PLANT EVOLUTION and the ORIGIN OF CROP SPECIES Plant Evolution and the Origin of Crop Species, 3rd Edition MIX FSC :from wfwvoloc. FSC C018575 This page intentionally left blank Plant Evolution and the Origin of Crop Species, 3rd Edition James F. Hancock Michigan State University, USA 0 IY) www.cabi.org CABI is a trading name of CAB International CABI CABI Nosworthy Way 875 Massachusetts Avenue Wallingford 7th Floor Oxfordshire OX10 8DE Cambridge, MA 02139 UK USA Tel: +44(0)1491832111 Tel: +1 6173954056 Fax: +44 (0)1491833508 Fax: +1 6173546875 E-mail: [email protected] E-mail: [email protected] Website: www.cabi.org © J.F. Hancock 2012. 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 Hancock, James E Plant evolution and the origin of crop species / James E Hancock. -- 3rd ed. p. cm. Includes bibliographical references and index. ISBN 978-1-84593-801-7 (alk. paper) 1. Crops--Evolution. 2. Crops--Origin. 3. Plants--Evolution. I. Title. SB106.074H36 2012 63 3 --dc2 3 2012001017 ISBN-13: 978 1 84593 801 7 Commissioning editor: Meredith Carroll Editorial assistants: Gwenan Spearing and Alexandra Lainsbury Production editor: Tracy Head Artwork provided by Marlene Cameron. Typeset by SPi, Pondicherry, India. Printed and bound in the UK by MPG Books Group. Contents Preface Acknowledgments PART IEVOLUTIONARY PROCESSES 1 Chromosome Structure and Genetic Variability 1 Introduction 1 Gene and Chromosome Structure 1 Types of Mutation 2 Measurement of Variability 11 Variation in Gene Expression Patterns 22 Tracing the Evolutionary and Geographical Origins of Crops 22 Construction of Genetic Maps and Genome Evolution 24 Summary 26 2Assortment of Genetic Variability 27 Introduction 27 Random Mating and Hardy-Weinberg Equilibrium 27 Migration 28 Selection 34 Types of Selection 35 Factors Limiting the Effect of Selection 38 Finding Loci Subject to Strong Selection 39 Coevolution 40 Genetic Drift 41 Evolution in Organelles 43 Interaction Between Forces 43 Summary 44 3The Multifactorial Genome 45 Introduction 45 Intra-genomic Interactions 45 Coadaptation 49 vi Contents Canalization 55 Paradox of Coadaptation 57 Summary 58 4Polyploidy and Gene Duplication 59 Introduction 59 Factors Enhancing the Establishment of Polyploids 60 Evolutionary Advantages of Polyploids 61 Genetic Differentiation in Polyploids 72 Chromosomal Repatterning 74 Genome Amplification and Chance 76 Summary 76 5 Speciation 77 Introduction 77 What is a Species? 77 Reproductive Isolating Barriers 80 Nature of Isolating Genes 84 Modes of Speciation 85 Genetic Differentiation During Speciation 90 Hybridization and Introgression 91 Hybridization and Extinction 95 Crop-Weed Hybridizations 96 Risk of Transgene Escape into the Environment 97 Summary 98 PART IIAGRICULTURAL ORIGINS AND CROP EVOLUTION 6Origins of Agriculture 99 Introduction 99 Rise of Our Food Crops 99 Evolution of Our Genus Homo 102 Spread of Homo sapiens 105 Agricultural Origins 106 Early Crop Dispersals 109 Transcontinental Crop Distributions 111 Summary 113 7 The Dynamics of Plant Domestication 114 Introduction 114 Evolution of Farming 115 Early Stages of Plant Domestication 116 Origins of Crops 119 Characteristics of Early Domesticants 119 Changes During the Domestication Process 120 Genetic Regulation of Domestication Syndromes 122 The Causative Changes in Domestication Genes 125 Rate of Domestication 125 Evolution of Weeds 126 Genetic Diversity and Domestication 127 Domestication and Native Diversity Patterns 128 Summary 130 Contents vii 8Cereal Grains 132 Introduction 132 Barley 132 Maize 134 Millets 137 Oat 139 Rice 140 Rye 142 Sorghum 143 Wheat 144 9Protein Plants 148 Introduction 148 Chickpea 148 Cowpea 149 Pea 150 Lentil 151 Phaseolus Beans 152 Faba Beans 155 Soybean 156 10Starchy Staples and Sugar 159 Introduction 159 Banana 159 Cassava 161 Potato 163 Sugarbeet 164 Sugarcane 165 Sweet Potato 166 Taro 167 Yam 168 11Fruits, Vegetables, Fibers and Oils 170 Introduction 170 Fruits 170 Vegetables 178 Fibers and Oils 185 12Postscript: Germplasm Resources 189 Introduction 189 Ex Situ Conservation 191 In Situ Conservation 192 References 193 Index 241 This page intentionally left blank Preface It has been almost 20 years since the first edition of this book was published, and the amount of information available on plant evolution and crop origins has skyrocketed, particularly in the molecular arena. Where the molecular technologies have had the greatest impact is in tracing crop origins - determining parental species, finding out where crops were domesticated and identifying the genes that made the domestications possible. Molecular studies have also played a key role in testing long-standing evolutionary theories. Most of the hypotheses of Anderson, Grant, Heiser and Stebbins have proven robust, even as experimental technologies have dramatically shifted from morphological and cytogenetic compari- sons to gene chips and genome sequencing. Hypotheses concerning hybrid speciation, polyploidy and the role of chromosome rearrangements have been tested, retested and expanded as each new technology has emerged. The molecular studies have generated some surprises, such as the amount of chromosome repatterning and gene expression alterations associated with interspecific hybridiza- tion, and the high level of gene duplication found in all sequenced genomes, but in general each new molecular technology has supported the evolutionary hypothesis formulated decades ago. In this book I have tried to use, whenever possible, the historical evidence of evolutionary phenomena and crop origins. This may give the book an "old fashioned" feel, but I think that the information is still relevant and should not be lost in a cloud of new technologies. I have chosen to work from the past up to the present, rather than the reverse. It is likely that the growing wealth of molecular information will necessitate an alternative approach in any future editions, but so far I think that I can hold my ground. ix Acknowledgments I would like to give special thanks to my wife Ann, who has so richly broadened my horizons with her passion and commitment to the living world around us. I would also like to thank the current crop of evolutionary biologists that I most admire: Norm Ellstrand, Loren Rieseberg, Tao Sang, Doug Schemske, Doug Soltis and Jonathan Wendel. x 1 Chromosome Structure and Genetic Variability Introduction are organized in chromosomes, and then we will discuss the kinds of genetic variability present Evolution is the force that shapes our livingand its measurement. world. Countless different kinds of plants and animals pack the earth and each species is itself composed of a wide range of morphologies and Gene and Chromosome Structure adaptations. These species are continually being modified as they face the realities of their par-Both gene and chromosome structure are ticular environments. complex. Genes are composed of coding regions In its simplest sense, evolution can becalled exons and non-coding regions called defined as a change in gene frequency over time. introns. Both the introns and the exons are tran- Genetic variability is produced by mutation and scribed, but the introns are removed from the then that variability is shuffled and sorted byfinal RNA product before translation (Fig. 1.1). the various evolutionary forces. The way organ-There are also short DNA sequences, both near isms evolve is dependent on their genetic char- and far from the coding region, that regulate acteristics and the type of environment theytranscription but are not transcribed them- must face. selves. "Promotor" sequences are found imme- A broad spectrum of evolutionary forces, diately before the protein coding region and play including migration,selection and random a role in the initiation of transcription, while chance, alter natural species. These same forces "enhancer" sequences are often located distant operated during the domestication of crops, asfrom the coding region and regulate levels of will be discussed in Chapter 6. In the next fourtranscription. chapters, we will describe these parameters and Each chromosome contains not only genes how they interact; but before we do this, weand regulatory sequences, but also a large will begin by discussing the different types ofnumber of short, repetitive sequences. Some of genetic variability that are found in plants. The these are concentrated near centromeres in the primary requirement for evolutionary change is densely stained portions of chromosomes called genetic variability, and mutation generates theseheterochromatic regions, and may play a role in building blocks. A wide range of mutations can the homologous pairing of chromosomes and occur at all levels of genetic organization fromtheir separation. However, there are numer- nucleotide sequence to chromosome structure. ous other repeating units that are more freely In this chapter, we will discuss how plant genesdispersed over chromosomes and do not appear J. F Hancock 2012. Plant Evolution and the Origin of Crop Species, 3rd Edn (J.F. Hancock) 1 2 Chapter 1 TATA exon exon 5' CAAT intron intron intron ATG TAR Initiation Stop of of translation translation Fig. 1.1. Organization of a typical eukaryotic gene. A precursor RNA molecule is produced