Quantitative Genetics, Genomics and Plant Breeding Second Edition Quantitative Genetics, Genomics and Plant Breeding Second Edition Edited by Manjit S. Kang Department of Plant Pathology, Kansas State University, Manhattan, KS, USA CABI is a trading name of CAB International CABI CABI Nosworthy Way 745 Atlantic Avenue Wallingford 8th Floor Oxfordshire OX10 8DE Boston, MA 02111 UK USA Tel: +44 (0)1491 832111 Tel: +1 (617)682-9015 Fax: +44 (0)1491 833508 E-mail: [email protected] E-mail: [email protected] Website: www.cabi.org © CAB International 2020. All rights reserved. No part of this publication may be reproduced in any form or by any means, electronically, mechanically, by photocopying, recording or otherwise, without the prior permission of the copyright owners. A catalogue record for this book is available from the British Library, London, UK. Library of Congress Cataloging-in-Publication Data Names: Kang, Manjit S., editor. Title: Quantitative genetics, genomics and plant breeding / Manjit S. Kang, Adjunct Professor (Quantitative Geneticist), Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA. Description: 2nd edition. | Wallingford, Oxfordshire ; Boston : CABI, [2020] | Includes bibliographical references and index. | Summary: “Quantitative genetics and breeding have made a major contribution to crop improvement over the years, but the genomics revolution has dramatically changed the field – this second edition of a popular book explains how traditional and genomic techniques have been combined to advance the field”– Provided by publisher. Identifiers: LCCN 2019047038 (print) | LCCN 2019047039 (ebook) | ISBN 9781789240214 (hardback) | ISBN 9781789242942 (ebk) | ISBN 9781789242959 (epub) Subjects: LCSH: Crops–Genetics. | Plant breeding. | Quantitative genetics. Classification: LCC SB123 .Q36 2020 (print) | LCC SB123 (ebook) | DDC 631.5/3–dc23 LC record available at https://lccn.loc.gov/2019047038 LC ebook record available at https://lccn.loc.gov/2019047039 References to Internet websites (URLs) were accurate at the time of writing. ISBN-13: 9781789240214 (hardback) 9781789242942 (ePDF) 9781789242959 (ePub) Commissioning Editor: David Hemming Editorial Assistant: Emma McCann Production Editor: Marta Patiño Typeset by SPi, Pondicherry, India Printed and bound in the UK by Severn, Gloucester Dr George P. Rédei, known among his colleagues and students as the ‘Encyclopedia of Genetics’, passed away on 10 November 2008. This edition of Quantitative Genetics, Genomics and Plant Breeding is dedicated to him. His chapter from the first edition of the book is being reproduced here. Contents Contributors ix Foreword xiii Preface xv 1 Vignettes of the History of Genetics 1 George P. Rédei Section I: Quantitative Genetics: Plant Breeding, Bioinformatics, Genome Editing and G×E Interaction 17 2 Food and Health: The Role of Plant Breeding 19 Salvatore Ceccarelli 3 The Importance of Plant Pan-genomes in Breeding 27 Soodeh Tirnaz, David Edwards and Jacqueline Batley 4 Genome Editing Technologies for Crop Improvement 33 Michael Pillay 5 Epigenome Editing in Crop Improvement 44 Gurbachan S. Miglani and Rajveer Singh 6 Bioinformatics and Plant Breeding 71 Robyn Anderson, Cassandria Tay Fernandez, Monica F. Danilevicz and David Edwards 7 Bioinformatics Approaches for Pathway Reconstruction in Orphan Crops – A New Paradigm 86 Dyfed Lloyd Evans and Shailesh Vinay Joshi 8 Advances in QTL Mapping and Cloning 124 Dharminder Bhatia and Darshan S. Brar 9 Genotype–Environment Interaction and Stability Analyses: An Update 140 Manjit S. Kang vii viii Contents 10 Biplot Analysis of Multi-environment Trial Data 162 Weikai Yan and L.A. Hunt 11 Design and Analysis of Multi-year Field Trials for Annual Crops 178 Vivi N. Arief, Ian H. DeLacy and Kaye E. Basford 12 Advances in the Definition of Adaptation Strategies and Yield-stability Targets in Plant Breeding 194 Paolo Annicchiarico Section II: Intersection of Breeding, Genetics and Genomics: Crop Examples 211 13 Prediction with Big Data in the Genomic and High-throughput Phenotyping Era: A Case Study with Wheat Data 213 Paulino Pérez-Rodríguez, Juan Burgueño, Osval A. Montesinos-López, Ravi P. Singh, Philomin Juliana, Suchismita Mondal and José Crossa 14 Quantitative Genetics in Improving Root and Tuber Crops 227 Hernán Ceballos 15 Genomic Selection in Rice: Empirical Results and Implications for Breeding 243 Nourollah Ahmadi, Jérôme Bartholomé, Tuong-Vi Cao and Cécile Grenier 16 Novel Breeding Approaches for Developing Climate-resilient Rice 259 Sandeep Chapagain, Lovepreet Singh and Prasanta K. Subudhi 17 Quantitative Genetics, Molecular Techniques and Agronomic Performance of Provitamin A Maize in Sub-Saharan Africa 276 Baffour Badu-Apraku, M.A.B. Fakorede, A.O. Talabi, E. Obeng-Bio, S.G.N. Tchala and S.A. Oyekale 18 Developments in Genomics Relative to Abiotic Stress-tolerance Breeding in Maize During the Past Decade 325 M.T. Labuschagne 19 Exploiting Alien Genetic Variation for Germplasm Enhancement in Brassica Oilseeds 338 Mehak Gupta and S.S. Banga 20 Biofortified Pearl Millet Cultivars Offer Potential Solution to Tackle Malnutrition in India 385 Mahalingam Govindaraj, Parminder S. Virk, Anand Kanatti, Binu Cherian, K.N. Rai, Meike S. Anderson and Wolfgang H. Pfeiffer Index 397 Contributors N. Ahmadi CIRAD, UMR AGAP, F-34398, Montpellier, France; AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France. M.S. Anderson HarvestPlus, c/o International Food Policy Research Institute (IFPRI), Washington DC, USA. R. Anderson School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, Australia. P. Annicchiarico Research Centre for Animal Production and Aquaculture, viale Piacenza 29, Lodi, Italy. V.N. Arief The University of Queensland, Brisbane, Australia. B. Badu-Apraku International Institute of Tropical Agriculture, Ibadan, Nigeria. S.S. Banga Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India. J. Bartholomé CIRAD, UMR AGAP, F-34398, Montpellier, France; AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France. K.E. Basford The University of Queensland, Brisbane, Australia. J. Batley School of Biological Sciences, University of Western Australia, Perth, Australia. D. Bhatia Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India. D.S. Brar School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India; Former Head, Plant Breeding, Genetics & Biotechnology Division, International Rice Research Institute, Manila, Philippines. J. Burgueño International Maize and Wheat Improvement Center (CIMMYT), México City, México. T.-V. Cao CIRAD, UMR AGAP, F-34398, Montpellier, France; AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France. ix