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McLeod L, Barchi L, Tumino G, Tripodi P, Salinier J, Gros C, Boyaci HF, Ozalp R, Borovsky Y, Schafleitner R, Barchenger D, Finkers R, Brouwer M, Stein N, Rabanus-Wallace MT, Giuliano G, Voorrips R, Paran I, Lefebvre V. Multi-environment association study highlights candidate genes for robust agronomic quantitative trait loci in a novel worldwide Capsicum core collection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1508-1528. [PMID: 37602679 DOI: 10.1111/tpj.16425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/13/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023]
Abstract
Investigating crop diversity through genome-wide association studies (GWAS) on core collections helps in deciphering the genetic determinants of complex quantitative traits. Using the G2P-SOL project world collection of 10 038 wild and cultivated Capsicum accessions from 10 major genebanks, we assembled a core collection of 423 accessions representing the known genetic diversity. Since complex traits are often highly dependent upon environmental variables and genotype-by-environment (G × E) interactions, multi-environment GWAS with a 10 195-marker genotypic matrix were conducted on a highly diverse subset of 350 Capsicum annuum accessions, extensively phenotyped in up to six independent trials from five climatically differing countries. Environment-specific and multi-environment quantitative trait loci (QTLs) were detected for 23 diverse agronomic traits. We identified 97 candidate genes potentially implicated in 53 of the most robust and high-confidence QTLs for fruit flavor, color, size, and shape traits, and for plant productivity, vigor, and earliness traits. Investigating the genetic architecture of agronomic traits in this way will assist the development of genetic markers and pave the way for marker-assisted selection. The G2P-SOL pepper core collection will be available upon request as a unique and universal resource for further exploitation in future gene discovery and marker-assisted breeding efforts by the pepper community.
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Affiliation(s)
- Louis McLeod
- INRAE, GAFL, Montfavet, France
- INRAE, A2M, Montfavet, France
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Giorgio Tumino
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Pasquale Tripodi
- Research Centre for Vegetable and Ornamental Crops, Council for Agricultural Research and Economics (CREA), Pontecagnano Faiano, Italy
| | | | | | | | - Ramazan Ozalp
- Bati Akdeniz Agricultural Research Institute (BATEM), Antalya, Türkiye
| | - Yelena Borovsky
- The Volcani Center, Institute of Plant Sciences, Agricultural Research Organization (ARO), Rishon LeZion, Israel
| | - Roland Schafleitner
- Vegetable Diversity and Improvement, World Vegetable Center, Shanhua, Taiwan
| | - Derek Barchenger
- Vegetable Diversity and Improvement, World Vegetable Center, Shanhua, Taiwan
| | - Richard Finkers
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Matthijs Brouwer
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Corre, Gatersleben, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany
| | | | - Giovanni Giuliano
- Casaccia Research Centre, Italian National Agency for New Technologies, Energy, and Sustainable Economic Development (ENEA), Rome, Italy
| | - Roeland Voorrips
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Ilan Paran
- The Volcani Center, Institute of Plant Sciences, Agricultural Research Organization (ARO), Rishon LeZion, Israel
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Wang Y, Shang B, Génard M, Hilbert-Masson G, Delrot S, Gomès E, Poni S, Keller M, Renaud C, Kong J, Chen J, Liang Z, Dai Z. Model-assisted analysis for tuning anthocyanin composition in grape berries. ANNALS OF BOTANY 2023; 132:1033-1050. [PMID: 37850481 PMCID: PMC10808033 DOI: 10.1093/aob/mcad165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
Anthocyanin composition is responsible for the red colour of grape berries and wines, and contributes to their organoleptic quality. However, anthocyanin biosynthesis is under genetic, developmental and environmental regulation, making its targeted fine-tuning challenging. We constructed a mechanistic model to simulate the dynamics of anthocyanin composition throughout grape ripening in Vitis vinifera, employing a consensus anthocyanin biosynthesis pathway. The model was calibrated and validated using six datasets from eight cultivars and 37 growth conditions. Tuning the transformation and degradation parameters allowed us to accurately simulate the accumulation process of each individual anthocyanin under different environmental conditions. The model parameters were robust across environments for each genotype. The coefficients of determination (R2) for the simulated versus observed values for the six datasets ranged from 0.92 to 0.99, while the relative root mean square errors (RRMSEs) were between 16.8 and 42.1 %. The leave-one-out cross-validation for three datasets showed R2 values of 0.99, 0.96 and 0.91, and RRMSE values of 28.8, 32.9 and 26.4 %, respectively, suggesting a high prediction quality of the model. Model analysis showed that the anthocyanin profiles of diverse genotypes are relatively stable in response to parameter perturbations. Virtual experiments further suggested that targeted anthocyanin profiles may be reached by manipulating a minimum of three parameters, in a genotype-dependent manner. This model presents a promising methodology for characterizing the temporal progression of anthocyanin composition, while also offering a logical foundation for bioengineering endeavours focused on precisely adjusting the anthocyanin composition of grapes.
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Affiliation(s)
- Yongjian Wang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Boxing Shang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Michel Génard
- INRAE, UR1115, Unité Plantes et Systèmes de Culture Horticoles, Avignon, France
| | | | - Serge Delrot
- EGFV, University of Bordeaux, Bordeaux-Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Eric Gomès
- EGFV, University of Bordeaux, Bordeaux-Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Stefano Poni
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Markus Keller
- Department of Viticulture and Enology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Christel Renaud
- EGFV, University of Bordeaux, Bordeaux-Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Junhua Kong
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Jinliang Chen
- Center for Agricultural Water Research in China, China Agricultural University, Beijing, 100083, China
| | - Zhenchang Liang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhanwu Dai
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Coussement JR, Villers SLY, Nelissen H, Inzé D, Steppe K. Turgor-time controls grass leaf elongation rate and duration under drought stress. PLANT, CELL & ENVIRONMENT 2021; 44:1361-1378. [PMID: 33373049 DOI: 10.1111/pce.13989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
The process of leaf elongation in grasses is characterized by the creation and transformation of distinct cell zones. The prevailing turgor pressure within these cells is one of the key drivers for the rate at which these cells divide, expand and differentiate, processes that are heavily impacted by drought stress. In this article, a turgor-driven growth model for grass leaf elongation is presented, which combines mechanistic growth from the basis of turgor pressure with the ontogeny of the leaf. Drought-induced reductions in leaf turgor pressure result in a simultaneous inhibition of both cell expansion and differentiation, lowering elongation rate but increasing elongation duration due to the slower transitioning of cells from the dividing and elongating zone to mature cells. Leaf elongation is, therefore, governed by the magnitude of, and time spent under, growth-enabling turgor pressure, a metric which we introduce as turgor-time. Turgor-time is able to normalize growth patterns in terms of varying water availability, similar to how thermal time is used to do so under varying temperatures. Moreover, additional inclusion of temperature dependencies within our model pioneers a novel concept enabling the general expression of growth regardless of water availability or temperature.
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Affiliation(s)
- Jonas R Coussement
- Laboratory of Plant Ecology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Selwyn L Y Villers
- Laboratory of Plant Ecology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kathy Steppe
- Laboratory of Plant Ecology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Cammarano D, Ronga D, Francia E, Akar T, Al-Yassin A, Benbelkacem A, Grando S, Romagosa I, Stanca AM, Pecchioni N. Genetic and Management Effects on Barley Yield and Phenology in the Mediterranean Basin. FRONTIERS IN PLANT SCIENCE 2021; 12:655406. [PMID: 33936140 PMCID: PMC8084452 DOI: 10.3389/fpls.2021.655406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Heading time in barley is considered a key developmental stage controlling adaptation to the environment and it affects grain yield; with the combination of agronomy (planting dates) and genetics being some of the determinants of adaptation to environmental conditions in order to escape late frost, heat, and terminal drought stresses. The objectives of this study are (i) to apply a gene-based characterization of 118 barley doubled haploid recombinants for vernalization, photoperiod, and earliness per se; (ii) use such information to quantify the optimal combination of genotype/sowing date that escapes extreme weather events; and (iii) how water and nitrogen management impact on grain yield. The doubled haploid barley genotypes with different allelic combinations for vernalization, photoperiod, and earliness per se were grown in eight locations across the Mediterranean basin. This information was linked with the crop growth model parameters. The photoperiod and earliness per se alleles modify the length of the phenological cycle, and this is more evident in combination with the recessive allele of the vernalization gene VRN-H2. In hot environments such as Algeria, Syria, and Jordan, early sowing dates (October 30 and December15) would be chosen to minimize the risk of exposing barley to heat stress. To maintain higher yields in the Mediterranean basin, barley breeding activities should focus on allelic combinations that have recessive VRN-H2 and EPS2 genes, since the risk of cold stress is much lower than the one represented by heat stress.
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Affiliation(s)
- Davide Cammarano
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Domenico Ronga
- Department of Life Science, Centre BIOGEST-SITEIA, University of Modena and Reggio Emilia, Reggio Emilia, Italy
- Department of Pharmacy, University of Salerno, Fisciano, Italy
| | - Enrico Francia
- Department of Life Science, Centre BIOGEST-SITEIA, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Taner Akar
- Department of Agronomy, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Adnan Al-Yassin
- National Agricultural Research Center (NCARE), Amman, Jordan
| | | | | | | | - Antonio Michele Stanca
- Department of Life Science, Centre BIOGEST-SITEIA, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops, CREA – Council for Agricultural Research and Economics, Foggia, Italy
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Deva CR, Urban MO, Challinor AJ, Falloon P, Svitákova L. Enhanced Leaf Cooling Is a Pathway to Heat Tolerance in Common Bean. FRONTIERS IN PLANT SCIENCE 2020; 11:19. [PMID: 32180776 PMCID: PMC7059850 DOI: 10.3389/fpls.2020.00019] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/10/2020] [Indexed: 05/26/2023]
Abstract
Common bean is the most consumed legume in the world and an important source of protein in Latin America, Eastern, and Southern Africa. It is grown in a variety of environments with mean air temperatures of between 14°C and 35°C and is more sensitive to high temperatures than other legumes. As global heating continues, breeding for heat tolerance in common bean is an urgent priority. Transpirational cooling has been shown to be an important mechanism for heat avoidance in many crops, and leaf cooling traits have been used to breed for both drought and heat tolerance. As yet, little is known about the magnitude of leaf cooling in common bean, nor whether this trait is functionally linked to heat tolerance. Accordingly, we explore the extent and genotypic variation of transpirational cooling in common bean. Our results show that leaf cooling is an important heat avoidance mechanism in common bean. On average, leaf temperatures are 5°C cooler than air temperatures, and can range from between 13°C cooler and 2°C warmer. We show that the magnitude of leaf cooling keeps leaf temperatures within a photosynthetically functional range. Heat tolerant genotypes cool more than heat sensitive genotypes and the magnitude of this difference increases at elevated temperatures. Furthermore, we find that differences in leaf cooling are largest at the top of the canopy where determinate bush beans are most sensitive to the impact of high temperatures during the flowering period. Our results suggest that heat tolerant genotypes cool more than heat sensitive genotypes as a result of higher stomatal conductance and enhanced transpirational cooling. We demonstrate that it is possible to accurately simulate the temperature of the leaf by genotype using only air temperature and relative humidity. Our work suggests that greater leaf cooling is a pathway to heat tolerance. Bean breeders can use the difference between air and leaf temperature to screen for genotypes with enhanced capacity for heat avoidance. Once evaluated for a particular target population of environments, breeders can use our model for modeling leaf temperatures by genotype to assess the value of selecting for cooler beans.
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Affiliation(s)
- Chetan R. Deva
- Climate Impacts Group, Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Milan O. Urban
- The International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Andrew J. Challinor
- Climate Impacts Group, Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Pete Falloon
- The Met Office Hadley Centre, Exeter, United Kingdom
| | - Lenka Svitákova
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
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Kanso H, Quilot-Turion B, Memah MM, Bernard O, Gouzé JL, Baldazzi V. Reducing a model of sugar metabolism in peach to catch different patterns among genotypes. Math Biosci 2020; 321:108321. [PMID: 32014417 DOI: 10.1016/j.mbs.2020.108321] [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: 08/02/2019] [Revised: 12/24/2019] [Accepted: 01/23/2020] [Indexed: 11/18/2022]
Abstract
Several studies have been conducted to understand the dynamic of primary metabolisms in fruit by translating them into mathematics models. An ODE kinetic model of sugar metabolism has been developed by Desnoues et al. (2018) to simulate the accumulation of different sugars during peach fruit development. Two major drawbacks of this model are (a) the number of parameters to calibrate and (b) its integration time that can be long due to non-linearity and time-dependent input functions. Together, these issues hamper the use of the model for a large panel of genotypes, for which few data are available. In this paper, we present a model reduction scheme that explicitly addresses the specificity of genetic studies in that: (i) it yields a reduced model that is adapted to the whole expected genetic diversity (ii) it maintains network structure and variable identity, in order to facilitate biological interpretation. The proposed approach is based on the combination and the systematic evaluation of different reduction methods. Thus, we combined multivariate sensitivity analysis, structural simplification and timescale-based approaches to simplify the number and the structure of ordinary differential equations of the model. The original and reduced models were compared based on three criteria, namely the corrected Aikake Information Criterion (AICC), the calibration time and the expected error of the reduced model over a progeny of virtual genotypes. The resulting reduced model not only reproduces the predictions of the original one but presents many advantages including a reduced number of parameters to be estimated and shorter calibration time, opening new promising perspectives for genetic studies and virtual breeding. The validity of the reduced model was further evaluated by calibration on 30 additional genotypes of an inter-specific peach progeny for which few data were available.
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Affiliation(s)
- Hussein Kanso
- INRAE, GAFL, Montfavet F-84143, France; INRAE, PSH, Avignon F-84914, France
| | | | | | - Olivier Bernard
- Université Côte d'Azur, Inria, INRAE, Sorbonne Université, BIOCORE, Sophia-Antipolis, France
| | - Jean-Luc Gouzé
- Université Côte d'Azur, Inria, INRAE, Sorbonne Université, BIOCORE, Sophia-Antipolis, France
| | - Valentina Baldazzi
- INRAE, PSH, Avignon F-84914, France; Université Côte d'Azur, INRAE, CNRS, ISA, Sophia-Antipolis, France; Université Côte d'Azur, Inria, INRAE, Sorbonne Université, BIOCORE, Sophia-Antipolis, France.
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7
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Barrasso C, Memah MM, Génard M, Quilot-Turion B. Model-based QTL detection is sensitive to slight modifications in model formulation. PLoS One 2019; 14:e0222764. [PMID: 31581203 PMCID: PMC6776317 DOI: 10.1371/journal.pone.0222764] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 09/07/2019] [Indexed: 12/25/2022] Open
Abstract
Classical crop models have been developed to predict crop yield and quality, and they are based on physiological and environmental inputs. After molecular discoveries, models should integrate genetic variation to allow predictions that are more genotype-dependent. An interesting approach, Quantitative Trait Locus (QTL)-based ecophysiological modeling, has shown promising results for the design of ideotypes that are adapted to biotic and abiotic stresses, but there are still limitations to attaining a fully integrated model. The aim of this case study is to clarify the impact of choosing different model equations (closely related and with different numbers of parameters) and optimization methods on the detection of QTLs controlling the parameters of crop growth. Different growth equations were parameterized based on a genetic population by following different approaches. The correlations between parameters were analyzed, and two different strategies were adopted to address the correlation issue. QTL analysis was performed on the optimized values of the parameters of the growth equations and on the observed dry mass (DM) data to validate the QTLs detected. Overall, models and strategies resulted in different QTLs being detected. Similar LOD profiles but with peaks of different heights were observed, some of which were significant, resulting in different numbers of QTLs. In some cases, peaks had slightly different positions or were absent. Even closely related growth models led to the detection of different QTLs. The goodness of fit and complexity of the growth models were found to be insufficient to select the best model. Calculating parameters independently of observed data may not be a good strategy, whereas setting parameters independent of the genotype is recommended. Given the large-scale global optimization problem and the strong correlations between parameters, the two algorithms tested showed poor performance. Currently, the lack of effective algorithms is the main obstacle to answering the question posed. The authors therefore suggest testing different model formulations and comparing the QTLs detected before choosing the best formulation to use in an ecophysiological modeling approach based on QTLs.
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Affiliation(s)
- Caterina Barrasso
- GAFL, INRA, 84143, Montfavet, France
- PSH, INRA, 84914, Avignon, France
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Kadam NN, Jagadish SVK, Struik PC, van der Linden CG, Yin X. Incorporating genome-wide association into eco-physiological simulation to identify markers for improving rice yields. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2575-2586. [PMID: 30882149 PMCID: PMC6487590 DOI: 10.1093/jxb/erz120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/11/2019] [Indexed: 05/22/2023]
Abstract
We explored the use of the eco-physiological crop model GECROS to identify markers for improved rice yield under well-watered (control) and water deficit conditions. Eight model parameters were measured from the control in one season for 267 indica genotypes. The model accounted for 58% of yield variation among genotypes under control and 40% under water deficit conditions. Using 213 randomly selected genotypes as the training set, 90 single nucleotide polymorphism (SNP) loci were identified using a genome-wide association study (GWAS), explaining 42-77% of crop model parameter variation. SNP-based parameter values estimated from the additive loci effects were fed into the model. For the training set, the SNP-based model accounted for 37% (control) and 29% (water deficit) of yield variation, less than the 78% explained by a statistical genomic prediction (GP) model for the control treatment. Both models failed in predicting yields of the 54 testing genotypes. However, compared with the GP model, the SNP-based crop model was advantageous when simulating yields under either control or water stress conditions in an independent season. Crop model sensitivity analysis ranked the SNP loci for their relative importance in accounting for yield variation, and the rank differed greatly between control and water deficit environments. Crop models have the potential to use single-environment information for predicting phenotypes under different environments.
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Affiliation(s)
- Niteen N Kadam
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & Research, AK Wageningen, The Netherlands
- International Rice Research Institute, Metro Manila, Philippines
| | - S V Krishna Jagadish
- International Rice Research Institute, Metro Manila, Philippines
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Paul C Struik
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & Research, AK Wageningen, The Netherlands
| | - C Gerard van der Linden
- Plant Breeding, Department of Plant Sciences, Wageningen University & Research, AJ Wageningen, The Netherlands
| | - Xinyou Yin
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & Research, AK Wageningen, The Netherlands
- Correspondence:
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Mathieu A, Vidal T, Jullien A, Wu Q, Chambon C, Bayol B, Cournède PH. A new methodology based on sensitivity analysis to simplify the recalibration of functional-structural plant models in new conditions. ANNALS OF BOTANY 2018; 122:397-408. [PMID: 29924295 PMCID: PMC6110344 DOI: 10.1093/aob/mcy080] [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: 11/30/2017] [Accepted: 04/24/2018] [Indexed: 05/13/2023]
Abstract
Background and Aims Functional-structural plant models (FSPMs) describe explicitly the interactions between plants and their environment at organ to plant scale. However, the high level of description of the structure or model mechanisms makes this type of model very complex and hard to calibrate. A two-step methodology to facilitate the calibration process is proposed here. Methods First, a global sensitivity analysis method was applied to the calibration loss function. It provided first-order and total-order sensitivity indexes that allow parameters to be ranked by importance in order to select the most influential ones. Second, the Akaike information criterion (AIC) was used to quantify the model's quality of fit after calibration with different combinations of selected parameters. The model with the lowest AIC gives the best combination of parameters to select. This methodology was validated by calibrating the model on an independent data set (same cultivar, another year) with the parameters selected in the second step. All the parameters were set to their nominal value; only the most influential ones were re-estimated. Key Results Sensitivity analysis applied to the calibration loss function is a relevant method to underline the most significant parameters in the estimation process. For the studied winter oilseed rape model, 11 out of 26 estimated parameters were selected. Then, the model could be recalibrated for a different data set by re-estimating only three parameters selected with the model selection method. Conclusions Fitting only a small number of parameters dramatically increases the efficiency of recalibration, increases the robustness of the model and helps identify the principal sources of variation in varying environmental conditions. This innovative method still needs to be more widely validated but already gives interesting avenues to improve the calibration of FSPMs.
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Affiliation(s)
- Amélie Mathieu
- UMR ECOSYS, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Tiphaine Vidal
- UMR ECOSYS, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Alexandra Jullien
- UMR ECOSYS, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - QiongLi Wu
- Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | - Camille Chambon
- UMR ECOSYS, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Benoit Bayol
- MICS laboratory, CentraleSupélec, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Paul-Henry Cournède
- MICS laboratory, CentraleSupélec, Université Paris-Saclay, Gif-sur-Yvette, France
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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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11
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Christensen AJ, Srinivasan V, Hart JC, Marshall-Colon A. Use of computational modeling combined with advanced visualization to develop strategies for the design of crop ideotypes to address food security. Nutr Rev 2018; 76:332-347. [PMID: 29562368 PMCID: PMC5892862 DOI: 10.1093/nutrit/nux076] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Sustainable crop production is a contributing factor to current and future food security. Innovative technologies are needed to design strategies that will achieve higher crop yields on less land and with fewer resources. Computational modeling coupled with advanced scientific visualization enables researchers to explore and interact with complex agriculture, nutrition, and climate data to predict how crops will respond to untested environments. These virtual observations and predictions can direct the development of crop ideotypes designed to meet future yield and nutritional demands. This review surveys modeling strategies for the development of crop ideotypes and scientific visualization technologies that have led to discoveries in "big data" analysis. Combined modeling and visualization approaches have been used to realistically simulate crops and to guide selection that immediately enhances crop quantity and quality under challenging environmental conditions. This survey of current and developing technologies indicates that integrative modeling and advanced scientific visualization may help overcome challenges in agriculture and nutrition data as large-scale and multidimensional data become available in these fields.
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Affiliation(s)
- A J Christensen
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Venkatraman Srinivasan
- Pacific Northwest National Laboratory, Richland, Washington, USA, and was with the Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - John C Hart
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Amy Marshall-Colon
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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12
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Pleban JR, Mackay DS, Aston TL, Ewers BE, Weinig C. Phenotypic Trait Identification Using a Multimodel Bayesian Method: A Case Study Using Photosynthesis in Brassica rapa Genotypes. FRONTIERS IN PLANT SCIENCE 2018; 9:448. [PMID: 29719545 PMCID: PMC5913710 DOI: 10.3389/fpls.2018.00448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 03/22/2018] [Indexed: 05/21/2023]
Abstract
Agronomists have used statistical crop models to predict yield on a genotype-by-genotype basis. Mechanistic models, based on fundamental physiological processes common across plant taxa, will ultimately enable yield prediction applicable to diverse genotypes and crops. Here, genotypic information is combined with multiple mechanistically based models to characterize photosynthetic trait differentiation among genotypes of Brassica rapa. Infrared leaf gas exchange and chlorophyll fluorescence observations are analyzed using Bayesian methods. Three advantages of Bayesian approaches are employed: a hierarchical model structure, the testing of parameter estimates with posterior predictive checks and a multimodel complexity analysis. In all, eight models of photosynthesis are compared for fit to data and penalized for complexity using deviance information criteria (DIC) at the genotype scale. The multimodel evaluation improves the credibility of trait estimates using posterior distributions. Traits with important implications for yield in crops, including maximum rate of carboxylation (Vcmax ) and maximum rate of electron transport (Jmax ) show genotypic differentiation. B. rapa shows phenotypic diversity in causal traits with the potential for genetic enhancement of photosynthesis. This multimodel screening represents a statistically rigorous method for characterizing genotypic differences in traits with clear biophysical consequences to growth and productivity within large crop breeding populations with application across plant processes.
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Affiliation(s)
- Jonathan R. Pleban
- Department of Geography, University at Buffalo, Buffalo, NY, United States
- *Correspondence: Jonathan R. Pleban
| | - D. Scott Mackay
- Department of Geography, University at Buffalo, Buffalo, NY, United States
| | - Timothy L. Aston
- Department of Botany, University of Wyoming, Laramie, WY, United States
| | - Brent E. Ewers
- Department of Botany, University of Wyoming, Laramie, WY, United States
- Program in Ecology, University of Wyoming, Laramie, WY, United States
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, United States
- Program in Ecology, University of Wyoming, Laramie, WY, United States
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States
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Rincent R, Kuhn E, Monod H, Oury FX, Rousset M, Allard V, Le Gouis J. Optimization of multi-environment trials for genomic selection based on crop models. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1735-1752. [PMID: 28540573 PMCID: PMC5511605 DOI: 10.1007/s00122-017-2922-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/11/2017] [Indexed: 05/20/2023]
Abstract
We propose a statistical criterion to optimize multi-environment trials to predict genotype × environment interactions more efficiently, by combining crop growth models and genomic selection models. Genotype × environment interactions (GEI) are common in plant multi-environment trials (METs). In this context, models developed for genomic selection (GS) that refers to the use of genome-wide information for predicting breeding values of selection candidates need to be adapted. One promising way to increase prediction accuracy in various environments is to combine ecophysiological and genetic modelling thanks to crop growth models (CGM) incorporating genetic parameters. The efficiency of this approach relies on the quality of the parameter estimates, which depends on the environments composing this MET used for calibration. The objective of this study was to determine a method to optimize the set of environments composing the MET for estimating genetic parameters in this context. A criterion called OptiMET was defined to this aim, and was evaluated on simulated and real data, with the example of wheat phenology. The MET defined with OptiMET allowed estimating the genetic parameters with lower error, leading to higher QTL detection power and higher prediction accuracies. MET defined with OptiMET was on average more efficient than random MET composed of twice as many environments, in terms of quality of the parameter estimates. OptiMET is thus a valuable tool to determine optimal experimental conditions to best exploit MET and the phenotyping tools that are currently developed.
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Affiliation(s)
- R Rincent
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, 63100, Clermont-Ferrand, France.
- Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 63178, Aubière Cedex, France.
| | - E Kuhn
- INRA, MaIAGE, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - H Monod
- INRA, MaIAGE, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - F-X Oury
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, 63100, Clermont-Ferrand, France
- Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 63178, Aubière Cedex, France
| | - M Rousset
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, 63100, Clermont-Ferrand, France
- Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 63178, Aubière Cedex, France
| | - V Allard
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, 63100, Clermont-Ferrand, France
- Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 63178, Aubière Cedex, France
| | - J Le Gouis
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, 63100, Clermont-Ferrand, France
- Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 63178, Aubière Cedex, France
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Génard M, Lescourret F, Bevacqua D, Boivin T. Genotype-by-Environment Interactions Emerge from Simple Assemblages of Mathematical Functions in Ecological Models. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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16
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Constantinescu D, Memmah MM, Vercambre G, Génard M, Baldazzi V, Causse M, Albert E, Brunel B, Valsesia P, Bertin N. Model-Assisted Estimation of the Genetic Variability in Physiological Parameters Related to Tomato Fruit Growth under Contrasted Water Conditions. FRONTIERS IN PLANT SCIENCE 2016; 7:1841. [PMID: 28018381 PMCID: PMC5145867 DOI: 10.3389/fpls.2016.01841] [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: 11/22/2016] [Indexed: 05/25/2023]
Abstract
Drought stress is a major abiotic stress threatening plant and crop productivity. In case of fleshy fruits, understanding mechanisms governing water and carbon accumulations and identifying genes, QTLs and phenotypes, that will enable trade-offs between fruit growth and quality under Water Deficit (WD) condition is a crucial challenge for breeders and growers. In the present work, 117 recombinant inbred lines of a population of Solanum lycopersicum were phenotyped under control and WD conditions. Plant water status, fruit growth and composition were measured and data were used to calibrate a process-based model describing water and carbon fluxes in a growing fruit as a function of plant and environment. Eight genotype-dependent model parameters were estimated using a multiobjective evolutionary algorithm in order to minimize the prediction errors of fruit dry and fresh mass throughout fruit development. WD increased the fruit dry matter content (up to 85%) and decreased its fresh weight (up to 60%), big fruit size genotypes being the most sensitive. The mean normalized root mean squared errors of the predictions ranged between 16-18% in the population. Variability in model genotypic parameters allowed us to explore diverse genetic strategies in response to WD. An interesting group of genotypes could be discriminated in which (i) the low loss of fresh mass under WD was associated with high active uptake of sugars and low value of the maximum cell wall extensibility, and (ii) the high dry matter content in control treatment (C) was associated with a slow decrease of mass flow. Using 501 SNP markers genotyped across the genome, a QTL analysis of model parameters allowed to detect three main QTLs related to xylem and phloem conductivities, on chromosomes 2, 4, and 8. The model was then applied to design ideotypes with high dry matter content in C condition and low fresh mass loss in WD condition. The ideotypes outperformed the RILs especially for large and medium fruit-size genotypes, by combining high pedicel conductance and high active uptake of sugars. Interestingly, five small fruit-size RILs were close to the selected ideotypes, and likely bear interesting traits and alleles for adaptation to WD.
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Affiliation(s)
- Dario Constantinescu
- Plantes et Systèmes de Culture Horticoles, Institut National de la Recherche Agronomique - Centre PACAAvignon, France
| | - Mohamed-Mahmoud Memmah
- Plantes et Systèmes de Culture Horticoles, Institut National de la Recherche Agronomique - Centre PACAAvignon, France
| | - Gilles Vercambre
- Plantes et Systèmes de Culture Horticoles, Institut National de la Recherche Agronomique - Centre PACAAvignon, France
| | - Michel Génard
- Plantes et Systèmes de Culture Horticoles, Institut National de la Recherche Agronomique - Centre PACAAvignon, France
| | - Valentina Baldazzi
- Plantes et Systèmes de Culture Horticoles, Institut National de la Recherche Agronomique - Centre PACAAvignon, France
| | - Mathilde Causse
- Unité Génétique et Amélioration des Fruits et Légumes, Institut National de la Recherche Agronomique – Centre PACAMontfavet, France
| | - Elise Albert
- Unité Génétique et Amélioration des Fruits et Légumes, Institut National de la Recherche Agronomique – Centre PACAMontfavet, France
| | - Béatrice Brunel
- Plantes et Systèmes de Culture Horticoles, Institut National de la Recherche Agronomique - Centre PACAAvignon, France
| | - Pierre Valsesia
- Plantes et Systèmes de Culture Horticoles, Institut National de la Recherche Agronomique - Centre PACAAvignon, France
| | - Nadia Bertin
- Plantes et Systèmes de Culture Horticoles, Institut National de la Recherche Agronomique - Centre PACAAvignon, France
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17
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Duan T, Chapman SC, Holland E, Rebetzke GJ, Guo Y, Zheng B. Dynamic quantification of canopy structure to characterize early plant vigour in wheat genotypes. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4523-34. [PMID: 27312669 PMCID: PMC4973728 DOI: 10.1093/jxb/erw227] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Early vigour is an important physiological trait to improve establishment, water-use efficiency, and grain yield for wheat. Phenotyping large numbers of lines is challenging due to the fast growth and development of wheat seedlings. Here we developed a new photo-based workflow to monitor dynamically the growth and development of the wheat canopy of two wheat lines with a contrasting early vigour trait. Multiview images were taken using a 'vegetation stress' camera at 2 d intervals from emergence to the sixth leaf stage. Point clouds were extracted using the Multi-View Stereo and Structure From Motion (MVS-SFM) algorithm, and segmented into individual organs using the Octree method, with leaf midribs fitted using local polynomial function. Finally, phenotypic parameters were calculated from the reconstructed point cloud including: tiller and leaf number, plant height, Haun index, phyllochron, leaf length, angle, and leaf elongation rate. There was good agreement between the observed and estimated leaf length (RMSE=8.6mm, R (2)=0.98, n=322) across both lines. Significant contrasts of phenotyping parameters were observed between the two lines and were consistent with manual observations. The early vigour line had fewer tillers (2.4±0.6) and larger leaves (308.0±38.4mm and 17.1±2.7mm for leaf length and width, respectively). While the phyllochron of both lines was quite similar, the non-vigorous line had a greater Haun index (more leaves on the main stem) on any date, as the vigorous line had slower development of its first two leaves. The workflow presented in this study provides an efficient method to phenotype individual plants using a low-cost camera (an RGB camera is also suitable) and could be applied in phenotyping for applications in both simulation modelling and breeding. The rapidity and accuracy of this novel method can characterize the results of specific selection criteria (e.g. width of leaf three, number of tillers, rate of leaf appearance) that have been or can now be utilized to breed for early leaf growth and tillering in wheat.
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Affiliation(s)
- T Duan
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China CSIRO Agriculture, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
| | - S C Chapman
- CSIRO Agriculture, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
| | - E Holland
- CSIRO Agriculture, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
| | - G J Rebetzke
- CSIRO Agriculture, PO Box 1600, Canberra, ACT 2601, Australia
| | - Y Guo
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - B Zheng
- CSIRO Agriculture, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
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18
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Dai Z, Wu H, Baldazzi V, van Leeuwen C, Bertin N, Gautier H, Wu B, Duchêne E, Gomès E, Delrot S, Lescourret F, Génard M. Inter-Species Comparative Analysis of Components of Soluble Sugar Concentration in Fleshy Fruits. FRONTIERS IN PLANT SCIENCE 2016; 7:649. [PMID: 27242850 PMCID: PMC4872523 DOI: 10.3389/fpls.2016.00649] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/28/2016] [Indexed: 05/03/2023]
Abstract
The soluble sugar concentration of fleshy fruit is a key determinant of fleshy fruit quality. It affects directly the sweetness of fresh fruits and indirectly the properties of processed products (e.g., alcohol content in wine). Despite considerable divergence among species, soluble sugar accumulation in a fruit results from the complex interplay of three main processes, namely sugar import, sugar metabolism, and water dilution. Therefore, inter-species comparison would help to identify common and/or species-specific modes of regulation in sugar accumulation. For this purpose, a process-based mathematical framework was used to compare soluble sugar accumulation in three fruits: grape, tomato, and peach. Representative datasets covering the time course of sugar accumulation during fruit development were collected. They encompassed 104 combinations of species (3), genotypes (30), and growing conditions (19 years and 16 nutrient and environmental treatments). At maturity, grape showed the highest soluble sugar concentrations (16.5-26.3 g/100 g FW), followed by peach (2.2 to 20 g/100 g FW) and tomato (1.4 to 5 g/100 g FW). Main processes determining soluble sugar concentration were decomposed into sugar importation, metabolism, and water dilution with the process-based analysis. Different regulation modes of soluble sugar concentration were then identified, showing either import-based, dilution-based, or import and dilution dual-based. Firstly, the higher soluble sugar concentration in grape than in tomato is a result of higher sugar importation. Secondly, the higher soluble sugar concentration in grape than in peach is due to a lower water dilution. The third mode of regulation is more complicated than the first two, with differences both in sugar importation and water dilution (grape vs. cherry tomato; cherry tomato vs. peach; peach vs. tomato). On the other hand, carbon utilization for synthesis of non-soluble sugar compounds (namely metabolism) was conserved among the three fruit species. These distinct modes appear to be quite species-specific, but the intensity of the effect may significantly vary depending on the genotype and management practices. These results provide novel insights into the drivers of differences in soluble sugar concentration among fleshy fruits.
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Affiliation(s)
- Zhanwu Dai
- EGFV, Bordeaux Sciences Agro, INRA, Université de BordeauxVillenave d’Ornon, France
| | - Huan Wu
- EGFV, Bordeaux Sciences Agro, INRA, Université de BordeauxVillenave d’Ornon, France
| | | | | | - Nadia Bertin
- INRA, UR1115, Plantes et Systèmes de Culture HorticolesAvignon, France
| | - Hélène Gautier
- INRA, UR1115, Plantes et Systèmes de Culture HorticolesAvignon, France
| | - Benhong Wu
- Institute of Botany – Chinese Academy of SciencesBeijing, China
| | | | - Eric Gomès
- EGFV, Bordeaux Sciences Agro, INRA, Université de BordeauxVillenave d’Ornon, France
| | - Serge Delrot
- EGFV, Bordeaux Sciences Agro, INRA, Université de BordeauxVillenave d’Ornon, France
| | | | - Michel Génard
- INRA, UR1115, Plantes et Systèmes de Culture HorticolesAvignon, France
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Jonas E, de Koning DJ. Goals and hurdles for a successful implementation of genomic selection in breeding programme for selected annual and perennial crops. Biotechnol Genet Eng Rev 2016; 32:18-42. [DOI: 10.1080/02648725.2016.1177377] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Elisabeth Jonas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Ulls väg 26, 75007 Uppsala, Sweden
| | - Dirk Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Ulls väg 26, 75007 Uppsala, Sweden
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20
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Casadebaig P, Zheng B, Chapman S, Huth N, Faivre R, Chenu K. Assessment of the Potential Impacts of Wheat Plant Traits across Environments by Combining Crop Modeling and Global Sensitivity Analysis. PLoS One 2016; 11:e0146385. [PMID: 26799483 PMCID: PMC4723307 DOI: 10.1371/journal.pone.0146385] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 12/16/2015] [Indexed: 12/02/2022] Open
Abstract
A crop can be viewed as a complex system with outputs (e.g. yield) that are affected by inputs of genetic, physiology, pedo-climatic and management information. Application of numerical methods for model exploration assist in evaluating the major most influential inputs, providing the simulation model is a credible description of the biological system. A sensitivity analysis was used to assess the simulated impact on yield of a suite of traits involved in major processes of crop growth and development, and to evaluate how the simulated value of such traits varies across environments and in relation to other traits (which can be interpreted as a virtual change in genetic background). The study focused on wheat in Australia, with an emphasis on adaptation to low rainfall conditions. A large set of traits (90) was evaluated in a wide target population of environments (4 sites × 125 years), management practices (3 sowing dates × 3 nitrogen fertilization levels) and CO2 (2 levels). The Morris sensitivity analysis method was used to sample the parameter space and reduce computational requirements, while maintaining a realistic representation of the targeted trait × environment × management landscape (∼ 82 million individual simulations in total). The patterns of parameter × environment × management interactions were investigated for the most influential parameters, considering a potential genetic range of +/- 20% compared to a reference cultivar. Main (i.e. linear) and interaction (i.e. non-linear and interaction) sensitivity indices calculated for most of APSIM-Wheat parameters allowed the identification of 42 parameters substantially impacting yield in most target environments. Among these, a subset of parameters related to phenology, resource acquisition, resource use efficiency and biomass allocation were identified as potential candidates for crop (and model) improvement.
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Affiliation(s)
| | - Bangyou Zheng
- CSIRO Agriculture, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, QLD 4067, Australia
| | - Scott Chapman
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, QLD 4350, Australia
| | - Neil Huth
- CSIRO Agriculture, 203 Tor Street, Toowoomba, QLD 4350, Australia
| | | | - Karine Chenu
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, 203 Tor Street, Toowoomba, QLD 4350, Australia
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21
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Cirilli M, Bassi D, Ciacciulli A. Sugars in peach fruit: a breeding perspective. HORTICULTURE RESEARCH 2016; 3:15067. [PMID: 26816618 PMCID: PMC4720000 DOI: 10.1038/hortres.2015.67] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/10/2015] [Accepted: 12/10/2015] [Indexed: 05/23/2023]
Abstract
The last decade has been characterized by a decrease in peach (Prunus persica) fruit consumption in many countries, foremost due to unsatisfactory quality. The sugar content is one of the most important quality traits perceived by consumers, and the development of novel peach cultivars with sugar-enhanced content is a primary objective of breeding programs to revert the market inertia. Nevertheless, the progress reachable through classical phenotypic selection is limited by the narrow genetic bases of peach breeding material and by the complex quantitative nature of the trait, which is deeply affected by environmental conditions and agronomical management. The development of molecular markers applicable in MAS or MAB has become an essential strategy to boost the selection efficiency. Despite the enormous advances in 'omics' sciences, providing powerful tools for plant genotyping, the identification of the genetic bases of sugar-related traits is hindered by the lack of adequate phenotyping methods that are able to address strong within-plant variability. This review provides an overview of the current knowledge of the metabolic pathways and physiological mechanisms regulating sugar accumulation in peach fruit, the main advances in phenotyping approaches and genetic background, and finally addressing new research priorities and prospective for breeders.
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Affiliation(s)
- Marco Cirilli
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Angelo Ciacciulli
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, 20133 Milan, Italy
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22
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Dai Z, Wu H, Baldazzi V, van Leeuwen C, Bertin N, Gautier H, Wu B, Duchêne E, Gomès E, Delrot S, Lescourret F, Génard M. Inter-Species Comparative Analysis of Components of Soluble Sugar Concentration in Fleshy Fruits. FRONTIERS IN PLANT SCIENCE 2016. [PMID: 27242850 DOI: 10.3389/fcls.2016.00649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The soluble sugar concentration of fleshy fruit is a key determinant of fleshy fruit quality. It affects directly the sweetness of fresh fruits and indirectly the properties of processed products (e.g., alcohol content in wine). Despite considerable divergence among species, soluble sugar accumulation in a fruit results from the complex interplay of three main processes, namely sugar import, sugar metabolism, and water dilution. Therefore, inter-species comparison would help to identify common and/or species-specific modes of regulation in sugar accumulation. For this purpose, a process-based mathematical framework was used to compare soluble sugar accumulation in three fruits: grape, tomato, and peach. Representative datasets covering the time course of sugar accumulation during fruit development were collected. They encompassed 104 combinations of species (3), genotypes (30), and growing conditions (19 years and 16 nutrient and environmental treatments). At maturity, grape showed the highest soluble sugar concentrations (16.5-26.3 g/100 g FW), followed by peach (2.2 to 20 g/100 g FW) and tomato (1.4 to 5 g/100 g FW). Main processes determining soluble sugar concentration were decomposed into sugar importation, metabolism, and water dilution with the process-based analysis. Different regulation modes of soluble sugar concentration were then identified, showing either import-based, dilution-based, or import and dilution dual-based. Firstly, the higher soluble sugar concentration in grape than in tomato is a result of higher sugar importation. Secondly, the higher soluble sugar concentration in grape than in peach is due to a lower water dilution. The third mode of regulation is more complicated than the first two, with differences both in sugar importation and water dilution (grape vs. cherry tomato; cherry tomato vs. peach; peach vs. tomato). On the other hand, carbon utilization for synthesis of non-soluble sugar compounds (namely metabolism) was conserved among the three fruit species. These distinct modes appear to be quite species-specific, but the intensity of the effect may significantly vary depending on the genotype and management practices. These results provide novel insights into the drivers of differences in soluble sugar concentration among fleshy fruits.
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Affiliation(s)
- Zhanwu Dai
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux Villenave d'Ornon, France
| | - Huan Wu
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux Villenave d'Ornon, France
| | | | | | - Nadia Bertin
- INRA, UR1115, Plantes et Systèmes de Culture Horticoles Avignon, France
| | - Hélène Gautier
- INRA, UR1115, Plantes et Systèmes de Culture Horticoles Avignon, France
| | - Benhong Wu
- Institute of Botany - Chinese Academy of Sciences Beijing, China
| | | | - Eric Gomès
- 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
| | | | - Michel Génard
- INRA, UR1115, Plantes et Systèmes de Culture Horticoles Avignon, France
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Jones JW, He J, Boote KJ, Wilkens P, Porter C, Hu Z. Estimating DSSAT Cropping System Cultivar-Specific Parameters Using Bayesian Techniques. METHODS OF INTRODUCING SYSTEM MODELS INTO AGRICULTURAL RESEARCH 2015. [DOI: 10.2134/advagricsystmodel2.c13] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
| | - Jianqiang He
- INRA, UMR1095, Génétique, Diversité et Ecophysiologie des Céréales; F-63100 Clermont-Ferrand France
| | | | - Paul Wilkens
- International Fertilizer Development Center; Muscle Shoals AL 35662
| | - C.H. Porter
- Dep. of Agricultural and Biological Engineering
| | - Z. Hu
- Dep. of Agricultural and Biological Engineering
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24
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Zheng B, Chapman SC, Christopher JT, Frederiks TM, Chenu K. Frost trends and their estimated impact on yield in the Australian wheatbelt. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3611-23. [PMID: 25922479 PMCID: PMC4463805 DOI: 10.1093/jxb/erv163] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Radiant spring frosts occurring during reproductive developmental stages can result in catastrophic yield loss for wheat producers. To better understand the spatial and temporal variability of frost, the occurrence and impact of frost events on rain-fed wheat production was estimated across the Australian wheatbelt for 1957-2013 using a 0.05 ° gridded weather data set. Simulated yield outcomes at 60 key locations were compared with those for virtual genotypes with different levels of frost tolerance. Over the last six decades, more frost events, later last frost day, and a significant increase in frost impact on yield were found in certain regions of the Australian wheatbelt, in particular in the South-East and West. Increasing trends in frost-related yield losses were simulated in regions where no significant trend of frost occurrence was observed, due to higher mean temperatures accelerating crop development and causing sensitive post-heading stages to occur earlier, during the frost risk period. Simulations indicated that with frost-tolerant lines the mean national yield could be improved by up to 20% through (i) reduced frost damage (~10% improvement) and (ii) the ability to use earlier sowing dates (adding a further 10% improvement). In the simulations, genotypes with an improved frost tolerance to temperatures 1 °C lower than the current 0 °C reference provided substantial benefit in most cropping regions, while greater tolerance (to 3 °C lower temperatures) brought further benefits in the East. The results indicate that breeding for improved reproductive frost tolerance should remain a priority for the Australian wheat industry, despite warming climates.
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Affiliation(s)
- Bangyou Zheng
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
| | - Scott C Chapman
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
| | - Jack T Christopher
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Leslie Research Facility, PO Box 2282 Toowoomba, QLD 4350, Australia
| | - Troy M Frederiks
- Queensland Department of Agriculture, Fisheries and Forestry (DAFFQ), Leslie Research Facility, PO Box 2282 Toowoomba, QLD 4350, Australia
| | - Karine Chenu
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), 203 Tor Street, Toowoomba, QLD 4350, Australia
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Martre P, He J, Le Gouis J, Semenov MA. In silico system analysis of physiological traits determining grain yield and protein concentration for wheat as influenced by climate and crop management. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3581-98. [PMID: 25810069 PMCID: PMC4463803 DOI: 10.1093/jxb/erv049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Genetic improvement of grain yield (GY) and grain protein concentration (GPC) is impeded by large genotype×environment×management interactions and by compensatory effects between traits. Here global uncertainty and sensitivity analyses of the process-based wheat model SiriusQuality2 were conducted with the aim of identifying candidate traits to increase GY and GPC. Three contrasted European sites were selected and simulations were performed using long-term weather data and two nitrogen (N) treatments in order to quantify the effect of parameter uncertainty on GY and GPC under variable environments. The overall influence of all 75 plant parameters of SiriusQuality2 was first analysed using the Morris method. Forty-one influential parameters were identified and their individual (first-order) and total effects on the model outputs were investigated using the extended Fourier amplitude sensitivity test. The overall effect of the parameters was dominated by their interactions with other parameters. Under high N supply, a few influential parameters with respect to GY were identified (e.g. radiation use efficiency, potential duration of grain filling, and phyllochron). However, under low N, >10 parameters showed similar effects on GY and GPC. All parameters had opposite effects on GY and GPC, but leaf and stem N storage capacity appeared as good candidate traits to change the intercept of the negative relationship between GY and GPC. This study provides a system analysis of traits determining GY and GPC under variable environments and delivers valuable information to prioritize model development and experimental work.
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Affiliation(s)
- Pierre Martre
- INRA, UMR1095 Genetic, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, Clermont-Ferrand F-63100, France Blaise Pascal University, UMR1095 Genetic, Diversity and Ecophysiology of Cereals, Aubière F-63177, France
| | - Jianqiang He
- INRA, UMR1095 Genetic, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, Clermont-Ferrand F-63100, France Blaise Pascal University, UMR1095 Genetic, Diversity and Ecophysiology of Cereals, Aubière F-63177, France
| | - Jacques Le Gouis
- INRA, UMR1095 Genetic, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, Clermont-Ferrand F-63100, France Blaise Pascal University, UMR1095 Genetic, Diversity and Ecophysiology of Cereals, Aubière F-63177, France
| | - Mikhail A Semenov
- Department of Computational and Systems Biology, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
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Reuning GA, Bauerle WL, Mullen JL, McKay JK. Combining quantitative trait loci analysis with physiological models to predict genotype-specific transpiration rates. PLANT, CELL & ENVIRONMENT 2015; 38:710-717. [PMID: 25124388 DOI: 10.1111/pce.12429] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 08/05/2014] [Accepted: 08/06/2014] [Indexed: 06/03/2023]
Abstract
Transpiration is controlled by evaporative demand and stomatal conductance (gs ), and there can be substantial genetic variation in gs . A key parameter in empirical models of transpiration is minimum stomatal conductance (g0 ), a trait that can be measured and has a large effect on gs and transpiration. In Arabidopsis thaliana, g0 exhibits both environmental and genetic variation, and quantitative trait loci (QTL) have been mapped. We used this information to create a genetically parameterized empirical model to predict transpiration of genotypes. For the parental lines, this worked well. However, in a recombinant inbred population, the predictions proved less accurate. When based only upon their genotype at a single g0 QTL, genotypes were less distinct than our model predicted. Follow-up experiments indicated that both genotype by environment interaction and a polygenic inheritance complicate the application of genetic effects into physiological models. The use of ecophysiological or 'crop' models for predicting transpiration of novel genetic lines will benefit from incorporating further knowledge of the genetic control and degree of independence of core traits/parameters underlying gs variation.
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Affiliation(s)
- Gretchen A Reuning
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523-1173, USA
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Martre P, Wallach D, Asseng S, Ewert F, Jones JW, Rötter RP, Boote KJ, Ruane AC, Thorburn PJ, Cammarano D, Hatfield JL, Rosenzweig C, Aggarwal PK, Angulo C, Basso B, Bertuzzi P, Biernath C, Brisson N, Challinor AJ, Doltra J, Gayler S, Goldberg R, Grant RF, Heng L, Hooker J, Hunt LA, Ingwersen J, Izaurralde RC, Kersebaum KC, Müller C, Kumar SN, Nendel C, O'leary G, Olesen JE, Osborne TM, Palosuo T, Priesack E, Ripoche D, Semenov MA, Shcherbak I, Steduto P, Stöckle CO, Stratonovitch P, Streck T, Supit I, Tao F, Travasso M, Waha K, White JW, Wolf J. Multimodel ensembles of wheat growth: many models are better than one. GLOBAL CHANGE BIOLOGY 2015; 21:911-25. [PMID: 25330243 DOI: 10.1111/gcb.12768] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 08/07/2014] [Accepted: 09/25/2014] [Indexed: 05/18/2023]
Abstract
Crop models of crop growth are increasingly used to quantify the impact of global changes due to climate or crop management. Therefore, accuracy of simulation results is a major concern. Studies with ensembles of crop models can give valuable information about model accuracy and uncertainty, but such studies are difficult to organize and have only recently begun. We report on the largest ensemble study to date, of 27 wheat models tested in four contrasting locations for their accuracy in simulating multiple crop growth and yield variables. The relative error averaged over models was 24-38% for the different end-of-season variables including grain yield (GY) and grain protein concentration (GPC). There was little relation between error of a model for GY or GPC and error for in-season variables. Thus, most models did not arrive at accurate simulations of GY and GPC by accurately simulating preceding growth dynamics. Ensemble simulations, taking either the mean (e-mean) or median (e-median) of simulated values, gave better estimates than any individual model when all variables were considered. Compared to individual models, e-median ranked first in simulating measured GY and third in GPC. The error of e-mean and e-median declined with an increasing number of ensemble members, with little decrease beyond 10 models. We conclude that multimodel ensembles can be used to create new estimators with improved accuracy and consistency in simulating growth dynamics. We argue that these results are applicable to other crop species, and hypothesize that they apply more generally to ecological system models.
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Affiliation(s)
- Pierre Martre
- INRA, UMR1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 chemin de Beaulieu, F-63 100, Clermont-Ferrand, France; Blaise Pascal University, UMR1095 GDEC, F-63 170, Aubière, France
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28
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Bogard M, Ravel C, Paux E, Bordes J, Balfourier F, Chapman SC, Le Gouis J, Allard V. Predictions of heading date in bread wheat (Triticum aestivum L.) using QTL-based parameters of an ecophysiological model. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5849-65. [PMID: 25148833 PMCID: PMC4203124 DOI: 10.1093/jxb/eru328] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Prediction of wheat phenology facilitates the selection of cultivars with specific adaptations to a particular environment. However, while QTL analysis for heading date can identify major genes controlling phenology, the results are limited to the environments and genotypes tested. Moreover, while ecophysiological models allow accurate predictions in new environments, they may require substantial phenotypic data to parameterize each genotype. Also, the model parameters are rarely related to all underlying genes, and all the possible allelic combinations that could be obtained by breeding cannot be tested with models. In this study, a QTL-based model is proposed to predict heading date in bread wheat (Triticum aestivum L.). Two parameters of an ecophysiological model (V sat and P base , representing genotype vernalization requirements and photoperiod sensitivity, respectively) were optimized for 210 genotypes grown in 10 contrasting location × sowing date combinations. Multiple linear regression models predicting V sat and P base with 11 and 12 associated genetic markers accounted for 71 and 68% of the variance of these parameters, respectively. QTL-based V sat and P base estimates were able to predict heading date of an independent validation data set (88 genotypes in six location × sowing date combinations) with a root mean square error of prediction of 5 to 8.6 days, explaining 48 to 63% of the variation for heading date. The QTL-based model proposed in this study may be used for agronomic purposes and to assist breeders in suggesting locally adapted ideotypes for wheat phenology.
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Affiliation(s)
- Matthieu Bogard
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - Catherine Ravel
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - Etienne Paux
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - Jacques Bordes
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - François Balfourier
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - Scott C Chapman
- CSIRO, Queensland Bioscience Precinct - St Lucia, 306 Carmody Road, St Lucia QLD 4067, Australia
| | - Jacques Le Gouis
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
| | - Vincent Allard
- INRA, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, 5 chemin de Beaulieu, F-63039 Clermont-Ferrand, France Université Blaise Pascal, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, F-63177 Aubière Cedex, France
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29
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Gu J, Yin X, Zhang C, Wang H, Struik PC. Linking ecophysiological modelling with quantitative genetics to support marker-assisted crop design for improved yields of rice (Oryza sativa) under drought stress. ANNALS OF BOTANY 2014; 114:499-511. [PMID: 24984712 PMCID: PMC4204662 DOI: 10.1093/aob/mcu127] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 05/08/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS Genetic markers can be used in combination with ecophysiological crop models to predict the performance of genotypes. Crop models can estimate the contribution of individual markers to crop performance in given environments. The objectives of this study were to explore the use of crop models to design markers and virtual ideotypes for improving yields of rice (Oryza sativa) under drought stress. METHODS Using the model GECROS, crop yield was dissected into seven easily measured parameters. Loci for these parameters were identified for a rice population of 94 introgression lines (ILs) derived from two parents differing in drought tolerance. Marker-based values of ILs for each of these parameters were estimated from additive allele effects of the loci, and were fed to the model in order to simulate yields of the ILs grown under well-watered and drought conditions and in order to design virtual ideotypes for those conditions. KEY RESULTS To account for genotypic yield differences, it was necessary to parameterize the model for differences in an additional trait 'total crop nitrogen uptake' (Nmax) among the ILs. Genetic variation in Nmax had the most significant effect on yield; five other parameters also significantly influenced yield, but seed weight and leaf photosynthesis did not. Using the marker-based parameter values, GECROS also simulated yield variation among 251 recombinant inbred lines of the same parents. The model-based dissection approach detected more markers than the analysis using only yield per se. Model-based sensitivity analysis ranked all markers for their importance in determining yield differences among the ILs. Virtual ideotypes based on markers identified by modelling had 10-36 % more yield than those based on markers for yield per se. CONCLUSIONS This study outlines a genotype-to-phenotype approach that exploits the potential value of marker-based crop modelling in developing new plant types with high yields. The approach can provide more markers for selection programmes for specific environments whilst also allowing for prioritization. Crop modelling is thus a powerful tool for marker design for improved rice yields and for ideotyping under contrasting conditions.
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Affiliation(s)
- Junfei Gu
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University, PO Box 430, 6700 AK Wageningen, The Netherlands
| | - Xinyou Yin
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University, PO Box 430, 6700 AK Wageningen, The Netherlands
| | - Chengwei Zhang
- Plant Breeding & Genetics, China Agricultural University, 100193 Beijing, PR China
| | - Huaqi Wang
- Plant Breeding & Genetics, China Agricultural University, 100193 Beijing, PR China
| | - Paul C Struik
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University, PO Box 430, 6700 AK Wageningen, The Netherlands
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30
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Ripoll J, Urban L, Staudt M, Lopez-Lauri F, Bidel LPR, Bertin N. Water shortage and quality of fleshy fruits--making the most of the unavoidable. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4097-117. [PMID: 24821951 DOI: 10.1093/jxb/eru197] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Extreme climatic events, including drought, are predicted to increase in intensity, frequency, and geographic extent as a consequence of global climate change. In general, to grow crops successfully in the future, growers will need to adapt to less available water and to take better advantage of the positive effects of drought. Fortunately, there are positive effects associated with drought. Drought stimulates the secondary metabolism, thereby potentially increasing plant defences and the concentrations of compounds involved in plant quality, particularly taste and health benefits. The role of drought on the production of secondary metabolites is of paramount importance for fruit crops. However, to manage crops effectively under conditions of limited water supply, for example by applying deficit irrigation, growers must consider not only the impact of drought on productivity but also on how plants manage the primary and secondary metabolisms. This question is obviously complex because during water deficit, trade-offs among productivity, defence, and quality depend upon the intensity, duration, and repetition of events of water deficit. The stage of plant development during the period of water deficit is also crucial, as are the effects of other stressors. In addition, growers must rely on relevant indicators of water status, i.e. parameters involved in the relevant metabolic processes, including those affecting quality. Although many reports on the effects of drought on plant function and crop productivity have been published, these issues have not been reviewed thus far. Here, we provide an up-to-date review of current knowledge of the effects of different forms of drought on fruit quality relative to the primary and secondary metabolisms and their interactions. We also review conventional and less conventional indicators of water status that could be used for monitoring purposes, such as volatile compounds. We focus on fruit crops owing to the importance of secondary metabolism in fruit quality and the importance of fruits in the human diet. The issue of defence is also briefly discussed.
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Affiliation(s)
- Julie Ripoll
- INRA - Centre d'Avignon, UR 1115 Plantes et Systèmes de culture Horticoles, Domaine Saint Paul - Site Agroparc, 228 route de l'Aérodrome, CS 40509, 84914 Avignon Cedex 9, France Laboratoire de Physiologie des Fruits et Légumes, Université d'Avignon et des Pays du Vaucluse, Bât. Agrosciences, 301 rue Baruch de Spinoza, B.p. 21239, F-84916 Avignon Cedex 9, France
| | - Laurent Urban
- Laboratoire de Physiologie des Fruits et Légumes, Université d'Avignon et des Pays du Vaucluse, Bât. Agrosciences, 301 rue Baruch de Spinoza, B.p. 21239, F-84916 Avignon Cedex 9, France
| | - Michael Staudt
- Centre d'Ecologie Fonctionnelle et Evolutive Montpellier, CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| | - Félicie Lopez-Lauri
- Laboratoire de Physiologie des Fruits et Légumes, Université d'Avignon et des Pays du Vaucluse, Bât. Agrosciences, 301 rue Baruch de Spinoza, B.p. 21239, F-84916 Avignon Cedex 9, France
| | - Luc P R Bidel
- INRA, UMR AGAP, Place P. Viala, F-34060 Montpellier, France
| | - Nadia Bertin
- INRA - Centre d'Avignon, UR 1115 Plantes et Systèmes de culture Horticoles, Domaine Saint Paul - Site Agroparc, 228 route de l'Aérodrome, CS 40509, 84914 Avignon Cedex 9, France
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31
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Fanciullino AL, Bidel LPR, Urban L. Carotenoid responses to environmental stimuli: integrating redox and carbon controls into a fruit model. PLANT, CELL & ENVIRONMENT 2014; 37:273-89. [PMID: 23777240 DOI: 10.1111/pce.12153] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 06/05/2013] [Accepted: 06/06/2013] [Indexed: 05/20/2023]
Abstract
Carotenoids play an important role in plant adaptation to fluctuating environments as well as in the human diet by contributing to the prevention of chronic diseases. Insights have been gained recently into the way individual factors, genetic, environmental or developmental, control the carotenoid biosynthetic pathway at the molecular level. The identification of the rate-limiting steps of carotenogenesis has paved the way for programmes of breeding, and metabolic engineering, aimed at increasing the concentration of carotenoids in different crop species. However, the complexity that arises from the interactions between the different factors as well as from the coordination between organs remains poorly understood. This review focuses on recent advances in carotenoid responses to environmental stimuli and discusses how the interactions between the modulation factors and between organs affect carotenoid build-up. We develop the idea that reactive oxygen species/redox status and sugars/carbon status can be considered as integrated factors that account for most effects of the major environmental factors influencing carotenoid biosynthesis. The discussion highlights the concept of carotenoids or carotenoid-derivatives as stress signals that may be involved in feedback controls. We propose a conceptual model of the effects of environmental and developmental factors on carotenoid build-up in fruits.
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Affiliation(s)
- A L Fanciullino
- UR 1115 Plantes et Systèmes de Culture Horticoles, INRA, Avignon, Cedex, 9, France
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32
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Kromdijk J, Bertin N, Heuvelink E, Molenaar J, de Visser PHB, Marcelis LFM, Struik PC. Crop management impacts the efficiency of quantitative trait loci (QTL) detection and use: case study of fruit load×QTL interactions. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:11-22. [PMID: 24227339 DOI: 10.1093/jxb/ert365] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Mapping studies using populations with introgressed marker-defined genomic regions are continuously increasing knowledge about quantitative trait loci (QTL) that correlate with variation in important crop traits. This knowledge is useful for plant breeding, although combining desired traits in one genotype might be complicated by the mode of inheritance and co-localization of QTL with antagonistic effects, and by physiological trade-offs, and feed-back or feed-forward mechanisms. Therefore, integrating advances at the genetic level with insight into influences of environment and crop management on crop performance remains difficult. Whereas mapping studies can pinpoint correlations between QTL and phenotypic traits for specific conditions, ignoring or overlooking the importance of environment or crop management can jeopardize the relevance of such assessments. Here, we focus on fruit load (a measure determining competition among fruits on one plant) and its strong modulation of QTL effects on fruit size and composition. Following an integral approach, we show which fruit traits are affected by fruit load, to which underlying processes these traits can be linked, and which processes at lower and higher integration levels are affected by fruit load (and subsequently influence fruit traits). This opinion paper (i) argues that a mechanistic framework to interpret interactions between fruit load and QTL effects is needed, (ii) pleads for consideration of the context of agronomic management when detecting QTL, (iii) makes a case for incorporating interacting factors in the experimental set-up of QTL mapping studies, and (iv) provides recommendations to improve efficiency in QTL detection and use, with particular focus on model-based marker-assisted breeding.
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Affiliation(s)
- J Kromdijk
- Wageningen UR Greenhouse Horticulture, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Zheng B, Biddulph B, Li D, Kuchel H, Chapman S. Quantification of the effects of VRN1 and Ppd-D1 to predict spring wheat (Triticum aestivum) heading time across diverse environments. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:3747-61. [PMID: 23873997 PMCID: PMC3745732 DOI: 10.1093/jxb/ert209] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Heading time is a major determinant of the adaptation of wheat to different environments, and is critical in minimizing risks of frost, heat, and drought on reproductive development. Given that major developmental genes are known in wheat, a process-based model, APSIM, was modified to incorporate gene effects into estimation of heading time, while minimizing degradation in the predictive capability of the model. Model parameters describing environment responses were replaced with functions of the number of winter and photoperiod (PPD)-sensitive alleles at the three VRN1 loci and the Ppd-D1 locus, respectively. Two years of vernalization and PPD trials of 210 lines (spring wheats) at a single location were used to estimate the effects of the VRN1 and Ppd-D1 alleles, with validation against 190 trials (~4400 observations) across the Australian wheatbelt. Compared with spring genotypes, winter genotypes for Vrn-A1 (i.e. with two winter alleles) had a delay of 76.8 degree days (°Cd) in time to heading, which was double the effect of the Vrn-B1 or Vrn-D1 winter genotypes. Of the three VRN1 loci, winter alleles at Vrn-B1 had the strongest interaction with PPD, delaying heading time by 99.0 °Cd under long days. The gene-based model had root mean square error of 3.2 and 4.3 d for calibration and validation datasets, respectively. Virtual genotypes were created to examine heading time in comparison with frost and heat events and showed that new longer-season varieties could be heading later (with potential increased yield) when sown early in season. This gene-based model allows breeders to consider how to target gene combinations to current and future production environments using parameters determined from a small set of phenotyping treatments.
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Affiliation(s)
- Bangyou Zheng
- CSIRO Plant Industry and Climate Adaptation Flagship, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, 4067, QLD, Australia
| | - Ben Biddulph
- Department of Agriculture and Food, Western Australia, 3 Baron-Hay Court, South Perth, 6151, WA, Australia
| | - Dora Li
- Department of Agriculture and Food, Western Australia, 3 Baron-Hay Court, South Perth, 6151, WA, Australia
| | - Haydn Kuchel
- Australian Grain Technologies Pty Ltd,Perkins Building, Roseworthy Campus, Roseworthy, 5371, WA, Australia
| | - Scott Chapman
- CSIRO Plant Industry and Climate Adaptation Flagship, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, 4067, QLD, Australia
- * To whom correspondence should be addressed.
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Etienne A, Génard M, Lobit P, Mbeguié-A-Mbéguié D, Bugaud C. What controls fleshy fruit acidity? A review of malate and citrate accumulation in fruit cells. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:1451-69. [PMID: 23408829 DOI: 10.1093/jxb/ert035] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Fleshy fruit acidity is an important component of fruit organoleptic quality and is mainly due to the presence of malic and citric acids, the main organic acids found in most ripe fruits. The accumulation of these two acids in fruit cells is the result of several interlinked processes that take place in different compartments of the cell and appear to be under the control of many factors. This review combines analyses of transcriptomic, metabolomic, and proteomic data, and fruit process-based simulation models of the accumulation of citric and malic acids, to further our understanding of the physiological mechanisms likely to control the accumulation of these two acids during fruit development. The effects of agro-environmental factors, such as the source:sink ratio, water supply, mineral nutrition, and temperature, on citric and malic acid accumulation in fruit cells have been reported in several agronomic studies. This review sheds light on the interactions between these factors and the metabolism and storage of organic acids in the cell.
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Affiliation(s)
- A Etienne
- Centre de Coopération International en Recherche Agronomique pour le Développement (CIRAD), UMR QUALISUD, Pôle de Recherche Agronomique de Martinique, BP 214, 97 285 Lamentin Cedex 2, France
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Dreccer MF, Chapman SC, Rattey AR, Neal J, Song Y, Christopher JJT, Reynolds M. Developmental and growth controls of tillering and water-soluble carbohydrate accumulation in contrasting wheat (Triticum aestivum L.) genotypes: can we dissect them? JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:143-60. [PMID: 23213136 PMCID: PMC3528026 DOI: 10.1093/jxb/ers317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
In wheat, tillering and water-soluble carbohydrates (WSCs) in the stem are potential traits for adaptation to different environments and are of interest as targets for selective breeding. This study investigated the observation that a high stem WSC concentration (WSCc) is often related to low tillering. The proposition tested was that stem WSC accumulation is plant density dependent and could be an emergent property of tillering, whether driven by genotype or by environment. A small subset of recombinant inbred lines (RILs) contrasting for tillering was grown at different plant densities or on different sowing dates in multiple field experiments. Both tillering and WSCc were highly influenced by the environment, with a smaller, distinct genotypic component; the genotype × environment range covered 350-750 stems m(-2) and 25-210 mg g(-1) WSCc. Stem WSCc was inversely related to stem number m(-2), but genotypic rankings for stem WSCc persisted when RILs were compared at similar stem density. Low tillering-high WSCc RILs had similar leaf area index, larger individual leaves, and stems with larger internode cross-section and wall area when compared with high tillering-low WSCc RILs. The maximum number of stems per plant was positively associated with growth and relative growth rate per plant, tillering rate and duration, and also, in some treatments, with leaf appearance rate and final leaf number. A common threshold of the red:far red ratio (0.39-0.44; standard error of the difference=0.055) coincided with the maximum stem number per plant across genotypes and plant densities, and could be effectively used in crop simulation modelling as a 'cut-off' rule for tillering. The relationship between tillering, WSCc, and their component traits, as well as the possible implications for crop simulation and breeding, is discussed.
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Affiliation(s)
- M Fernanda Dreccer
- CSIRO Plant Industry, Cooper Laboratory, PO Box 863, University of Queensland, Warrego Highway, Gatton, QLD 4343, Australia.
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White JW, Andrade-Sanchez P, Gore MA, Bronson KF, Coffelt TA, Conley MM, Feldmann KA, French AN, Heun JT, Hunsaker DJ, Jenks MA, Kimball BA, Roth RL, Strand RJ, Thorp KR, Wall GW, Wang G. Field-based phenomics for plant genetics research. FIELD CROPS RESEARCH 2012; 133:101-112. [PMID: 0 DOI: 10.1016/j.fcr.2012.04.003] [Citation(s) in RCA: 231] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
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Gu J, Yin X, Struik PC, Stomph TJ, Wang H. Using chromosome introgression lines to map quantitative trait loci for photosynthesis parameters in rice (Oryza sativa L.) leaves under drought and well-watered field conditions. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:455-69. [PMID: 21984650 PMCID: PMC3245479 DOI: 10.1093/jxb/err292] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 07/25/2011] [Accepted: 08/18/2011] [Indexed: 05/21/2023]
Abstract
Photosynthesis is fundamental to biomass production, but sensitive to drought. To understand the genetics of leaf photosynthesis, especially under drought, upland rice cv. Haogelao, lowland rice cv. Shennong265, and 94 of their introgression lines (ILs) were studied at flowering and grain filling under drought and well-watered field conditions. Gas exchange and chlorophyll fluorescence measurements were conducted to evaluate eight photosynthetic traits. Since these traits are very sensitive to fluctuations in microclimate during measurements under field conditions, observations were adjusted for microclimatic differences through both a statistical covariant model and a physiological approach. Both approaches identified leaf-to-air vapour pressure difference as the variable influencing the traits most. Using the simple sequence repeat (SSR) linkage map for the IL population, 1-3 quantitative trait loci (QTLs) were detected per trait-stage-treatment combination, which explained between 7.0% and 30.4% of the phenotypic variance of each trait. The clustered QTLs near marker RM410 (the interval from 57.3 cM to 68.4 cM on chromosome 9) were consistent over both development stages and both drought and well-watered conditions. This QTL consistency was verified by a greenhouse experiment under a controlled environment. The alleles from the upland rice at this interval had positive effects on net photosynthetic rate, stomatal conductance, transpiration rate, quantum yield of photosystem II (PSII), and the maximum efficiency of light-adapted open PSII. However, the allele of another main QTL from upland rice was associated with increased drought sensitivity of photosynthesis. These results could potentially be used in breeding programmes through marker-assisted selection to improve drought tolerance and photosynthesis simultaneously.
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Affiliation(s)
- Junfei Gu
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University, PO Box 430, 6700 AK Wageningen, The Netherlands
| | - Xinyou Yin
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University, PO Box 430, 6700 AK Wageningen, The Netherlands
| | - Paul C. Struik
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University, PO Box 430, 6700 AK Wageningen, The Netherlands
| | - Tjeerd Jan Stomph
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University, PO Box 430, 6700 AK Wageningen, The Netherlands
| | - Huaqi Wang
- Plant Breeding & Genetics, China Agricultural University, 100193 Beijing, PR China
- To whom correspondence should be addressed.
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Martre P, Bertin N, Salon C, Génard M. Modelling the size and composition of fruit, grain and seed by process-based simulation models. THE NEW PHYTOLOGIST 2011; 191:601-618. [PMID: 21649661 DOI: 10.1111/j.1469-8137.2011.03747.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Understanding what determines the size and composition of fruit, grain and seed in response to the environment and genotype is challenging, as these traits result from several linked processes controlled at different levels of organization, from the subcellular to the crop level, with subtle interactions occurring at or between the levels of organization. Process-based simulation models (PBSMs) implement algorithms to simulate metabolic and biophysical aspects of cell, tissue and organ behaviour. In this review, fruit, grain and seed PBSMs describing the main phases of growth, development and storage metabolism are discussed. From this concurrent work, it is possible to identify generic storage organ processes which can be modelled similarly for fruit, grain and seed. Spatial heterogeneity at the tissue and whole-plant level is found to be a key consideration in modelling the effects of the environment and genotype on fruit, grain and seed end-use value. In the future, PBSMs may well become the main link between studies at the molecular and whole-plant levels. To bridge this phenotype-to-genotype gap, future models need to remain plastic without becoming overparameterized.
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Affiliation(s)
- Pierre Martre
- INRA, UMR 1095 Genetics, Diversity, and Ecophysiology of Cereals (GDEC), 234 Avenue du Brezet, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR 1095 GDEC, F-63177 Aubière, France
| | - Nadia Bertin
- INRA, UR 1115 Plantes et Systèmes de Culture Horticoles, F-84914 Avignon, France
| | - Christophe Salon
- INRA, UMR 102 Génétique et Ecophysiologie des Légumineuses (LEG), BP 86510, F-21065 Dijon, France
- AgroSup Dijon, UMR102 LEG, F-21065 Dijon, France
| | - Michel Génard
- INRA, UR 1115 Plantes et Systèmes de Culture Horticoles, F-84914 Avignon, France
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Messina CD, Podlich D, Dong Z, Samples M, Cooper M. Yield-trait performance landscapes: from theory to application in breeding maize for drought tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:855-68. [PMID: 21041371 DOI: 10.1093/jxb/erq329] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The effectiveness of breeding strategies to increase drought resistance in crops could be increased further if some of the complexities in gene-to-phenotype (G → P) relations associated with epistasis, pleiotropy, and genotype-by-environment interactions could be captured in realistic G → P models, and represented in a quantitative manner useful for selection. This paper outlines a promising methodology. First, the concept of landscapes was extended from the study of fitness landscapes used in evolutionary genetics to the characterization of yield-trait-performance landscapes for agricultural environments and applications in plant breeding. Second, the E(NK) model of trait genetic architecture was extended to incorporate biophysical, physiological, and statistical components. Third, a graphical representation is proposed to visualize the yield-trait performance landscape concept for use in selection decisions. The methodology was demonstrated at a particular stage of a maize breeding programme with the objective of improving the drought tolerance of maize hybrids for the US Western Corn-Belt. The application of the framework to the genetic improvement of drought tolerance in maize supported selection of Doubled Haploid (DH) lines with improved levels of drought tolerance based on physiological genetic knowledge, prediction of test-cross yield within the target population of environments, and their predicted potential to sustain further genetic progress with additional cycles of selection. The existence of rugged yield-performance landscapes with multiple peaks and intervening valleys of lower performance, as shown in this study, supports the proposition that phenotyping strategies, and the directions emphasized in genomic selection can be improved by creating knowledge of the topology of yield-trait performance landscapes.
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Affiliation(s)
- Carlos D Messina
- Pioneer Hi-Bred, A DuPont Business, 7250 NW 62nd Avenue, Johnston, IA 50131, USA.
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