony Whitbread
- Research Program- Innovation System for Drylands, ICRISAT, Patancheru, India
| | - Mamta Sharma
- Research Program- Asia, ICRISAT, Patancheru, India
| | - Rajeev K Varshney
- Research Program- Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
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12
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Wang C, Linderholm HW, Song Y, Wang F, Liu Y, Tian J, Xu J, Song Y, Ren G. Impacts of Drought on Maize and Soybean Production in Northeast China During the Past Five Decades. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E2459. [PMID: 32260284 PMCID: PMC7177764 DOI: 10.3390/ijerph17072459] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/29/2020] [Accepted: 04/02/2020] [Indexed: 11/16/2022]
Abstract
Climate change has a distinct impact on agriculture in China, particularly in the northeast, a key agriculture area sensitive to extreme hydroclimate events. Using monthly climate and agriculture data, the influence of drought on maize and soybean yields-two of the main crops in the region-in northeast China since 1961 to 2017 were investigated. The results showed that the temperature in the growing season increased by 1.0 °C from the period 1998-2017 to the period 1961-1980, while the annual precipitation decreased slightly. However, precipitation trends varied throughout the growing season (May-September), increasing slightly in May and June, but decreasing in July, August and September, associated with the weakening of the East Asian summer monsoon. Consequently, the annual and growing season drought frequency increased by 15%, and 25%, respectively, in the period 1998-2017 relative to the period 1961-1980. The highest drought frequency (55%) was observed in September. At the same time, the drought intensity during the growing season increased by 7.8%. The increasing frequency and intensity of drought had negative influences on the two crops. During moderate drought years in the period 1961-2017, 3.2% and 10.4% of the provincial maize and soybean yields were lost, respectively. However, during more severe drought years, losses doubled for soybean (21.8%), but increased more than four-fold for maize (14.0%). Moreover, in comparison to the period 1961-1980, a higher proportion of the yields were lost in the period 1998-2017, particularly for maize, which increased by 15% (increase for soybean was 2.4%). This change largely depends on increasing droughts in August and September, when both crops are in their filling stages. The impact of drought on maize and soybean production was different during different growth stages, where a strong relationship was noted between drought and yield loss of soybean in its filling stage. Given the sensitivity of maize and soybean yields in northeast China to drought, and the observed production trends, climate change will likely have significant negative impacts on productivity in the future.
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Affiliation(s)
- Chunyi Wang
- State Key Laboratory of Severe Weather, Chinese Academy of Meteorological Sciences, Beijing 100081, China; (Y.S.); (F.W.)
| | - Hans W. Linderholm
- Department of Earth Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Department of Geography, University of Cambridge, Cambridge CB2 3EN, UK
| | - Yanling Song
- State Key Laboratory of Severe Weather, Chinese Academy of Meteorological Sciences, Beijing 100081, China; (Y.S.); (F.W.)
| | - Fang Wang
- State Key Laboratory of Severe Weather, Chinese Academy of Meteorological Sciences, Beijing 100081, China; (Y.S.); (F.W.)
| | - Yanju Liu
- National Climate Center, China Meteorological Administration, Beijing 100081, China; (Y.L.); (G.R.)
| | - Jinfeng Tian
- Faculty of Agricultural and Nutritional Sciences, Kiel University, 24118 Kiel, Germany;
| | - Jinxia Xu
- Climate Center of Sichuan Province, China Meteorological Administration, Chengdu 610072, China;
| | - Yingbo Song
- National Meteorological Center, China Meteorological Administration, Beijing 100081, China;
| | - Guoyu Ren
- National Climate Center, China Meteorological Administration, Beijing 100081, China; (Y.L.); (G.R.)
- Department of Atmospheric Sciences, School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
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13
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Peng B, Guan K, Tang J, Ainsworth EA, Asseng S, Bernacchi CJ, Cooper M, Delucia EH, Elliott JW, Ewert F, Grant RF, Gustafson DI, Hammer GL, Jin Z, Jones JW, Kimm H, Lawrence DM, Li Y, Lombardozzi DL, Marshall-Colon A, Messina CD, Ort DR, Schnable JC, Vallejos CE, Wu A, Yin X, Zhou W. Towards a multiscale crop modelling framework for climate change adaptation assessment. NATURE PLANTS 2020; 6:338-348. [PMID: 32296143 DOI: 10.1038/s41477-020-0625-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/24/2020] [Indexed: 05/18/2023]
Abstract
Predicting the consequences of manipulating genotype (G) and agronomic management (M) on agricultural ecosystem performances under future environmental (E) conditions remains a challenge. Crop modelling has the potential to enable society to assess the efficacy of G × M technologies to mitigate and adapt crop production systems to climate change. Despite recent achievements, dedicated research to develop and improve modelling capabilities from gene to global scales is needed to provide guidance on designing G × M adaptation strategies with full consideration of their impacts on both crop productivity and ecosystem sustainability under varying climatic conditions. Opportunities to advance the multiscale crop modelling framework include representing crop genetic traits, interfacing crop models with large-scale models, improving the representation of physiological responses to climate change and management practices, closing data gaps and harnessing multisource data to improve model predictability and enable identification of emergent relationships. A fundamental challenge in multiscale prediction is the balance between process details required to assess the intervention and predictability of the system at the scales feasible to measure the impact. An advanced multiscale crop modelling framework will enable a gene-to-farm design of resilient and sustainable crop production systems under a changing climate at regional-to-global scales.
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Affiliation(s)
- Bin Peng
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Kaiyu Guan
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Jinyun Tang
- Climate Sciences Department, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Elizabeth A Ainsworth
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Senthold Asseng
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, FL, USA
| | - Carl J Bernacchi
- Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mark Cooper
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | - Evan H Delucia
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joshua W Elliott
- Department of Computer Science, University of Chicago, Chicago, IL, USA
| | - Frank Ewert
- Crop Science Group, INRES, University of Bonn, Bonn, Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Robert F Grant
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | | | - Graeme L Hammer
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
- Australian Research Council Centre of Excellence for Translational Photosynthesis, The University of Queensland, Brisbane, Queensland, Australia
| | - Zhenong Jin
- Department of Bioproducts and Biosystems Engineering, University of Minnesota-Twin Cities, St. Paul, MN, USA
| | - James W Jones
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, FL, USA
| | - Hyungsuk Kimm
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Yan Li
- State Key Laboratory of Earth Surface Processes and Resources Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | | | - Amy Marshall-Colon
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Donald R Ort
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Crop Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - James C Schnable
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - C Eduardo Vallejos
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - Alex Wu
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
- Australian Research Council Centre of Excellence for Translational Photosynthesis, The University of Queensland, Brisbane, Queensland, Australia
| | - Xinyou Yin
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & Research, Wageningen, The Netherlands
| | - Wang Zhou
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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He L, Jin N, Yu Q. Impacts of climate change and crop management practices on soybean phenology changes in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 707:135638. [PMID: 31780168 DOI: 10.1016/j.scitotenv.2019.135638] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/09/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
Crop phenology is determined by both climatic factors and agronomic management practices such as sowing date and cultivar characteristics. Exploring the interactive effects of climate change and crop management practices on crop phenology can be used to devise adaptation strategies to mitigate climate change. The objectives of this study were to: 1) examined trends in soybean (Glycine max L.) phenological development in China from 1981 to 2010; 2) isolate and quantify impacts of climate change and crop management on changes in soybean phenology; 3) determine the relative contribution of climate change and crop management to observed changes in soybean phenology; and 4) determine the relative contribution of temperature, precipitation, and sunshine hours to changes in soybean phenology. Changes in soybean phenology were observed across the major soybean producing area of eastern China during 1981-2010. Observed dates of sowing, emergence, anthesis, and maturity were delayed by an average of 1.78, 0.83, 0.19, and 0.62 days decade-1, respectively. Additionally, the lengths of the vegetative growth period and the soybean growing season were shortened by an average of 0.62 and 1.16 days decade-1, respectively. Conversely, the reproductive period was lengthened by an average of 0.43 days decade-1. Crop management practices had greater influence on sowing, emergence, and maturity dates than climate change. The direction of the changes to phenology trends created by management and climate change were opposite to each other. The relative influence of climate change on dates of anthesis, lengths of the vegetative and reproductive growth periods and growing season was larger than the influence of crop management practices. Mean temperature was the dominant climatic factor influencing most soybean phenological stages and phases. Delayed sowing dates and use of longer-duration cultivars are management adaptations that farmers have used to adapt to climate change occurring in past decades and that can continue to be used. These results indicate that farmers have a wider sowing window in spring and can select cultivars with long growing season duration and frost-tolerance to mitigate detrimental effects of a future warmer climate.
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Affiliation(s)
- Liang He
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China; National Meteorological Center, Beijing 100081, China.
| | - Ning Jin
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China
| | - Qiang Yu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China; School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia
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15
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Haas M, Sprenger H, Zuther E, Peters R, Seddig S, Walther D, Kopka J, Hincha DK, Köhl KI. Can Metabolite- and Transcript-Based Selection for Drought Tolerance in Solanum tuberosum Replace Selection on Yield in Arid Environments? FRONTIERS IN PLANT SCIENCE 2020; 11:1071. [PMID: 32793257 PMCID: PMC7385397 DOI: 10.3389/fpls.2020.01071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 06/30/2020] [Indexed: 05/09/2023]
Abstract
Climate models predict an increased likelihood of drought, demanding efficient selection for drought tolerance to maintain yield stability. Classic tolerance breeding relies on selection for yield in arid environments, which depends on yield trials and takes decades. Breeding could be accelerated by marker-assisted selection (MAS). As an alternative to genomic markers, transcript and metabolite markers have been suggested for important crops but also for orphan corps. For potato, we suggested a random-forest-based model that predicts tolerance from leaf metabolite and transcript levels with a precision of more than 90% independent of the agro-environment. To find out how the model based selection compares to yield-based selection in arid environments, we applied this approach to a population of 200 tetraploid Solanum tuberosum ssp. tuberosum lines segregating for drought tolerance. Twenty-four lines were selected into a phenotypic subpopulation (PPt) for superior tolerance based on relative tuber starch yield data from three drought stress trials. Two subpopulations with superior (MPt) and inferior (MPs) tolerance were selected based on drought tolerance predictions based on leaf metabolite and transcript levels from two sites. The 60 selected lines were phenotyped for yield and drought tolerance in 10 multi-environment drought stress trials representing typical Central European drought scenarios. Neither selection affected development or yield potential. Lines with superior drought tolerance and high yields under stress were over-represented in both populations selected for superior tolerance, with a higher number in PPt compared to MPt. However, selection based on leaf metabolites may still be an alternative to yield-based selection in arid environments as it works on leaves sampled in breeder's fields independent of drought trials. As the selection against low tolerance was ineffective, the method is best used in combination with tools that select against sensitive genotypes. Thus, metabolic and transcript marker-based selection for drought tolerance is a viable alternative to the selection on yield in arid environments.
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Affiliation(s)
- Manuela Haas
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Heike Sprenger
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Ellen Zuther
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Rolf Peters
- Versuchsstation Dethlingen, Landwirtschaftskammer Niedersachsen, Munster, Germany
| | - Sylvia Seddig
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius-Kühn Institut, Sanitz, Germany
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Dirk K. Hincha
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Karin I. Köhl
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- *Correspondence: Karin I. Köhl,
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16
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Larue F, Fumey D, Rouan L, Soulié JC, Roques S, Beurier G, Luquet D. Modelling tiller growth and mortality as a sink-driven process using Ecomeristem: implications for biomass sorghum ideotyping. ANNALS OF BOTANY 2019; 124:675-690. [PMID: 30953443 PMCID: PMC6821234 DOI: 10.1093/aob/mcz038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/28/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS Plant modelling can efficiently support ideotype conception, particularly in multi-criteria selection contexts. This is the case for biomass sorghum, implying the need to consider traits related to biomass production and quality. This study evaluated three modelling approaches for their ability to predict tiller growth, mortality and their impact, together with other morphological and physiological traits, on biomass sorghum ideotype prediction. METHODS Three Ecomeristem model versions were compared to evaluate whether tillering cessation and mortality were source (access to light) or sink (age-based hierarchical access to C supply) driven. They were tested using a field data set considering two biomass sorghum genotypes at two planting densities. An additional data set comparing eight genotypes was used to validate the best approach for its ability to predict the genotypic and environmental control of biomass production. A sensitivity analysis was performed to explore the impact of key genotypic parameters and define optimal parameter combinations depending on planting density and targeted production (sugar and fibre). KEY RESULTS The sink-driven control of tillering cessation and mortality was the most accurate, and represented the phenotypic variability of studied sorghum genotypes in terms of biomass production and partitioning between structural and non-structural carbohydrates. Model sensitivity analysis revealed that light conversion efficiency and stem diameter are key traits to target for improving sorghum biomass within existing genetic diversity. Tillering contribution to biomass production appeared highly genotype and environment dependent, making it a challenging trait for designing ideotypes. CONCLUSIONS By modelling tiller growth and mortality as sink-driven processes, Ecomeristem could predict and explore the genotypic and environmental variability of biomass sorghum production. Its application to larger sorghum genetic diversity considering water deficit regulations and its coupling to a genetic model will make it a powerful tool to assist ideotyping for current and future climatic scenario.
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Affiliation(s)
- Florian Larue
- CIRAD, UMR AGAP, PAM, Montpellier, France
- UMR AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Lauriane Rouan
- CIRAD, UMR AGAP, PAM, Montpellier, France
- UMR AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jean-Christophe Soulié
- CIRAD, UR Recycling & Risk, Montpellier, France
- Recycling & Risk Unit, University of Montpellier, CIRAD, Montpellier, France
| | - Sandrine Roques
- CIRAD, UMR AGAP, PAM, Montpellier, France
- UMR AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Grégory Beurier
- CIRAD, UMR AGAP, PAM, Montpellier, France
- UMR AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Delphine Luquet
- CIRAD, UMR AGAP, PAM, Montpellier, France
- UMR AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
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17
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Muller B, Martre P. Plant and crop simulation models: powerful tools to link physiology, genetics, and phenomics. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2339-2344. [PMID: 31091319 DOI: 10.1093/jxb/erz175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Affiliation(s)
- Bertrand Muller
- UMR LEPSE, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Pierre Martre
- UMR LEPSE, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
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18
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Parent B, Millet EJ, Tardieu F. The use of thermal time in plant studies has a sound theoretical basis provided that confounding effects are avoided. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2359-2370. [PMID: 31091318 DOI: 10.1093/jxb/ery402] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
The use of thermal time is essential in plant studies and crop growth modeling because correcting time for temperature allows working in fluctuating conditions as if temperature was constant. However, thermal time is often seen as a loose concept because of a multitude of thermal functions and case-specific parameter values. Our hypothesis is that these different formalisms and parameterization could emerge from common principles and a common response of plant development to temperature, but with several counfounding factors which are not taken into account. We first show that these calculations of thermal time are based on sound common principles and mathematical formalisms. We test, via a modelling exercise of nine case studies using maize plants grown in three field sites, how a given "ground truth" response of plant development rate to temperature can be affected if an experimenter either considers or ignores confounding factors. We also show that apparent differences in temperature responses between phenological stages of the growth cycle, between day and night, or between plant genotypes may be due to the confounding effects of evaporative demand, the range of temperatures, and the time interval at which measurements are taken. On the basis of our findings, we propose that the critical point in the use of a given formalism of thermal time calculation is to ensure that the chosen model is compatible with the temporal definition, temperature range, and environmental scenario in the considered dataset.
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Affiliation(s)
- Boris Parent
- LEPSE, Université Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Emilie J Millet
- LEPSE, Université Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - François Tardieu
- LEPSE, Université Montpellier, INRA, Montpellier SupAgro, Montpellier, France
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19
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Wang E, Brown HE, Rebetzke GJ, Zhao Z, Zheng B, Chapman SC. Improving process-based crop models to better capture genotype×environment×management interactions. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2389-2401. [PMID: 30921457 DOI: 10.1093/jxb/erz092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 03/05/2019] [Indexed: 05/07/2023]
Abstract
In spite of the increasing expectation for process-based crop modelling to capture genotype (G) by environment (E) by management (M) interactions to support breeding selections, it remains a challenge to use current crop models to accurately predict phenotypes from genotypes or from candidate genes. We use wheat as a target crop and the APSIM farming systems model (Holzworth et al., 2014) as an example to analyse the current status of process-based crop models with a major focus on need to improve simulation of specific eco-physiological processes and their linkage to underlying genetic controls. For challenging production environments in Australia, we examine the potential opportunities to capture physiological traits, and to integrate genetic and molecular approaches for future model development and applications. Model improvement will require both reducing the uncertainty in simulating key physiological processes and enhancing the capture of key observable traits and underlying genetic control of key physiological responses to environment. An approach consisting of three interactive stages is outlined to (i) improve modelling of crop physiology, (ii) develop linkage from model parameter to genotypes and further to loci or alleles, and (iii) further link to gene expression pathways. This helps to facilitate the integration of modelling, phenotyping, and functional gene detection and to effectively advance modelling of G×E×M interactions. While gene-based modelling is not always needed to simulate G×E×M, including well-understood gene effects can improve the estimation of genotype effects and prediction of phenotypes. Specific examples are given for enhanced modelling of wheat in the APSIM framework.
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Affiliation(s)
- Enli Wang
- CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Hamish E Brown
- The New Zealand Institute for Plant & Food Research Limited, Private Bag, Christchurch, New Zealand
| | | | - Zhigan Zhao
- CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Bangyou Zheng
- CSIRO Agriculture & Food, Queensland Biosciences Precinct, St Lucia, QLD, Australia
| | - Scott C Chapman
- CSIRO Agriculture & Food, Queensland Biosciences Precinct, St Lucia, QLD, Australia
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD, Australia
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20
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Zardilis A, Hume A, Millar AJ. A multi-model framework for the Arabidopsis life cycle. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2463-2477. [PMID: 31091320 PMCID: PMC6487595 DOI: 10.1093/jxb/ery394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 11/20/2018] [Indexed: 05/04/2023]
Abstract
Linking our understanding of biological processes at different scales is a major conceptual challenge in biology and aggravated by differences in research methods. Modelling can be a useful approach to consolidating our understanding across traditional research domains. The laboratory model species Arabidopsis is very widely used to study plant growth processes and has also been tested more recently in ecophysiology and population genetics. However, approaches from crop modelling that might link these domains are rarely applied to Arabidopsis. Here, we combine plant growth models with phenology models from ecophysiology, using the agent-based modelling language Chromar. We introduce a simpler Framework Model of vegetative growth for Arabidopsis, FM-lite. By extending this model to include inflorescence and fruit growth and seed dormancy, we present a whole-life-cycle, multi-model FM-life, which allows us to simulate at the population level in various genotype × environment scenarios. Environmental effects on plant growth distinguish between the simulated life history strategies that were compatible with previously described Arabidopsis phenology. Our results simulate reproductive success that is founded on the broad range of physiological processes familiar from crop models and suggest an approach to simulating evolution directly in future.
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Affiliation(s)
- Argyris Zardilis
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alastair Hume
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- EPCC, University of Edinburgh, Edinburgh, UK
| | - Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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21
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Yates S, Jaškūnė K, Liebisch F, Nagelmüller S, Kirchgessner N, Kölliker R, Walter A, Brazauskas G, Studer B. Phenotyping a Dynamic Trait: Leaf Growth of Perennial Ryegrass Under Water Limiting Conditions. FRONTIERS IN PLANT SCIENCE 2019; 10:344. [PMID: 30967891 PMCID: PMC6440318 DOI: 10.3389/fpls.2019.00344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 03/05/2019] [Indexed: 05/30/2023]
Abstract
Water limitation is one of the major factors reducing crop productivity worldwide. In order to develop efficient breeding strategies to improve drought tolerance, accurate methods to identify when a plant reduces growth as a consequence of water deficit have yet to be established. In perennial ryegrass (Lolium perenne L.), an important forage grass of the Poaceae family, leaf elongation is a key factor determining plant growth and hence forage yield. Although leaf elongation has been shown to be temperature-dependent under non-stress conditions, the impact of water limitation on leaf elongation in perennial ryegrass is poorly understood. We describe a method for quantifying tolerance to water deficit based on leaf elongation in relation to temperature and soil moisture in perennial ryegrass. With decreasing soil moisture, three growth response phases were identified: first, a "normal" phase where growth is mainly determined by temperature, second a "slow" phase where leaf elongation decreases proportionally to soil water potential and third an "arrest" phase where leaf growth terminates. A custom R function was able to quantify the points which demarcate these phases and can be used to describe the response of plants to water deficit. Applied to different perennial ryegrass genotypes, this function revealed significant genotypic variation in the response of leaf growth to temperature and soil moisture. Dynamic phenotyping of leaf elongation can be used as a tool to accurately quantify tolerance to water deficit in perennial ryegrass and to improve this trait by breeding. Moreover, the tools presented here are applicable to study the plant response to other stresses in species with linear, graminoid leaf morphology.
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Affiliation(s)
- Steven Yates
- Molecular Plant Breeding, Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Kristina Jaškūnė
- Laboratory of Genetics and Physiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Akademija, Lithuania
| | - Frank Liebisch
- Crop Science, Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Sebastian Nagelmüller
- Crop Science, Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Norbert Kirchgessner
- Crop Science, Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Roland Kölliker
- Molecular Plant Breeding, Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Achim Walter
- Crop Science, Institute of Agricultural Sciences, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Gintaras Brazauskas
- Laboratory of Genetics and Physiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Akademija, Lithuania
| | - Bruno Studer
- Molecular Plant Breeding, Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
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Bolger AM, Poorter H, Dumschott K, Bolger ME, Arend D, Osorio S, Gundlach H, Mayer KFX, Lange M, Scholz U, Usadel B. Computational aspects underlying genome to phenome analysis in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:182-198. [PMID: 30500991 PMCID: PMC6849790 DOI: 10.1111/tpj.14179] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/06/2018] [Accepted: 11/16/2018] [Indexed: 05/18/2023]
Abstract
Recent advances in genomics technologies have greatly accelerated the progress in both fundamental plant science and applied breeding research. Concurrently, high-throughput plant phenotyping is becoming widely adopted in the plant community, promising to alleviate the phenotypic bottleneck. While these technological breakthroughs are significantly accelerating quantitative trait locus (QTL) and causal gene identification, challenges to enable even more sophisticated analyses remain. In particular, care needs to be taken to standardize, describe and conduct experiments robustly while relying on plant physiology expertise. In this article, we review the state of the art regarding genome assembly and the future potential of pangenomics in plant research. We also describe the necessity of standardizing and describing phenotypic studies using the Minimum Information About a Plant Phenotyping Experiment (MIAPPE) standard to enable the reuse and integration of phenotypic data. In addition, we show how deep phenotypic data might yield novel trait-trait correlations and review how to link phenotypic data to genomic data. Finally, we provide perspectives on the golden future of machine learning and their potential in linking phenotypes to genomic features.
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Affiliation(s)
- Anthony M. Bolger
- Institute for Biology I, BioSCRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Hendrik Poorter
- Forschungszentrum Jülich (FZJ) Institute of Bio‐ and Geosciences (IBG‐2) Plant SciencesWilhelm‐Johnen‐Straße52428JülichGermany
- Department of Biological SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | - Kathryn Dumschott
- Institute for Biology I, BioSCRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Marie E. Bolger
- Forschungszentrum Jülich (FZJ) Institute of Bio‐ and Geosciences (IBG‐2) Plant SciencesWilhelm‐Johnen‐Straße52428JülichGermany
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstraße 306466SeelandGermany
| | - Sonia Osorio
- Department of Molecular Biology and BiochemistryInstituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasCampus de Teatinos29071MálagaSpain
| | - Heidrun Gundlach
- Plant Genome and Systems Biology (PGSB)Helmholtz Zentrum München (HMGU)Ingolstädter Landstraße 185764NeuherbergGermany
| | - Klaus F. X. Mayer
- Plant Genome and Systems Biology (PGSB)Helmholtz Zentrum München (HMGU)Ingolstädter Landstraße 185764NeuherbergGermany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstraße 306466SeelandGermany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstraße 306466SeelandGermany
| | - Björn Usadel
- Institute for Biology I, BioSCRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- Forschungszentrum Jülich (FZJ) Institute of Bio‐ and Geosciences (IBG‐2) Plant SciencesWilhelm‐Johnen‐Straße52428JülichGermany
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23
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Agronomic Management for Enhancing Plant Tolerance to Abiotic Stresses: High and Low Values of Temperature, Light Intensity, and Relative Humidity. HORTICULTURAE 2018. [DOI: 10.3390/horticulturae4030021] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Abiotic stresses have direct effects on plant growth and development. In agriculture, sub-optimal values of temperature, light intensity, and relative humidity can limit crop yield and reduce product quality. Temperature has a direct effect on whole plant metabolism, and low or high temperatures can reduce growth or induce crop damage. Solar radiation is the primary driver of crop production, but light intensity can also have negative effects, especially if concurrent with water stress and high temperature. Relative humidity also plays an important role by regulating transpiration and water balance of crops. In this review, the main effects of these abiotic stresses on crop performance are reported, and agronomic strategies used to avoid or mitigate the effects of these stresses are discussed.
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Tardieu F, Cabrera-Bosquet L, Pridmore T, Bennett M. Plant Phenomics, From Sensors to Knowledge. Curr Biol 2018; 27:R770-R783. [PMID: 28787611 DOI: 10.1016/j.cub.2017.05.055] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Major improvements in crop yield are needed to keep pace with population growth and climate change. While plant breeding efforts have greatly benefited from advances in genomics, profiling the crop phenome (i.e., the structure and function of plants) associated with allelic variants and environments remains a major technical bottleneck. Here, we review the conceptual and technical challenges facing plant phenomics. We first discuss how, given plants' high levels of morphological plasticity, crop phenomics presents distinct challenges compared with studies in animals. Next, we present strategies for multi-scale phenomics, and describe how major improvements in imaging, sensor technologies and data analysis are now making high-throughput root, shoot, whole-plant and canopy phenomic studies possible. We then suggest that research in this area is entering a new stage of development, in which phenomic pipelines can help researchers transform large numbers of images and sensor data into knowledge, necessitating novel methods of data handling and modelling. Collectively, these innovations are helping accelerate the selection of the next generation of crops more sustainable and resilient to climate change, and whose benefits promise to scale from physiology to breeding and to deliver real world impact for ongoing global food security efforts.
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Affiliation(s)
- François Tardieu
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, F34060, Montpellier, France.
| | - Llorenç Cabrera-Bosquet
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, F34060, Montpellier, France
| | - Tony Pridmore
- School of Computer Science, University of Nottingham, NG8 1BB, UK
| | - Malcolm Bennett
- Plant & Crop Sciences, School of Biosciences, University of Nottingham, LE12 3RD, UK.
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25
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Peccoux A, Loveys B, Zhu J, Gambetta GA, Delrot S, Vivin P, Schultz HR, Ollat N, Dai Z. Dissecting the rootstock control of scion transpiration using model-assisted analyses in grapevine. TREE PHYSIOLOGY 2018; 38:1026-1040. [PMID: 29228360 DOI: 10.1093/treephys/tpx153] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 10/31/2017] [Indexed: 05/06/2023]
Abstract
How rootstocks contribute to the control of scion transpiration under drought is poorly understood. We investigated the role of root characteristics, hydraulic conductance and chemical signals (abscisic acid, ABA) in the response of stomatal conductance (gs) and transpiration (E) to drought in Cabernet Sauvignon (Vitis vinifera) grafted onto drought-sensitive (Vitis riparia) and drought-tolerant (Vitis berlandieri × Vitis rupestris 110R) rootstocks. All combinations showed a concomitant reduction in gs and E, and an increase in xylem sap ABA concentration during the drought cycle. Cabernet Sauvignon grafted onto 110R exhibited higher gs and E under well-watered and moderate water deficit, but all combinations converged as water deficit increased. These results were integrated into three permutations of a whole-plant transpiration model that couples both chemical (i.e., ABA) and hydraulic signals in the modelling of stomatal control. Model comparisons revealed that both hydraulic and chemical signals were important for rootstock-specific stomatal regulation. Moreover, model parameter comparison and sensitivity analysis highlighted two major parameters differentiating the rootstocks: (i) ABA biosynthetic activity and (ii) the hydraulic conductance between the rhizosphere and soil-root interface determined by root system architecture. These differences in root architecture, specifically a higher root length area in 110R, likely explain its higher E and gs observed at low and moderate water deficit.
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Affiliation(s)
- Anthony Peccoux
- EGFV, Bordeaux Sciences Agro, CNRS, INRA, ISVV, Université de Bordeaux, Villenave d'Ornon, France
- Hochschule Geisenheim University, von-Lade-Straße 1, Geisenheim, Germany
| | - Brian Loveys
- CSIRO Plant Industry, Glen Osmond, SA, Australia
| | - Junqi Zhu
- EGFV, Bordeaux Sciences Agro, CNRS, INRA, ISVV, Université de Bordeaux, Villenave d'Ornon, France
| | - Gregory A Gambetta
- EGFV, Bordeaux Sciences Agro, CNRS, INRA, ISVV, Université de Bordeaux, Villenave d'Ornon, France
| | - Serge Delrot
- EGFV, Bordeaux Sciences Agro, CNRS, INRA, ISVV, Université de Bordeaux, Villenave d'Ornon, France
| | - Philippe Vivin
- EGFV, Bordeaux Sciences Agro, CNRS, INRA, ISVV, Université de Bordeaux, Villenave d'Ornon, France
| | - Hans R Schultz
- Hochschule Geisenheim University, von-Lade-Straße 1, Geisenheim, Germany
| | - Nathalie Ollat
- EGFV, Bordeaux Sciences Agro, CNRS, INRA, ISVV, Université de Bordeaux, Villenave d'Ornon, France
| | - Zhanwu Dai
- EGFV, Bordeaux Sciences Agro, CNRS, INRA, ISVV, Université de Bordeaux, Villenave d'Ornon, France
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26
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Varshney RK, Thudi M, Pandey MK, Tardieu F, Ojiewo C, Vadez V, Whitbread AM, Siddique KHM, Nguyen HT, Carberry PS, Bergvinson D. Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3293-3312. [PMID: 29514298 DOI: 10.1093/jxb/ery088] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/22/2018] [Indexed: 05/23/2023]
Abstract
Grain legumes form an important component of the human diet, provide feed for livestock, and replenish soil fertility through biological nitrogen fixation. Globally, the demand for food legumes is increasing as they complement cereals in protein requirements and possess a high percentage of digestible protein. Climate change has enhanced the frequency and intensity of drought stress, posing serious production constraints, especially in rainfed regions where most legumes are produced. Genetic improvement of legumes, like other crops, is mostly based on pedigree and performance-based selection over the past half century. To achieve faster genetic gains in legumes in rainfed conditions, this review proposes the integration of modern genomics approaches, high throughput phenomics, and simulation modelling in support of crop improvement that leads to improved varieties that perform with appropriate agronomy. Selection intensity, generation interval, and improved operational efficiencies in breeding are expected to further enhance the genetic gain in experimental plots. Improved seed access to farmers, combined with appropriate agronomic packages in farmers' fields, will deliver higher genetic gains. Enhanced genetic gains, including not only productivity but also nutritional and market traits, will increase the profitability of farming and the availability of affordable nutritious food especially in developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Francois Tardieu
- French National Institute for Agricultural Research (INRA), Monpellier, France
| | - Chris Ojiewo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Institut de recherche pour le développement (IRD), Montpellier, France
| | - Anthony M Whitbread
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | | | - Peter S Carberry
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - David Bergvinson
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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27
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Tricker PJ, ElHabti A, Schmidt J, Fleury D. The physiological and genetic basis of combined drought and heat tolerance in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3195-3210. [PMID: 29562265 DOI: 10.1093/jxb/ery081] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/14/2018] [Indexed: 05/03/2023]
Abstract
Drought and heat stress cause losses in wheat productivity in major growing regions worldwide, and both the occurrence and the severity of these events are likely to increase with global climate change. Water deficits and high temperatures frequently occur simultaneously at sensitive growth stages, reducing wheat yields by reducing grain number or weight. Although genetic variation and underlying quantitative trait loci for either individual stress are known, the combination of the two stresses has rarely been studied. Complex and often antagonistic physiology means that genetic loci underlying tolerance to the combined stress are likely to differ from those for drought or heat stress tolerance alone. Here, we review what is known of the physiological traits and genetic control of drought and heat tolerance in wheat and discuss potential physiological traits to study for combined tolerance. We further place this knowledge in the context of breeding for new, more tolerant varieties and discuss opportunities and constraints. We conclude that a fine control of water relations across the growing cycle will be beneficial for combined tolerance and might be achieved through fine management of spatial and temporal gas exchange.
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Affiliation(s)
- Penny J Tricker
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Abdeljalil ElHabti
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Jessica Schmidt
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Delphine Fleury
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
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Araus JL, Kefauver SC, Zaman-Allah M, Olsen MS, Cairns JE. Translating High-Throughput Phenotyping into Genetic Gain. TRENDS IN PLANT SCIENCE 2018; 23:451-466. [PMID: 29555431 PMCID: PMC5931794 DOI: 10.1016/j.tplants.2018.02.001] [Citation(s) in RCA: 272] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 01/23/2018] [Accepted: 02/01/2018] [Indexed: 05/18/2023]
Abstract
Inability to efficiently implement high-throughput field phenotyping is increasingly perceived as a key component that limits genetic gain in breeding programs. Field phenotyping must be integrated into a wider context than just choosing the correct selection traits, deployment tools, evaluation platforms, or basic data-management methods. Phenotyping means more than conducting such activities in a resource-efficient manner; it also requires appropriate trial management and spatial variability handling, definition of key constraining conditions prevalent in the target population of environments, and the development of more comprehensive data management, including crop modeling. This review will provide a wide perspective on how field phenotyping is best implemented. It will also outline how to bridge the gap between breeders and 'phenotypers' in an effective manner.
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Affiliation(s)
- José Luis Araus
- Unit of Plant Physiology, Faculty of Biology, University of Barcelona, Barcelona, Spain.
| | - Shawn C Kefauver
- Unit of Plant Physiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Mainassara Zaman-Allah
- Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT) Southern Africa Regional Office, Harare, Zimbabwe
| | | | - Jill E Cairns
- Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT) Southern Africa Regional Office, Harare, Zimbabwe
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29
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Tardieu F, Simonneau T, Muller B. The Physiological Basis of Drought Tolerance in Crop Plants: A Scenario-Dependent Probabilistic Approach. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:733-759. [PMID: 29553801 DOI: 10.1146/annurev-arplant-042817-040218] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Drought tolerance involves mechanisms operating at different spatial and temporal scales, from rapid stomatal closure to maintenance of crop yield. We review how short-term mechanisms are controlled for stabilizing shoot water potential and how long-term processes have been constrained by evolution or breeding to fit into acclimation strategies for specific drought scenarios. These short- or long-term feedback processes participate in trade-offs between carbon accumulation and the risk of deleterious soil water depletion. Corresponding traits and alleles may therefore have positive or negative effects on crop yield depending on drought scenarios. We propose an approach that analyzes the genetic architecture of traits in phenotyping platforms and of yield in tens of field experiments. A combination of modeling and genomic prediction is then used to estimate the comparative interests of combinations of alleles depending on drought scenarios. Hence, drought tolerance is understood probabilistically by estimating the benefit and risk of each combination of alleles.
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Affiliation(s)
- François Tardieu
- INRA, Université Montpellier, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, F-34060 Montpellier, France;
| | - Thierry Simonneau
- INRA, Université Montpellier, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, F-34060 Montpellier, France;
| | - Bertrand Muller
- INRA, Université Montpellier, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, F-34060 Montpellier, France;
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30
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Zhu J, Dai Z, Vivin P, Gambetta GA, Henke M, Peccoux A, Ollat N, Delrot S. A 3-D functional-structural grapevine model that couples the dynamics of water transport with leaf gas exchange. ANNALS OF BOTANY 2018; 121:833-848. [PMID: 29293870 PMCID: PMC5906973 DOI: 10.1093/aob/mcx141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/01/2017] [Indexed: 05/03/2023]
Abstract
Background and Aims Predicting both plant water status and leaf gas exchange under various environmental conditions is essential for anticipating the effects of climate change on plant growth and productivity. This study developed a functional-structural grapevine model which combines a mechanistic understanding of stomatal function and photosynthesis at the leaf level (i.e. extended Farqhuhar-von Caemmerer-Berry model) and the dynamics of water transport from soil to individual leaves (i.e. Tardieu-Davies model). Methods The model included novel features that account for the effects of xylem embolism (fPLC) on leaf hydraulic conductance and residual stomatal conductance (g0), variable root and leaf hydraulic conductance, and the microclimate of individual organs. The model was calibrated with detailed datasets of leaf photosynthesis, leaf water potential, xylem sap abscisic acid (ABA) concentration and hourly whole-plant transpiration observed within a soil drying period, and validated with independent datasets of whole-plant transpiration under both well-watered and water-stressed conditions. Key Results The model well captured the effects of radiation, temperature, CO2 and vapour pressure deficit on leaf photosynthesis, transpiration, stomatal conductance and leaf water potential, and correctly reproduced the diurnal pattern and decline of water flux within the soil drying period. In silico analyses revealed that decreases in g0 with increasing fPLC were essential to avoid unrealistic drops in leaf water potential under severe water stress. Additionally, by varying the hydraulic conductance along the pathway (e.g. root and leaves) and changing the sensitivity of stomatal conductance to ABA and leaf water potential, the model can produce different water use behaviours (i.e. iso- and anisohydric). Conclusions The robust performance of this model allows for modelling climate effects from individual plants to fields, and for modelling plants with complex, non-homogenous canopies. In addition, the model provides a basis for future modelling efforts aimed at describing the physiology and growth of individual organs in relation to water status.
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Affiliation(s)
- Junqi Zhu
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Zhanwu Dai
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Philippe Vivin
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Gregory A Gambetta
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Michael Henke
- Department of Ecoinformatics, Biometrics and Forest Growth, University of Göttingen, Göttingen, Germany
| | - Anthony Peccoux
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Nathalie Ollat
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Serge Delrot
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
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32
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Priya R, Ramesh D. Adaboost.RT Based Soil N-P-K Prediction Model for Soil and Crop Specific Data: A Predictive Modelling Approach. BIG DATA ANALYTICS 2018. [DOI: 10.1007/978-3-030-04780-1_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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33
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Water (stress) models and deficit irrigation: System-theoretical description and causality mapping. Ecol Modell 2017. [DOI: 10.1016/j.ecolmodel.2017.07.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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34
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Antle JM, Basso B, Conant RT, Godfray HCJ, Jones JW, Herrero M, Howitt RE, Keating BA, Munoz-Carpena R, Rosenzweig C, Tittonell P, Wheeler TR. Towards a new generation of agricultural system data, models and knowledge products: Design and improvement. AGRICULTURAL SYSTEMS 2017; 155:255-268. [PMID: 28701817 PMCID: PMC5485644 DOI: 10.1016/j.agsy.2016.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 10/01/2016] [Accepted: 10/04/2016] [Indexed: 05/11/2023]
Abstract
This paper presents ideas for a new generation of agricultural system models that could meet the needs of a growing community of end-users exemplified by a set of Use Cases. We envision new data, models and knowledge products that could accelerate the innovation process that is needed to achieve the goal of achieving sustainable local, regional and global food security. We identify desirable features for models, and describe some of the potential advances that we envisage for model components and their integration. We propose an implementation strategy that would link a "pre-competitive" space for model development to a "competitive space" for knowledge product development and through private-public partnerships for new data infrastructure. Specific model improvements would be based on further testing and evaluation of existing models, the development and testing of modular model components and integration, and linkages of model integration platforms to new data management and visualization tools.
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35
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Jin Z, Zhuang Q, Wang J, Archontoulis SV, Zobel Z, Kotamarthi VR. The combined and separate impacts of climate extremes on the current and future US rainfed maize and soybean production under elevated CO 2. GLOBAL CHANGE BIOLOGY 2017; 23:2687-2704. [PMID: 28063186 DOI: 10.1111/gcb.13617] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 12/24/2016] [Accepted: 12/27/2016] [Indexed: 05/16/2023]
Abstract
Heat and drought are two emerging climatic threats to the US maize and soybean production, yet their impacts on yields are collectively determined by the magnitude of climate change and rising atmospheric CO2 concentrations. This study quantifies the combined and separate impacts of high temperature, heat and drought stresses on the current and future US rainfed maize and soybean production and for the first time characterizes spatial shifts in the relative importance of individual stress. Crop yields are simulated using the Agricultural Production Systems Simulator (APSIM), driven by high-resolution (12 km) dynamically downscaled climate projections for 1995-2004 and 2085-2094. Results show that maize and soybean yield losses are prominent in the US Midwest by the late 21st century under both Representative Concentration Pathway (RCP) 4.5 and RCP8.5 scenarios, and the magnitude of loss highly depends on the current vulnerability and changes in climate extremes. Elevated atmospheric CO2 partially but not completely offsets the yield gaps caused by climate extremes, and the effect is greater in soybean than in maize. Our simulations suggest that drought will continue to be the largest threat to US rainfed maize production under RCP4.5 and soybean production under both RCP scenarios, whereas high temperature and heat stress take over the dominant stress of drought on maize under RCP8.5. We also reveal that shifts in the geographic distributions of dominant stresses are characterized by the increase in concurrent stresses, especially for the US Midwest. These findings imply the importance of considering heat and drought stresses simultaneously for future agronomic adaptation and mitigation strategies, particularly for breeding programs and crop management. The modeling framework of partitioning the total effects of climate change into individual stress impacts can be applied to the study of other crops and agriculture systems.
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Affiliation(s)
- Zhenong Jin
- Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Qianlai Zhuang
- Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, West Lafayette, IN, 47907, USA
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Jiali Wang
- Environmental Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | | | - Zachary Zobel
- Department of Atmospheric Sciences, University of Illinois Champaign-Urbana, Urbana, IL, 61801, USA
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Tardieu F, Parent B. Predictable 'meta-mechanisms' emerge from feedbacks between transpiration and plant growth and cannot be simply deduced from short-term mechanisms. PLANT, CELL & ENVIRONMENT 2017; 40:846-857. [PMID: 27569520 DOI: 10.1111/pce.12822] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 05/19/2023]
Abstract
Growth under water deficit is controlled by short-term mechanisms but, because of numerous feedbacks, the combination of these mechanisms over time often results in outputs that cannot be deduced from the simple inspection of individual mechanisms. It can be analysed with dynamic models in which causal relationships between variables are considered at each time-step, allowing calculation of outputs that are routed back to inputs for the next time-step and that can change the system itself. We first review physiological mechanisms involved in seven feedbacks of transpiration on plant growth, involving changes in tissue hydraulic conductance, stomatal conductance, plant architecture and underlying factors such as hormones or aquaporins. The combination of these mechanisms over time can result in non-straightforward conclusions as shown by examples of simulation outputs: 'over production of abscisic acid (ABA) can cause a lower concentration of ABA in the xylem sap ', 'decreasing root hydraulic conductance when evaporative demand is maximum can improve plant performance' and 'rapid root growth can decrease yield'. Systems of equations simulating feedbacks over numerous time-steps result in logical and reproducible emergent properties that can be viewed as 'meta-mechanisms' at plant level, which have similar roles as mechanisms at cell level.
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Affiliation(s)
- François Tardieu
- INRA, UMR759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Montpellier, F-34060, France
| | - Boris Parent
- INRA, UMR759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Montpellier, F-34060, France
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Urban MO, Vašek J, Klíma M, Krtková J, Kosová K, Prášil IT, Vítámvás P. Proteomic and physiological approach reveals drought-induced changes in rapeseeds: Water-saver and water-spender strategy. J Proteomics 2016; 152:188-205. [PMID: 27838467 DOI: 10.1016/j.jprot.2016.11.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/21/2016] [Accepted: 11/03/2016] [Indexed: 01/05/2023]
Abstract
The cultivar-dependent differences in Brassica napus L. seed yield are significantly affected by drought stress. Here, the response of leaf proteome to long-term drought (28days) was studied in cultivars (cvs): Californium (C), Cadeli (D), Navajo (N), and Viking (V). Analysis of twenty-four 2-D DIGE gels revealed 134 spots quantitatively changed at least 2-fold; from these, 79 proteins were significantly identified by MALDI-TOF/TOF. According to the differences in water use, the cultivars may be assigned to two categories: water-savers or water-spenders. In the water-savers group (cvs C+D), proteins related to nitrogen assimilation, ATP and redox homeostasis were increased under stress, while in the water-spenders category (cvs N+V), carbohydrate/energy, photosynthesis, stress related and rRNA processing proteins were increased upon stress. Taking all data together, we indicated cv C as a drought-adaptable water-saver, cv D as a medium-adaptable water-saver, cv N as a drought-adaptable water-spender, and cv V as a low-adaptable drought sensitive water-spender rapeseed. Proteomic data help to evaluate the impact of drought and the extent of genotype-based adaptability and contribute to the understanding of their plasticity. These results provide new insights into the provenience-based drought acclimation/adaptation strategy of contrasting winter rapeseeds and link data at gasometric, biochemical, and proteome level. SIGNIFICANCE Soil moisture deficit is a real problem for every crop. The data in this study demonstrates for the first time that in stem-prolongation phase cultivars respond to progressive drought in different ways and at different levels. Analysis of physiological and proteomic data showed two different water regime-related strategies: water-savers and spenders. However, not only water uptake rate itself, but also individual protein abundances, gasometric and biochemical parameters together with final biomass accumulation after stress explained genotype-based responses. Interestingly, under a mixed climate profile, both water-use patterns (savers or spenders) can be appropriate for drought adaptation. These data suggest, than complete "acclimation image" of rapeseeds in stem-prolongation phase under drought could be reached only if these characteristics are taken, explained and understood together.
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Affiliation(s)
- Milan Oldřich Urban
- Crop Research Institute, Department of Genetics and Plant Breeding, Drnovská 507/73, Prague, Czech Republic; Charles University, Department of Experimental Plant Biology, Viničná 5, Prague, Czech Republic.
| | - Jakub Vašek
- Czech University of Life Sciences Prague, Department of Genetics and Breeding, Kamýcká 129, Prague, Czech Republic
| | - Miroslav Klíma
- Crop Research Institute, Department of Genetics and Plant Breeding, Drnovská 507/73, Prague, Czech Republic
| | - Jana Krtková
- Charles University, Department of Experimental Plant Biology, Viničná 5, Prague, Czech Republic
| | - Klára Kosová
- Crop Research Institute, Department of Genetics and Plant Breeding, Drnovská 507/73, Prague, Czech Republic
| | - Ilja Tom Prášil
- Crop Research Institute, Department of Genetics and Plant Breeding, Drnovská 507/73, Prague, Czech Republic
| | - Pavel Vítámvás
- Crop Research Institute, Department of Genetics and Plant Breeding, Drnovská 507/73, Prague, Czech Republic
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Wu A, Song Y, van Oosterom EJ, Hammer GL. Connecting Biochemical Photosynthesis Models with Crop Models to Support Crop Improvement. FRONTIERS IN PLANT SCIENCE 2016; 7:1518. [PMID: 27790232 PMCID: PMC5061851 DOI: 10.3389/fpls.2016.01518] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/26/2016] [Indexed: 05/18/2023]
Abstract
The next advance in field crop productivity will likely need to come from improving crop use efficiency of resources (e.g., light, water, and nitrogen), aspects of which are closely linked with overall crop photosynthetic efficiency. Progress in genetic manipulation of photosynthesis is confounded by uncertainties of consequences at crop level because of difficulties connecting across scales. Crop growth and development simulation models that integrate across biological levels of organization and use a gene-to-phenotype modeling approach may present a way forward. There has been a long history of development of crop models capable of simulating dynamics of crop physiological attributes. Many crop models incorporate canopy photosynthesis (source) as a key driver for crop growth, while others derive crop growth from the balance between source- and sink-limitations. Modeling leaf photosynthesis has progressed from empirical modeling via light response curves to a more mechanistic basis, having clearer links to the underlying biochemical processes of photosynthesis. Cross-scale modeling that connects models at the biochemical and crop levels and utilizes developments in upscaling leaf-level models to canopy models has the potential to bridge the gap between photosynthetic manipulation at the biochemical level and its consequences on crop productivity. Here we review approaches to this emerging cross-scale modeling framework and reinforce the need for connections across levels of modeling. Further, we propose strategies for connecting biochemical models of photosynthesis into the cross-scale modeling framework to support crop improvement through photosynthetic manipulation.
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Affiliation(s)
- Alex Wu
- Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, The University of QueenslandBrisbane, QLD, Australia
- ARC Centre of Excellence for Translational Photosynthesis, The University of QueenslandBrisbane, QLD, Australia
| | - Youhong Song
- Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, The University of QueenslandBrisbane, QLD, Australia
- ARC Centre of Excellence for Translational Photosynthesis, The University of QueenslandBrisbane, QLD, Australia
| | - Erik J. van Oosterom
- Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, The University of QueenslandBrisbane, QLD, Australia
- ARC Centre of Excellence for Translational Photosynthesis, The University of QueenslandBrisbane, QLD, Australia
| | - Graeme L. Hammer
- Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, The University of QueenslandBrisbane, QLD, Australia
- ARC Centre of Excellence for Translational Photosynthesis, The University of QueenslandBrisbane, QLD, Australia
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Cabrera-Bosquet L, Fournier C, Brichet N, Welcker C, Suard B, Tardieu F. High-throughput estimation of incident light, light interception and radiation-use efficiency of thousands of plants in a phenotyping platform. THE NEW PHYTOLOGIST 2016; 212:269-81. [PMID: 27258481 DOI: 10.1111/nph.14027] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/22/2016] [Indexed: 05/22/2023]
Abstract
Light interception and radiation-use efficiency (RUE) are essential components of plant performance. Their genetic dissections require novel high-throughput phenotyping methods. We have developed a suite of methods to evaluate the spatial distribution of incident light, as experienced by hundreds of plants in a glasshouse, by simulating sunbeam trajectories through glasshouse structures every day of the year; the amount of light intercepted by maize (Zea mays) plants via a functional-structural model using three-dimensional (3D) reconstructions of each plant placed in a virtual scene reproducing the canopy in the glasshouse; and RUE, as the ratio of plant biomass to intercepted light. The spatial variation of direct and diffuse incident light in the glasshouse (up to 24%) was correctly predicted at the single-plant scale. Light interception largely varied between maize lines that differed in leaf angles (nearly stable between experiments) and area (highly variable between experiments). Estimated RUEs varied between maize lines, but were similar in two experiments with contrasting incident light. They closely correlated with measured gas exchanges. The methods proposed here identified reproducible traits that might be used in further field studies, thereby opening up the way for large-scale genetic analyses of the components of plant performance.
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Affiliation(s)
| | | | - Nicolas Brichet
- UMR LEPSE, INRA, Montpellier SupAgro, F-34060, Montpellier, France
| | - Claude Welcker
- UMR LEPSE, INRA, Montpellier SupAgro, F-34060, Montpellier, France
| | - Benoît Suard
- UMR LEPSE, INRA, Montpellier SupAgro, F-34060, Montpellier, France
| | - François Tardieu
- UMR LEPSE, INRA, Montpellier SupAgro, F-34060, Montpellier, France
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40
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Jin Z, Zhuang Q, Tan Z, Dukes JS, Zheng B, Melillo JM. Do maize models capture the impacts of heat and drought stresses on yield? Using algorithm ensembles to identify successful approaches. GLOBAL CHANGE BIOLOGY 2016; 22:3112-26. [PMID: 27251794 DOI: 10.1111/gcb.13376] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/25/2016] [Accepted: 05/04/2016] [Indexed: 05/06/2023]
Abstract
Stresses from heat and drought are expected to increasingly suppress crop yields, but the degree to which current models can represent these effects is uncertain. Here we evaluate the algorithms that determine impacts of heat and drought stress on maize in 16 major maize models by incorporating these algorithms into a standard model, the Agricultural Production Systems sIMulator (APSIM), and running an ensemble of simulations. Although both daily mean temperature and daylight temperature are common choice of forcing heat stress algorithms, current parameterizations in most models favor the use of daylight temperature even though the algorithm was designed for daily mean temperature. Different drought algorithms (i.e., a function of soil water content, of soil water supply to demand ratio, and of actual to potential transpiration ratio) simulated considerably different patterns of water shortage over the growing season, but nonetheless predicted similar decreases in annual yield. Using the selected combination of algorithms, our simulations show that maize yield reduction was more sensitive to drought stress than to heat stress for the US Midwest since the 1980s, and this pattern will continue under future scenarios; the influence of excessive heat will become increasingly prominent by the late 21st century. Our review of algorithms in 16 crop models suggests that the impacts of heat and drought stress on plant yield can be best described by crop models that: (i) incorporate event-based descriptions of heat and drought stress, (ii) consider the effects of nighttime warming, and (iii) coordinate the interactions among multiple stresses. Our study identifies the proficiency with which different model formulations capture the impacts of heat and drought stress on maize biomass and yield production. The framework presented here can be applied to other modeled processes and used to improve yield predictions of other crops with a wide variety of crop models.
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Affiliation(s)
- Zhenong Jin
- Department of Earth, Atmospheric and Planetary Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Qianlai Zhuang
- Department of Earth, Atmospheric and Planetary Sciences, Purdue University, West Lafayette, IN, 47907, USA
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Climate Change Research Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Zeli Tan
- Department of Earth, Atmospheric and Planetary Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Jeffrey S Dukes
- Purdue Climate Change Research Center, Purdue University, West Lafayette, IN, 47907, USA
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Bangyou Zheng
- CSRIO Agriculture, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Qld, 4067, Australia
| | - Jerry M Melillo
- The Marine Biological Laboratory, The Ecosystems Center, Woods Hole, MA, 02536, USA
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Parent B, Vile D, Violle C, Tardieu F. Towards parsimonious ecophysiological models that bridge ecology and agronomy. THE NEW PHYTOLOGIST 2016; 210:380-382. [PMID: 26805609 DOI: 10.1111/nph.13811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- Boris Parent
- INRA, UMR759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Place Viala, F-34060, Montpellier, France
| | - Denis Vile
- INRA, UMR759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Place Viala, F-34060, Montpellier, France
| | - Cyrille Violle
- CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE, 1919 route de Mende, F-34293, Montpellier, CEDEX 5, France
| | - François Tardieu
- INRA, UMR759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Place Viala, F-34060, Montpellier, France
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Quilot-Turion B, Génard M, Valsesia P, Memmah MM. Optimization of Allelic Combinations Controlling Parameters of a Peach Quality Model. FRONTIERS IN PLANT SCIENCE 2016; 7:1873. [PMID: 28066450 PMCID: PMC5167719 DOI: 10.3389/fpls.2016.01873] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/28/2016] [Indexed: 05/08/2023]
Abstract
Process-based models are effective tools to predict the phenotype of an individual in different growing conditions. Combined with a quantitative trait locus (QTL) mapping approach, it is then possible to predict the behavior of individuals with any combinations of alleles. However the number of simulations to explore the realm of possibilities may become infinite. Therefore, the use of an efficient optimization algorithm to intelligently explore the search space becomes imperative. The optimization algorithm has to solve a multi-objective problem, since the phenotypes of interest are usually a complex of traits, to identify the individuals with best tradeoffs between those traits. In this study we proposed to unroll such a combined approach in the case of peach fruit quality described through three targeted traits, using a process-based model with seven parameters controlled by QTL. We compared a current approach based on the optimization of the values of the parameters with a more evolved way to proceed which consists in the direct optimization of the alleles controlling the parameters. The optimization algorithm has been adapted to deal with both continuous and combinatorial problems. We compared the spaces of parameters obtained with different tactics and the phenotype of the individuals resulting from random simulations and optimization in these spaces. The use of a genetic model enabled the restriction of the dimension of the parameter space toward more feasible combinations of parameter values, reproducing relationships between parameters as observed in a real progeny. The results of this study demonstrated the potential of such an approach to refine the solutions toward more realistic ideotypes. Perspectives of improvement are discussed.
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Affiliation(s)
- William J Davies
- Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster, LA1 4YQ, UK
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
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Wuyts N, Dhondt S, Inzé D. Measurement of plant growth in view of an integrative analysis of regulatory networks. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:90-97. [PMID: 26002069 DOI: 10.1016/j.pbi.2015.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/17/2015] [Accepted: 05/01/2015] [Indexed: 05/29/2023]
Abstract
As the regulatory networks of growth at the cellular level are elucidated at a fast pace, their complexity is not reduced; on the contrary, the tissue, organ and even whole-plant level affect cell proliferation and expansion by means of development-induced and environment-induced signaling events in growth regulatory processes. Measurement of growth across different levels aids in gaining a mechanistic understanding of growth, and in defining the spatial and temporal resolution of sampling strategies for molecular analyses in the model Arabidopsis thaliana and increasingly also in crop species. The latter claim their place at the forefront of plant research, since global issues and future needs drive the translation from laboratory model-acquired knowledge of growth processes to improvements in crop productivity in field conditions.
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Affiliation(s)
- Nathalie Wuyts
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Stijn Dhondt
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium.
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Rossi M, Bermudez L, Carrari F. Crop yield: challenges from a metabolic perspective. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:79-89. [PMID: 26002068 DOI: 10.1016/j.pbi.2015.05.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 04/24/2015] [Accepted: 05/01/2015] [Indexed: 05/03/2023]
Abstract
Considering the dual use of plants, as bio-factories for foods and feedstock for bio-refining, along with a rising world population, the plant biotechnology field is currently facing a dramatic challenge to develop crops with higher yield. Furthermore, convergent studies predict that global changes in climate will influence crop productivity by modifying most yield-associated traits. Here, we review recent advances in the understanding of plant metabolism directly or indirectly impacting on yield and provide an update of the different pathways proposed as targets for metabolic engineering aiming to optimize source-sink relationships.
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Affiliation(s)
- Magdalena Rossi
- Departamento de Botânica-IB-USP, Rua do Matão, 277, 05508-090, São Paulo, SP, Brazil
| | - Luisa Bermudez
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), B1712WAA Castelar, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), B1712WAA Castelar, Argentina; Facultad de Agronomía, Universidad de Buenos Aires, Argentina
| | - Fernando Carrari
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), B1712WAA Castelar, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), B1712WAA Castelar, Argentina; Facultad de Agronomía, Universidad de Buenos Aires, Argentina.
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Tardieu F, Simonneau T, Parent B. Modelling the coordination of the controls of stomatal aperture, transpiration, leaf growth, and abscisic acid: update and extension of the Tardieu-Davies model. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2227-37. [PMID: 25770586 PMCID: PMC4986722 DOI: 10.1093/jxb/erv039] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/09/2015] [Accepted: 01/14/2015] [Indexed: 05/19/2023]
Abstract
Stomatal aperture, transpiration, leaf growth, hydraulic conductance, and concentration of abscisic acid in the xylem sap ([ABA]xyl) vary rapidly with time of day. They follow deterministic relations with environmental conditions and interact in such a way that a change in any one of them affects all the others. Hence, approaches based on measurements of one variable at a given time or on paired correlations are prone to a confusion of effects, in particular for studying their genetic variability. A dynamic model allows the simulation of environmental effects on the variables, and of multiple feedbacks between them at varying time resolutions. This paper reviews the control of water movement through the plant, stomatal aperture and growth, and translates them into equations in a model. It includes recent progress in understanding the intrinsic and environmental controls of tissue hydraulic conductance as a function of transpiration rate, circadian rhythms, and [ABA]xyl. Measured leaf water potential is considered as the water potential of a capacitance representing mature tissues, which reacts more slowly to environmental cues than xylem water potential and expansive growth. Combined with equations for water and ABA fluxes, it results in a dynamic model able to simulate variables with genotype-specific parameters. It allows adaptive roles for hydraulic processes to be proposed, in particular the circadian oscillation of root hydraulic conductance. The script of the model, in the R language, is included together with appropriate documentation and examples.
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Affiliation(s)
- François Tardieu
- INRA, UMR759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Place Viala, F-34060 Montpellier, France
| | - Thierry Simonneau
- INRA, UMR759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Place Viala, F-34060 Montpellier, France
| | - Boris Parent
- INRA, UMR759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, Place Viala, F-34060 Montpellier, France
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Hu X, Wu L, Zhao F, Zhang D, Li N, Zhu G, Li C, Wang W. Phosphoproteomic analysis of the response of maize leaves to drought, heat and their combination stress. FRONTIERS IN PLANT SCIENCE 2015. [PMID: 25999967 DOI: 10.3389/flps.2015.00298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Drought and heat stress, especially their combination, greatly affect crop production. Many studies have described transcriptome, proteome and phosphoproteome changes in response of plants to drought or heat stress. However, the study about the phosphoproteomic changes in response of crops to the combination stress is scare. To understand the mechanism of maize responses to the drought and heat combination stress, phosphoproteomic analysis was performed on maize leaves by using multiplex iTRAQ-based quantitative proteomic and LC-MS/MS methods. Five-leaf-stage maize was subjected to drought, heat or their combination, and the leaves were collected. Globally, heat, drought and the combined stress significantly changed the phosphorylation levels of 172, 149, and 144 phosphopeptides, respectively. These phosphopeptides corresponded to 282 proteins. Among them, 23 only responded to the combined stress and could not be predicted from their responses to single stressors; 30 and 75 only responded to drought and heat, respectively. Notably, 19 proteins were phosphorylated on different sites in response to the single and combination stresses. Of the seven significantly enriched phosphorylation motifs identified, two were common for all stresses, two were common for heat and the combined stress, and one was specific to the combined stress. The signaling pathways in which the phosphoproteins were involved clearly differed among the three stresses. Functional characterization of the phosphoproteins and the pathways identified here could lead to new targets for the enhancement of crop stress tolerance, which will be particularly important in the face of climate change and the increasing prevalence of abiotic stressors.
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Affiliation(s)
- Xiuli Hu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University Zhengzhou, China
| | - Liuji Wu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University Zhengzhou, China
| | - Feiyun Zhao
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University Zhengzhou, China
| | - Dayong Zhang
- Jiangsu Academy of Agricultural Sciences Institute of Biotechnology Nanjing, China
| | - Nana Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University Zhengzhou, China
| | - Guohui Zhu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University Guangzhou, China
| | - Chaohao Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University Zhengzhou, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University Zhengzhou, China
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Hu X, Wu L, Zhao F, Zhang D, Li N, Zhu G, Li C, Wang W. Phosphoproteomic analysis of the response of maize leaves to drought, heat and their combination stress. FRONTIERS IN PLANT SCIENCE 2015; 6:298. [PMID: 25999967 PMCID: PMC4419667 DOI: 10.3389/fpls.2015.00298] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/14/2015] [Indexed: 05/18/2023]
Abstract
Drought and heat stress, especially their combination, greatly affect crop production. Many studies have described transcriptome, proteome and phosphoproteome changes in response of plants to drought or heat stress. However, the study about the phosphoproteomic changes in response of crops to the combination stress is scare. To understand the mechanism of maize responses to the drought and heat combination stress, phosphoproteomic analysis was performed on maize leaves by using multiplex iTRAQ-based quantitative proteomic and LC-MS/MS methods. Five-leaf-stage maize was subjected to drought, heat or their combination, and the leaves were collected. Globally, heat, drought and the combined stress significantly changed the phosphorylation levels of 172, 149, and 144 phosphopeptides, respectively. These phosphopeptides corresponded to 282 proteins. Among them, 23 only responded to the combined stress and could not be predicted from their responses to single stressors; 30 and 75 only responded to drought and heat, respectively. Notably, 19 proteins were phosphorylated on different sites in response to the single and combination stresses. Of the seven significantly enriched phosphorylation motifs identified, two were common for all stresses, two were common for heat and the combined stress, and one was specific to the combined stress. The signaling pathways in which the phosphoproteins were involved clearly differed among the three stresses. Functional characterization of the phosphoproteins and the pathways identified here could lead to new targets for the enhancement of crop stress tolerance, which will be particularly important in the face of climate change and the increasing prevalence of abiotic stressors.
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Affiliation(s)
- Xiuli Hu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| | - Liuji Wu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| | - Feiyun Zhao
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| | - Dayong Zhang
- Jiangsu Academy of Agricultural Sciences Institute of BiotechnologyNanjing, China
| | - Nana Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| | - Guohui Zhu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural UniversityGuangzhou, China
| | - Chaohao Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
- *Correspondence: Wei Wang, State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University, 63 Nongye Road, Zhengzhou 450002, China
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Tuberosa R, Turner NC, Cakir M. Preface: two decades of InterDrought conferences: are we bridging the genotype-to-phenotype gap? JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6137-6139. [PMID: 25544976 DOI: 10.1093/jxb/eru407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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