Crop Systems Biology

Xinyou Yin • Paul C. Struik Editors

Crop Systems Biology Narrowing the Gaps between Crop Modelling and Genetics

Editors Xinyou Yin Department of Plant Sciences, Centre for Crop Systems Analysis Wageningen University Wageningen, The Netherlands

Paul C. Struik Department of Plant Sciences, Centre for Crop Systems Analysis Wageningen University Wageningen, The Netherlands

ISBN 978-3-319-20561-8 ISBN 978-3-319-20562-5 DOI 10.1007/978-3-319-20562-5

(eBook)

Library of Congress Control Number: 2015953437 Springer Cham Heidelberg New York Dordrecht London © Springer International Publishing Switzerland 2016 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper Springer International Publishing AG Switzerland is part of Springer Science+Business Media (www. springer.com)

Preface

The sequencing of genomes has been completed for an increasing number of crop species, and researchers have now succeeded in isolating and characterising many important genes and quantitative trait loci. High expectations from genomics, however, are waving back towards the recognition that crop physiology is also important for realistic improvement of crop productivity. Complex processes and networks along various hierarchical levels of crop growth can be thoroughly understood with the help of their mathematical description – modelling. The further practical application of these understandings also requires the discovery of emerging properties and quantitative predictions. In order to better support design, engineering and breeding for new crops and cultivars for improving agricultural production under global warming and climate change, there is an increasing call for an interdisciplinary research approach, which combines modern genetics and genomics, traditional physiology and biochemistry and advanced bioinformatics and crop modelling. Recently we coined a term ‘crop systems biology’ to describe such an interdisciplinary approach. Such an interdisciplinary research has been practised in various research groups across the globe. However, it does not seem to be fully covered in the format of book publications. We, therefore, initiated this book project on ‘crop systems biology – narrowing the gaps between crop modelling and genetics’, in response to an invitation by Springer Science + Business Media. Nine chapters written by leading groups active in this field are presented in the book, representing the state of the art in the realm of this research covering various traits in several crops. Baldazzi et al. describe gene regulatory and metabolic networks, link these networks to crop models and show how to integrate different temporal and spatial scales within a single model, thus illustrating the perspectives for multi-scale modelling. Xu and Buck-Sorlin describe a three-dimensional modelling approach called Functional-Structural Plant Modelling and link it to quantitative trait loci analysis in rice. They use this framework to analyse opportunities and pitfalls to advance breeding for architectural traits. Bustos et al. discuss prediction strategies for genotype-by-environment interactions using statistical models, crop growth models and combinations of v

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Preface

model types. They illustrate how prediction accuracy can profit from the large data sets available on environmental and genotypic variables by integrating physiological and statistical knowledge. Génard et al. show how knowledge generated by in silico profiling can be used to unravel genotype × environment × management interactions and to construct plant ideotypes for particular conditions, using examples for fruit quality, sensitivity to diseases and root system architecture. Luquet et al. describe a model that combines characteristics of functionalstructural modelling approaches with classical crop growth models. They use this model to analyse the trade-off between early vigour and drought tolerance in rice and to design rice ideotypes that combine the two traits. Sinclair et al. describe the steps of modelling-physiology-transcriptomicsgenetic screening they followed in developing soybean cultivars with restricted transpiration. The yield increases obtained in experiments and in model simulations for years with limited rainfall prove that this trait is highly desirable. Hammer et al. argue that crop ecophysiology and functional modelling can effectively link processes at the molecular and organism levels. They provide a physiological framework and examples, illustrating that their integrated functional modelling and molecular genetics approach holds promise for closing the genotypeto-phenotype gap. Boote et al. show opportunities and challenges of linking genetics to processoriented crop modelling, with the objective of predicting field performance of grain legumes as a function of genes. They also show how to link model input parameters with allelic effects of several known genes to predict growth and seed yield in the common bean. Yin et al. describe the most active research line within crop systems biology over the last 15 years: quantitative trait loci-based crop modelling; they provide a comprehensive overview of recent experiences and future prospects within this field. In the last chapter, the editors outline how these research activities contribute to the development of crop systems biology within the context of crop improvement programmes. The book is meant for those scientists and graduate students from the domains of, and interested in bridging, fundamental plant biology and applied crop science. As presented in the book, crop systems biology is a dynamically evolving concept and research realm. We appreciate receiving any response and feedback from readers. Please do not hesitate to contact us if you have suggestions or comments. We thank the authors of individual chapters for their valuable contribution. We also thank Maryse Elliott, Melanie van Overbeek and Anja Smykowski of Springer Science + Business Media B.V. for inviting us to initiate this project and for their subsequent support in realising it. Wageningen, The Netherlands March 2015

Xinyou Yin Paul C. Struik

Contents

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Challenges in Integrating Genetic Control in Plant and Crop Models ..................................................................................... Valentina Baldazzi, Nadia Bertin, Michel Génard, Hélène Gautier, Elsa Desnoues, and Bénédicte Quilot-Turion Simulating Genotype-Phenotype Interaction Using Extended Functional-Structural Plant Models: Approaches, Applications and Potential Pitfalls ........................................................ Lifeng Xu and Gerhard Buck-Sorlin Modelling of Genotype by Environment Interaction and Prediction of Complex Traits across Multiple Environments as a Synthesis of Crop Growth Modelling, Genetics and Statistics ............................................................................ Daniela Bustos-Korts, Marcos Malosetti, Scott Chapman, and Fred van Eeuwijk Process-Based Simulation Models Are Essential Tools for Virtual Profiling and Design of Ideotypes: Example of Fruit and Root..................................................................................... Michel Génard, Mohamed-Mahmoud Memmah, Bénédicte Quilot-Turion, Gilles Vercambre, Valentina Baldazzi, Jacques Le Bot, Nadia Bertin, Hélène Gautier, Françoise Lescourret, and Loïc Pagès

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Heuristic Exploration of Theoretical Margins for Improving Adaptation of Rice through Crop-Model Assisted Phenotyping ........ 105 Delphine Luquet, Camila Rebolledo, Lauriane Rouan, Jean-Christophe Soulie, and Michael Dingkuhn

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Limited-Transpiration Trait for Increased Yield for Water-Limited Soybean: From Model to Phenotype to Genotype to Cultivars......................................................................... 129 Thomas R. Sinclair, Jyostna M. Devi, and Thomas E. Carter Jr.

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Molecular Breeding for Complex Adaptive Traits: How Integrating Crop Ecophysiology and Modelling Can Enhance Efficiency.......................................................................... 147 Graeme Hammer, Charlie Messina, Erik van Oosterom, Scott Chapman, Vijaya Singh, Andrew Borrell, David Jordan, and Mark Cooper

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Crop Modeling Approaches for Predicting Phenotype of Grain Legumes with Linkage to Genetic Information .................... 163 Kenneth J. Boote, C. Eduardo Vallejos, James W. Jones, and Melanie J. Correll

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Modelling QTL-Trait-Crop Relationships: Past Experiences and Future Prospects .............................................................................. 193 Xinyou Yin, Paul C. Struik, Junfei Gu, and Huaqi Wang

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Crop Systems Biology: Where Are We and Where to Go?.................. 219 Xinyou Yin and Paul C. Struik

Index ................................................................................................................. 229

Contributors

Valentina Baldazzi INRA, UR1115 Plantes et Systèmes de Culture Horticoles, Avignon, France Nadia Bertin INRA, UR1115 Plantes et Systèmes de Culture Horticoles, Avignon, France Kenneth J. Boote Agronomy Department, University of Florida, Gainesville, FL, USA Andrew Borrell Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, Hermitage Research Facility, The University of Queensland, Warwick, Australia Jacques Le Bot INRA, UR1115 Plantes et Systèmes de Culture Horticoles, Avignon, France Gerhard Buck-Sorlin UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST, Angers Cedex 01, France Daniela Bustos-Korts Biometris, Wageningen University & Research Centre, Wageningen, The Netherlands C.T. de Wit Graduate School for Production Ecology and Resource Conservation (PE&RC), Wageningen, The Netherlands Thomas E. Carter Jr. Agricultural Research Service, US Department of Agriculture, Raleigh, NC, USA Scott Chapman CSIRO Plant Industry and Climate Adaptation Flagship, Queensland Bioscience Precinct, St Lucia, QLD, Australia Mark Cooper DuPont-Pioneer, Johnston, IA, USA Melanie J. Correll Agricultural and Biological Engineering Department, University of Florida, Gainesville, FL, USA ix

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Contributors

Elsa Desnoues INRA, UR1115 Plantes et Systèmes de Culture Horticoles, Avignon, France Jyostna M. Devi Crop Science Department, North Carolina State University, Raleigh, NC, USA Michael Dingkuhn UMR AGAP, CIRAD, Montpellier, France CESD Division, IRRI, Metro Manila, Philippines Fred van Eeuwijk Biometris, Wageningen University & Research Centre, Wageningen, The Netherlands Hélène Gautier INRA, UR1115 Plantes et Systèmes de Culture Horticoles, Avignon, France Michel Génard INRA, UR1115 Plantes et Systèmes de Culture Horticoles, Avignon, France Junfei Gu Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, Jiangsu, China Graeme Hammer Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia James W. Jones Agricultural and Biological Engineering Department, University of Florida, Gainesville, FL, USA David Jordan Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, Hermitage Research Facility, The University of Queensland, Warwick, Australia Françoise Lescourret INRA, UR1115 Plantes et Systèmes de Culture Horticoles, Avignon, France Delphine Luquet UMR AGAP, CIRAD, Montpellier, France Marcos Malosetti Biometris, Wageningen University & Research Centre, Wageningen, The Netherlands Mohamed-Mahmoud Memmah INRA, UR1115 Plantes et Systèmes de Culture Horticoles, Avignon, France Charlie Messina DuPont-Pioneer, Johnston, IA, USA Erik van Oosterom Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia Loïc Pagès INRA, UR1115 Plantes et Systèmes de Culture Horticoles, Avignon, France

Contributors

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Bénédicte Quilot-Turion INRA, UR1052 Génétique et Amélioration des Fruit et Légumes, Avignon, France Camila Rebolledo CIAT, Agrobiodiversity, Cali, Colombia Lauriane Rouan UMR AGAP, CIRAD, Montpellier, France Thomas R. Sinclair Crop Science Department, North Carolina State University, Raleigh, NC, USA Vijaya Singh Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia Jean-Christophe Soulie UMR AGAP, CIRAD, Montpellier, France Paul C. Struik Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands C. Eduardo Vallejos Horticultural Sciences Department, University of Florida, Gainesville, FL, USA Gilles Vercambre INRA, UR1115 Plantes et Systèmes de Culture Horticoles, Avignon, France Huaqi Wang Plant Breeding and Genetics, China Agricultural University, Beijing, People’s Republic of China Lifeng Xu College of Computer Science & Technology, Zhejiang University of Technology, Hangzhou, People’s Republic of China Xinyou Yin Department of Plant Sciences, Centre for Crop Systems Analysis, Wageningen University, Wageningen, The Netherlands