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Principles of Plant Genetics and Breeding Dedication To my parents Shiloh and Ernestina With love and admiration Principles of Plant Genetics and Breeding George Acquaah Copyright © 2007 by George Acquaah BLACKWELL PUBLISHING 350 Main Street, Malden, MA 02148-5020, USA 9600 Garsington Road, Oxford OX4 2DQ, UK 550 Swanston Street, Carlton, Victoria 3053, Australia The right of George Acquaah to be identified as the Author of this Work has been asserted in accordance with the UK Copyright, Designs, and Patents Act 1988 All rights reserved No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs, and Patents Act 1988, without the prior permission of the publisher First published 2007 by Blackwell Publishing Ltd 2007 Library of Congress Cataloging-in-Publication Data Acquaah, George Principles of plant genetics and breeding / George Acquaah p cm Includes bibliographical references and index ISBN-13: 978-1-4051-3646-4 (hardback : alk paper) ISBN-10: 1-4051-3646-4 (hardback : alk paper) Plant breeding Plant genetics I Title SB123.A334 2007 631.5′233—dc22 2006004754 A catalogue record for this title is available from the British Library Set in 10/12pt Galliard by Graphicraft Limited, Hong Kong Printed and bound in UK by TJ International Ltd The publisher’s policy is to use permanent paper from mills that operate a sustainable forestry policy, and which has been manufactured from pulp processed using acid-free and elementary chlorine-free practices Furthermore, the publisher ensures that the text paper and cover board used have met acceptable environmental accreditation standards For further information on Blackwell Publishing, visit our website: www.blackwellpublishing.com Contents Industry highlights boxes, vii Industry highlights box authors, ix Preface, xi Acknowledgments, xiii Part I Underlying science and methods of plant breeding, Section Historical perspectives and importance of plant breeding, History and role of plant breeding in society, Section General biological concepts, 16 The art and science of plant breeding, 17 Plant cellular organization and genetic structure: an overview, 35 Plant reproductive systems, 55 Section Germplasm issues, 74 Variation: types, origin, and scale, 75 Plant genetic resources for plant breeding, 87 Section Genetic analysis in plant breeding, 108 Introduction to concepts of population genetics, 109 Introduction to quantitative genetics, 121 Common statistical methods in plant breeding, 146 Section Tools in plant breeding, 163 10 Sexual hybridization and wide crosses in plant breeding, 164 11 Tissue culture and the breeding of clonally propagated plants, 181 12 Mutagenesis in plant breeding, 199 13 Polyploidy in plant breeding, 214 14 Biotechnology in plant breeding, 231 15 Issues in the application of biotechnology in plant breeding, 257 Section Classic methods of plant breeding, 281 16 Breeding self-pollinated species, 282 17 Breeding cross-pollinated species, 313 18 Breeding hybrid cultivars, 334 Section Selected breeding objectives, 351 19 Breeding for physiological and morphological traits, 352 20 Breeding for resistance to diseases and insect pests, 367 21 Breeding for resistance to abiotic stresses, 385 22 Breeding compositional traits and added value, 404 Section Cultivar release and commercial seed production, 417 23 Performance evaluation for crop cultivar release, 418 24 Seed certification and commercial seed multiplication, 435 vi CONTENTS 25 International plant breeding efforts, 450 26 Emerging concepts in plant breeding, 462 Part II Breeding selected crops, 471 27 28 29 30 31 32 33 34 Breeding wheat, 472 Breeding corn, 485 Breeding rice, 498 Breeding sorghum, 509 Breeding soybean, 519 Breeding peanut, 529 Breeding potato, 537 Breeding cotton, 546 Glossary, 556 Appendix 1: Internet resources, 561 Appendix 2: Conversion rates, 563 Index, 564 Industry highlights boxes Chapter Normal Ernest Borlaug: the man and his passion George Acquaah Chapter Introduction and adaptation of new crops Jaime Prohens, Adrián Rodríguez-Burruezo, and Fernando Nuez Chapter No box Chapter Maize × Tripsacum hybridization and the transfer of apomixis: historical review Bryan Kindiger Chapter 12 Current apple breeding programs to release apple scabresistant scion cultivars F Laurens Chapter 13 Application of tissue culture for tall wheatgrass improvement Kanyand Matand and George Acquaah Chapter 14 Bioinformatics for sequence and genomic data Hugh B Nicholas, Jr., David W Deerfield II, and Alexander J Ropelewski Chapter No box Chapter 15 The intersection of science and policy in risk analysis of genetically engineered plants David A Lee and Laura E Bartley Chapter Plant genetic resources for breeding K Hammer, F Heuser, K Khoshbakht, and Y Teklu Chapter 16 Barley breeding in the United Kingdom W T B Thomas Chapter No box Chapter 17 Developing a new cool-season perennial grass forage: interspecific hybrids of Poa arachnifera × Poa secunda Bryan Kindiger Chapter Recurrent selection with soybean Joe W Burton Chapter Multivariate analyses procedures: applications in plant breeding, genetics, and agronomy A A Jaradat Chapter 10 The use of the wild potato species, Solanum etuberosum, in developing virus- and insect-resistant potato varieties Richard Novy Chapter 11 Haploids and doubled haploids: their generation and application in plant breeding Sergey Chalyk Chapter 18 Pioneer Hi-Bred International, Inc.: bringing seed value to the grower Jerry Harrington Chapter 19 Bringing Roundup Ready® technology to wheat Sally Metz Chapter 20 Genetic improvement of cassava through biotechnology Nigel J Taylor Chapter 21 Discovering genes for drought adaptation in sorghum Andrew Borrell, David Jordan, John Mullet, Patricia viii INDUSTRY HIGHLIGHTS BOXES Klein, Robert Klein, Henry Nguyen, Darrell Rosenow, Graeme Hammer, and Bob Henzell A Fritz, B S Gill, K S Gill, S Haley, K K Kidwell, S F Kianian, N Lapitan, H Ohm, D Santra, M Sorrells, M Soria, E Souza, and L Talbert Chapter 22 QPM: enhancing protein nutrition in sub-Saharan Africa Twumasi Afriyie Chapter 28 Hybrid breeding in maize F J Betrán Chapter 23 MSTAT: a software program for plant breeders Russell Freed Chapter 29 Breeding rice Anna Myers McClung Chapter 24 Public release and registration of “Prolina” soybean Joe W Burton and Plant variety protection in Canada B Riché and D J Donnelly Chapter 30 Sorghum breeding William Rooney Chapter 25 Plant breeding research at ICRISAT P M Gaur, K B Saxena, S N Nigam, B V S Reddy, K N Rai, C L L Gowda, and H D Upadhyaya Chapter 26 An example of participatory plant breeding: barley at ICARDA S Ceccarelli and S Grando Chapter 27 Bringing genomics to the wheat fields K A Garland-Campbell, J Dubcovsky, J A Anderson, P S Baenziger, G Brown-Guedira, X Chen, E Elias, Chapter 31 Estimating inheritance factors and developing cultivars for tolerance to charcoal rot in soybean James R Smith Chapter 32 Peanut (Arachis hypogaea L.) breeding and root-knot nematode resistance Charles Simpson Chapter 33 The breeding of potato John E Bradshaw Chapter 34 Cotton breeding Don L Keim Industry highlights box authors Acquaah, G., Department of Agriculture and Natural Resources, Langston University, Langston, OK 73050, USA Afriyie, T., International Maize and Wheat Improvement Center (CIMMYT), PO Box 5689, Addis Ababa, Ethiopia Anderson, J A., Department of Agronomy and Plant Genetics, University of Minnesota, Twin Cities, St Paul, MN 55108, USA Baenziger, P S., Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA Bartley, L E., USDA-APHIS Biotechnology Regulatory Services, Riverdale, MD 20737, USA Betrán, F J., Texas A&M University, College Station, TX 77843, USA Borrell, A., Department of Primary Industries and Fisheries, Hermitage Research Station, Warwick, Queensland 4370, Australia Bradshaw, J E., Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK Brown-Guedira, G., USDA-ARS Plant Science Research Unit, North Carolina State University, Raleigh, NC 27606, USA Burton, J W., USDA Plant Science Building, 3127 Ligon Street, Raleigh, NC 27607, USA Ceccarelli, S., International Center for Agricultural Research in the Dry Areas (ICARDA), PO Box 5466, Aleppo, Syria Chalyk, S., 12 Goldfinch Court, Apt 1007, Toronto M2R 2C4, Canada Chen, X., USDA-ARS Wheat Genetics, Quality, Physiology, and Disease Research Unit, Washington State University, Pullman WA 99164, USA Deerfield, D W II, Pittsburgh Supercomputing Center, Pittsburgh, PA 15213, USA Donnelly, D J., Plant Science Department, McGill University, Ste Anne de Bellevue, QC H9X 3V9, Canada Dubcovsky, J., Department of Agronomy and Range Science, University of California at Davis, Davis, CA 95616, USA Elias, E., Department of Plant Sciences, North Dakota State University, Fargo, ND 58105, USA Freed, R., Department of Crop and Soil Science, Michigan State University, East Lansing, MI 48824, USA Fritz, A., Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA Garland-Campbell, K A., USDA-ARS Wheat Genetics, Quality, Physiology, and Disease Research Unit, Washington State University, Pullman, WA 99164, USA Gaur, P M., International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, AP, India Gill, B S., Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA Gill, K S., Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA Gowda, C L L., International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, AP, India Grando, S., International Center for Agricultural Research in the Dry Areas (ICARDA), PO Box 5466, Aleppo, Syria Haley, S., Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80526, USA Hammer, G., School of Land and Food, University of Queensland, Queensland 4072, Australia Hammer, K., Institute of Crop Science, Agrobiodiversity Department, University Kassel, D-37213 Witzenhausen, Germany Harrington, J., Pioneer Hi-Bred International, Des Moines, IA 50307, USA Henzell, R., Department of Primary Industries and Fisheries, Hermitage Research Station, Warwick, Queensland 4370, Australia Heuser, F., Institute of Crop Science, Agrobiodiversity Department, University Kassel, D-37213 Witzenhausen, Germany Jaradat, A A., USDA-ARS, Morris, 56267 MN, USA Jordan, D., Department of Primary Industries and Fisheries, Hermitage Research Station, Warwick, Queensland 4370, Australia Keim, D L., Delta and Pine Land Company, One Cotton Row, PO Box 157, Scott, MS 38772, USA Khoshbakht, K., Institute of Crop Science, Agrobiodiversity Department, University Kassel, D-37213 Witzenhausen, Germany Kianian, S F., Department of Plant Sciences, North Dakota State University, Fargo, ND 58105, USA Kidwell, K K., Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA Kindiger, B., USDA-ARS Grazinglands Research Laboratory, El Reno, OK 73036, USA Klein, P., Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA Klein, R., USDA-ARS Southern Agricultural Research Station, College Station, TX 77843, USA Lapitan, N., Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80526, USA Laurens, F., UMR Génétique et Horticulture (GenHort) (INRA/INH/UA), INRA Centre d’Angers, 49070 Beaucouzé, France Lee, D A., EPA Office of Research and Development, 8623N, Washington, DC 20460, USA Matand, K., Department of Agriculture and Applied Sciences, Langston University, Langston, OK 73050, USA 266 CHAPTER 15 Service (USDA-APHIS) uses the authority of the Plant Protection Act to regulate GE organisms This law gives USDA the authority to restrict introduction into the environment of plant pests, which are defined as living organisms that cause disease in or damage to plants not including humans and non-parasitic plants (US Congress 2000) The current USDA-APHIS regulations use this “plant pest authority” to regulate GE organisms based on the potential plant pest risk caused by the use of plant pest (e.g., viral) sequences or vectors (e.g., Agrobacterium) in the creation of many GE plants (USDA-APHIS 1997) For plants created through biolistic transformation that not have plant pest sequences, the regulations can be imposed on articles that USDA has “reason to believe” pose a plant pest risk (USDA-APHIS 1997) Technically, it may be possible that the use of plant pest components in the creation of a GE plant could create a new plant pest or increase the GE plant’s susceptibility to a disease However, the rarity of these effects in GE plants and the dependence on the reason to believe clause, causes some to be concerned that the current regulations are tenuous (National Research Council 2002) In order for a GE plant to be released into the environment in an unconfined manner and thus sold commercially, USDA-APHIS will evaluate a petition for non-regulated status to determine if the GE product does not pose a plant pest risk or cause other environmental harm, as evaluated under the National Environmental Policy Act Because granting non-regulated status takes the product out from all USDA-APHIS oversight, this feature has drawn criticism as it may limit USDA-APHIS actions in terms of monitoring and other risk management activities Also, while much information in petitions is available to the public, applicants may claim portions are confidential business information under the Freedom of Information Act, reducing the transparency of the USDA-APHIS system In part to address some of the issues discussed above, USDA-APHIS initiated a process in 2004 to revise its regulations based on the so-called “noxious weed authority” in the Plant Protection Act (USDA-APHIS 2004) This authority gives USDA-APHIS the ability to restrict introduction into the environment of noxious weeds, which are defined quite broadly as “any plant or plant product that can directly or indirectly injure or cause damage to crops, other interests of agriculture, natural resources of the United States, public health, or the environment” (US Congress 2000) The revised regulations would regulate based on potential noxious weed risk of GE plants, greatly expanding the reasons for USDA-APHIS to assert its authority In contrast to the somewhat limited abilities of USDA-APHIS under its current regulations, the EPA broadly uses its authority under the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) to regulate GE plants that contain pesticidal elements To use this law to regulate GE plants, the EPA defined a new pesticide type, the plant-incorporated protectant (PIP), as “a pesticidal substance produced by the plants and the genetic material necessary for them to produce the substance” (EPA 2001) This allows the EPA to retain authority over approved products and it often requests additional data from applicants as a condition of continued registration, thereby reducing the data gaps present during risk assessment FIFRA provides special protections for information regarding the health effects of products that might be claimed as confidential under other statutes, and requires that the EPA submit major decisions to a panel of external experts, called a scientific advisory panel Thus, relative to other agencies, the EPA has a more transparent and understandable regulatory process However, some have criticized the EPA for too restrictively regulating PIPs by establishing requirements that are not commensurate with the risks posed by GE plants and are unnecessarily burdensome for applicants, especially since conventionally bred PIPs are exempted from regulation Nonetheless, the EPA’s efforts may improve acceptability of the technology, and, in the case of Bt crops, extend the lifetime of their benefits to agriculture by requiring insect-resistance management The FDA regulates foods derived from GE products under the Federal Food Drug and Cosmetic Act (FFDCA) As published in 1992, FDA policy is that it will regulate foods derived from GE products in the same way as those derived from conventionally developed products (FDA 1992) The FDA’s regulation is based on whether the product has altered nutritional properties or contains a food additive, which is defined as a substance introduced into food that is not a pesticide and is not “generally recognized as safe” (GRAS) (FDA 1992) As for conventionally developed foods, FFDCA makes it the responsibility of the developer to determine that GE-derived foods are safe and any substances new to the variety are GRAS, but the FDA provides a voluntary consultation process to help developers determine this The consultation process, through which developers submit data to FDA scientists until the FDA has no more questions regarding safety, is available for both conventional and GE products The voluntary nature of the consultations makes some observers very uncomfortable with the FDA’s regulation of GE foods On the other hand, FDA records show that all GE products currently approved in the United States have completed such a consultation, but, because it is voluntary, none of the information submitted to the FDA is available for public scrutiny Therefore, while the FDA’s regulation is most genuinely product-based, the transparency of the system is the lowest among the three agencies GE risk assessment concerns and typical data and information evaluation Given the peculiarities of the US regulatory system for GE crops, how does it actually work? Here, we discuss the risk assessment concerns and information that the regulatory agencies regularly examine before approving a GE variety for widespread use To evaluate the safety of GE crops before approval for food, feed, or planting in the United States, the USDA, EPA, and FDA consider the potential impact of a large number of environmental- and health-related effects of the GE crops Notably, the list of concerns that the agencies evaluate includes all of the potential environmental hazards a recent National Research Council (2002) panel identified that GE plants could cause: The GE trait could be passed to a wild or weedy relative and increase its weediness or invasiveness, or the GE plant itself could become weedy or invasive ISSUES IN THE APPLICATION OF BIOTECHNOLOGY IN PLANT BREEDING 267 The GE trait could negatively impact non-target organisms in the environment Organisms that the GE trait is intended to harm could develop resistance to the trait Currently, agency scientists and risk managers evaluate each submission on a case-by-case basis and determine the specific data the applicant should submit depending on the product However, as shown in Table 1, there are a number of concerns Table Risk assessment concerns and information used by the Food and Drug Administration (FDA), Environmental Protection Agency (EPA), and US Department of Agriculture (USDA) Agency Risk assessment concerns Typical data1 and information2 used in assessment FDA, EPA, and/or USDA-APHIS3 Characterization of inserted DNA Characterization of expressed protein(s) Data from Southern blots and/or sequencing Data from western blots or ELISA assays often with multiple plant tissues; data from phenotypic analyses; data on peptide modification in vivo Data from Southern blots and/or phenotypic analysis over multiple generations Data on measurements of amino acids, minerals, fatty acids, carbohydrates, water, etc., including amounts of any toxins and antinutrients that are typically found in the plant Data on in vitro digestibility, heat stability; data on sequence similarity to known allergens Stable inheritance of the transgene Plant composition Allergenicity of expressed protein EPA and USDA-APHIS Effects on non-target organisms Gene flow to wild and weedy relatives Potential weediness of engineered plant Threatened and endangered species impact Data from toxicity assays on non-target insects, soil organisms, birds, mammals, and fish; in some instances, data from surveys of non-target invertebrates in the field Information on hybridization potential and distributions of wild and weedy relatives; in some instances, data on hybridization potential Data describing plant characteristics relative to a comparator plant line Information on distributions of threatened and endangered species that are related to the target organism or could otherwise be affected USDA-APHIS Plant pest risk Agronomic management Data on incidence of plant pests in field trials Agency assessments4; information on alternative agricultural management options EPA Acute toxicity Transgenic protein fate in environment Cost benefit analysis Mammalian toxicity assay Half-life of protein under soil conditions Agency assessments; information on alternative agricultural management options with respect to pesticide use Agency assessments; data on effective dosage compared with protein expression in the plant; information on target insect biology and behavior Insect Resistance Management “Data” refers to original data, in the form of formal or informal observations, submitted by the applicant “Information” refers to information that is not typically generated by the applicant (i.e., not original data), typically public information from the scientific or agronomic literature All three agencies evaluate molecular characterization data FDA and USDA-APHIS examine plant composition FDA and EPA evaluate allergenicity potential of the expressed protein(s) “Agency assessments” signify a particular reliance on agency risk assessment expertise and information that is not generated by the applicant APHIS, Animal and Plant Health Inspection Service; ELISA, enzyme-linked immunosorbent assay 268 CHAPTER 15 that the agencies typically evaluate for every product that falls under their purview All of the agencies evaluate a detailed molecular and genetic characterization of the product to obtain information about the identity of the GE plant and confirm that the inserted gene is functioning as intended In addition, the FDA and USDA-APHIS examine plant composition to gauge unintended, pleiotropic changes due to transgenesis, and the FDA and EPA evaluate the allergenicity potential of the expressed protein(s) USDA-APHIS determines the potential of a GE plant to become an agricultural weed, or to cause damage to agriculture through the introduction of a novel plant pathogen produced by the transgenic plant or a change in plant susceptibility to pests Under FIFRA the benefits of products as well as their potential risks are evaluated in the registration process, so the EPA assesses the potential economic impact of the introduction of the PIP product, along with the environmental and human health benefits of the altered pesticide-use regime When appropriate, the EPA evaluates insect resistance management (IRM) plans proposed by applicants to confirm that the plan will be sufficient to delay resistance development to Bt Both EPA and USDA-APHIS are concerned with the potential for gene flow to occur from the transgenic plant to wild relatives (Table 1) In the case of plants engineered to produce a PIP, USDA-APHIS and EPA evaluate whether there will be toxicity to non-target organisms that might come into contact with the crop or its residues Using science for risk management: the insect-resistance management example In addition to the data provided to the agencies during their assessment of specific products during the approval process, both the EPA and USDA fund active research programs to continue studying the environmental and human health impacts of GE crop plants An example of the use of science in determining regulatory policy is that of the EPA’s IRM plan for PIPs utilizing proteins produced by the bacterium Bacillus thuringiensis (Bt), which are the most common PIPs engineered into plants Insect populations exposed to pesticides over a long enough timeframe will develop resistance (Feyereisen 1995), so because preparations of the bacteria that express Bt toxins are an important pest management tool for the organic farming industry, concerns were raised that the development of resistance to Bt would deprive the agricultural community of a safe, environmentally friendly pesticide Due to the adverse health and environmental effects of having to use conventional pesticides instead of Bt, the EPA has required a very stringent IRM plan for the use of Bt-PIP-containing crops to delay resistance development, in contrast to almost all other pesticides After studying insect-resistance models and experimental data, the EPA developed a program to delay resistance development based on a 50 : 50 refuge in 80 : 20 external “high dose/structured refuge” approach This strategy relies on resistcotton growing areas refuge ance to Bt being a genetically recessive trait and the initial frequency of (a) the resistance allele being very low When this is the case, refuges for susceptible insects can be designed so that in principle any resistant insects that arise in the population will almost certainly mate with a susceptible individual so that the heterozygous offspring will be susceptible to the PIP The high dose requirement for PIP products necessitates that the plant expresses a level of Bt protein at least 25-fold greater than that needed to kill 99% of susceptible insects in laboratory assays The basic structured refuge requirements for Bt crops are satisfied in general by planting 20% of the field as a contiguous non-Bt refuge that should be located within 0.8 km of the Bt crop fields (Figure 1) However, if Bt corn is planted in cotton-producing areas then the non-Bt refuge should be 50% of the corn acreage because cotton pests could feed on both 80 : 20 external 95 : embedded cotton and corn and develop resistance more rapidly refuge refuge Monitoring for insect-resistance development has always been a (b) requirement by the EPA for registrants, who inform the EPA of the results of their monitoring program on an annual basis, along with any grower observations of increased crop damage by insects normally susFigure Examples of refuge strategies for Bt ceptible to Bt toxins In addition, academic researchers have performed crops that are acceptable to the EPA: (a) corn recent studies in Arizona, North Carolina, and Iowa to measure resistrefuge requirements and (b) cotton refuge ance development in Bt corn and cotton fields over multiple growing requirements Light areas represent fields of Bt seasons (Tabashnik et al 2003) In most cases, the initial frequency of crops, which the dark areas represent non-Bt resistance alleles to particular GE Bt-containing plants in the target poprefuges In all cases, the refuge can be sprayed ulations was very low (