Second Edition - Breeding for Quantitative Traits in …

1 Breeding for Quantitative Traits in PLANTS Second Edition Rex Bernardo University of Minnesota Twin Cities Stemma Press Woodbury, Minnesota 2010 by Rex Bernardo All rights reserved. No part of this book may be reproduced, stored, or transmitted by any means without written permission from the author. The information in this book is deemed highly reliable, but the author and the publisher cannot be held responsible for any consequences of using the information it contains.

2 Printed in the United States of America Stemma Press 1938 Bowsens Lane Woodbury, MN 55125 ISBN 978-0-9720724-1-0 Library of Congress Control Number: 2010906366 Cover photo courtesy of Scott Bauer, USDA Agricultural Research Service The author used Scientific WorkPlace version to write and typeset this book ContentsI Plant Breeding and Population Genetics11 PlantBreedingandQuantitativeTraits .. genetic EffectsandtheOne-LocusModel .. Breeding Self-Pollinated and Cross-Pollinated 102 Genetics of Breeding GenotypeandAlleleFrequenciesinaPopulatio n.

3 Hardy-Weinberg Linkage .. Linkage Disequilibrium and Lack of Random MolecularMarkersandLinkageMaps .. SmallPopulations .. InbreedingandRelatedness .. IdentitybyDescentinPedigrees .. Estimating Relatedness with Molecular Markers .. 45ivContentsII Means of Genotypes and Breeding Populations 513 Phenotypic and Genotypic PhenotypeasaFunctionofGenesandEnvironmen t .. EffectsofAlleles .. Means and Values Two-Locus Model: Epistatic Testcross General and SpecificCombiningAbility.

4 704 Selecting Parents to Maximize Mean ParentalSelectioninInbredDevelopment .. FixationofFavorableAlleles .. 815 Mapping Quantitative Trait LinkageMappingofQTL .. GeneralApproach .. Single-FactorAnalysisandIntervalMapping .. Multiple-MarkerAnalysis .. SignificanceTestsandFalseDiscoveryRate .. Marker-Trait Associations and Population Structure Linkage Gene Expression CandidateGenesandComparativeMapping .. 110 III Variation in Breeding Populations1136 Phenotypic and genetic VariationduetoGenesandEnvironment.

5 AdditiveVarianceandDominanceVariance .. EpistaticVariance .. GeneticVariancesfromaFactorialModel .. Variance among Testcross, Half-Sib, and Full-Sib Families . CovariancebetweenSingleCrosses .. Covariance between Selfed Relatives in anF2 Population .. Heritability .. Maintenance 1437 Estimating genetic DoBreedersNeedtoEstimateGeneticVariances ? .. Approach .. Assumptions .. One-FactorDesign .. FactorialDesign .. PrecisionofEstimatesofGeneticVariances.

6 ConfidenceIntervals .. EpistaticVariance .. 1738 Genotype Environment Genotypic Values in Coping with Genotype EnvironmentInteraction .. ,VGE, and Number of Replications and Environments .. Partitioning Environments into Homogeneous Subgroups .. ClusterAnalysis .. MultiplicativeModels .. SitesRegressionAnalysis .. QTL EnvironmentInteraction .. 202IV Selection in Breeding Populations2059 Inbred and Testcross VarianceamongandwithinSelfedFamilies .. Variance at Different Selection among versus within Selection inF2versusBC1 Populations.

7 EarlyversusLateTestinginHybridCrops .. ChoosingaSuitableTester .. 22510 Recurrent .. Theoretical .. 25511 Best Linear Unbiased .. BLUP for Self-Pollinated Crops: Interpretation of Random Properties ofb BLUP for Cross-PollinatedCrops: Single Crosses .. genetic .. for Multiple Subpopulations .. Marker-Based Selection without QTL Mapping .. Non-BLUP Methods for Genomewide Selection .. 29812 Heterosis and Hybrid .. Initial Approaches for Predicting Hybrid Performance.

8 ,DoubleCrosses,andSynthetics .. 32013 Selection for Multiple .. Tandem Selection and Independent Culling Levels .. 33414 Epilogue: Designing a Breeding Program337 References341 Index380viiiContentsPrefaceBreeding for Quantitative Traits in Plantswas written as a textbookfor a graduate course in the application of Quantitative genetics to plantbreeding. I hope it will also be useful as a reference for practicing plantbreeders. My goal was to write a book that would help a student of plantbreeding achieve the following objectives:1.

9 Understand fundamental concepts in plant Breeding and populationgenetics;2. Explore how Quantitative genetics principles and modern tools canhelp a plant breeder design and implement a Breeding program; and3. Appreciate the theory, experimental approaches, and evidence thatcomprise the basis for these concepts and Breeding Edition of this book, published in 2002, grew out of lecturenotes for a class I twice taught at Purdue University. I wrote it from theperspective of one who has worked as a scientist at a seed company (1988to 1997) and as a professor at a public university (since 1997).

10 Thefirstedition, which I used as a textbook in my graduate course at the Universityof Minnesota, presented molecular-marker applications mainly in the lasttwo chapters. But rapid developments since thefirst Edition was publishedhave made molecular markers increasingly cheap and abundant, to theextent that molecular markers should no longer be considered as simply anadd-on to a Breeding program. Molecular-marker applications are thereforeintegrated throughout the text in this Second coverage of the subject assumes that the reader has taken a graduate-credit course in plant Breeding and a graduate-credit course in of basic matrix algebra is required; a brief introduction to ma-trix algebra is included for those without this background.