Xinyou Yin · Paul C. Struik Editors Crop Systems Biology Narrowing the Gaps between Crop Modelling and Genetics Crop Systems Biology Xinyou Yin (cid:129) Paul C. Struik Editors Crop Systems Biology Narrowing the Gaps between Crop Modelling and Genetics Editors Xinyou Yin Paul C. Struik Department of Plant Sciences, Department of Plant Sciences, Centre for Crop Systems Analysis Centre for Crop Systems Analysis Wageningen University Wageningen University Wageningen , The Netherlands Wageningen , The Netherlands ISBN 978-3-319-20561-8 ISBN 978-3-319-20562-5 (eBook) DOI 10.1007/978-3-319-20562-5 Library of Congress Control Number: 2015953437 Springer Cham Heidelberg New York Dordrecht London © Springer International Publishing Switzerland 2016 T his work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfi lms 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. T he use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specifi c statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. T he 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) Pref ace 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, how- ever, 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 applica- tion 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 warm- ing 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 biol- ogy – 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 fi eld 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 net- works 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. X u 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 breed- ing for architectural traits. B ustos et al. discuss prediction strategies for genotype-by-environment i nteractions using statistical models, crop growth models and combinations of v vi Preface model types. They illustrate how prediction accuracy can profi t from the large data sets available on environmental and genotypic variables by integrating physiologi- cal and statistical knowledge. G énard et al. show how knowledge generated by in silico profi ling 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 functional- structural 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-transcriptomics- genetic 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 effec- tively link processes at the molecular and organism levels. They provide a physio- logical framework and examples, illustrating that their integrated functional modelling and molecular genetics approach holds promise for closing the genotype- to- phenotype gap. Boote et al. show opportunities and challenges of linking genetics to process- oriented crop modelling, with the objective of predicting fi eld 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 com- prehensive overview of recent experiences and future prospects within this fi eld. I n 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 con- cept 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 Xinyou Yin March 2015 Paul C. Struik Contents 1 Challenges in Integrating Genetic Control in Plant and Crop Models ..................................................................................... 1 Valentina Baldazzi, Nadia Bertin, Michel Génard, Hélène Gautier, Elsa Desnoues, and Bénédicte Quilot-Turion 2 Simulating Genotype-Phenotype Interaction Using Extended Functional-Structural Plant Models: Approaches, Applications and Potential Pitfalls ........................................................ 33 Lifeng Xu and Gerhard Buck-Sorlin 3 Modelling of Genotype by Environment Interaction and Prediction of Complex Traits across Multiple Environments as a Synthesis of Crop Growth Modelling, Genetics and Statistics ............................................................................ 55 Daniela Bustos-Korts , Marcos Malosetti , Scott Chapman , and Fred van Eeuwijk 4 Process-Based Simulation Models Are Essential Tools for Virtual Profiling and Design of Ideotypes: Example of Fruit and Root ..................................................................................... 83 Michel Génard , Mohamed-Mahmoud Memmah , Bénédicte Quilot-Turion , Gilles Vercambre , Valentina Baldazzi , Jacques Le Bot , Nadia Bertin , Hélène Gautier , Françoise Lescourret , and Loïc Pagès 5 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 vii viii Contents 6 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. 7 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 8 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 9 Modelling QTL-Trait-Crop Relationships: Past Experiences and Future Prospects .............................................................................. 193 Xinyou Yin , Paul C. Struik , Junfei Gu , and Huaqi Wang 10 Crop Systems Biology: Where Are We and Where to Go? .................. 219 Xinyou Yin and Paul C. Struik Index ................................................................................................................. 229 Contributors Valentina Baldazzi I NRA, 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 C entre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, Hermitage Research Facility, T he University of Queensland, Warwick , Australia Jacques Le Bot INRA, UR1115 Plantes et Systèmes de Culture Horticoles , Avignon , France Gerhard Buck-Sorlin U MR 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 C SIRO Plant Industry and Climate Adaptation Flagship, Queensland Bioscience Precinct , St Lucia , QLD , Australia Mark Cooper DuPont-Pioneer , Johnston , IA , USA Melanie J. Correll A gricultural and Biological Engineering Department, University of Florida , Gainesville , FL , USA ix