GGGGGEEEEENNNNNEEEEETTTTTIIIIICCCCCSSSSS,,,,, GGGGGEEEEENNNNNOOOOOMMMMMIIIIICCCCCSSSSS AAAAANNNNNDDDDD BBBBBRRRRREEEEEEEEEEDDDDDIIIIINNNNNGGGGG OOOOOFFFFF SSSSSUUUUUNNNNNFFFFFLLLLLOOOOOWWWWWEEEEERRRRR Genetics, Genomics and Breeding of Crop Plants Series Editor Chittaranjan Kole Department of Genetics and Biochemistry Clemson University Clemson, SC USA Books in this Series: Published or in Press: • Jinguo Hu, Gerald Seiler & Chittaranjan Kole: Sunflower (cid:129) Kristin D. Bilyeu, Milind B. Ratnaparkhe & Chittaranjan Kole: Soybean (cid:129) Robert Henry & Chittaranjan Kole: Sugarcane Books under preparation: (cid:129) Jan Sadowsky & Chittaranjan Kole: Vegetable Brassicas (cid:129) C.P. Joshi, Stephen DiFazio & Chittaranjan Kole: Poplar (cid:129) Kevin Folta & Chittaranjan Kole: Berries GENETICS, GENOMICS AND BREEDING OF SUNFLOWER Editors Jinguo Hu USDA-Agricultural Research Service Western Regional Plant Introduction Station Pullman, WA USA Gerald Seiler USDA-Agricultural Research Service Northern Crop Science Laboratory Fargo, ND USA Chittaranjan Kole Department of Genetics and Biochemistry Clemson University Clemson, SC USA CRC Press 6Su0i0te0 3B0ro0k, eBno Scoau nRda tPoanr,k FwLa y3, 3N4W87 Science Publishers Taylor & Francis Group 270 Madison Avenue an informa business N2 ePwar Yk oSrqk,u NarYe ,1 M00il1to6n Park Enfield, New Hampshire www.crcpress.com Abingdon, Oxon OX 14 4RN, UK iv Genetics, Genomics and Breeding of Sunflower Published by Science Publishers, P.O. Box 699, Enfield, NH 03748, USA An imprint of Edenbridge Ltd., British Channel Islands E-mail: [email protected] Website: www.scipub.net Marketed and distributed by: CRC Press 6Su0i0te0 3B0ro0k, eBno Scoau nRda tPoanr,k FwLa y3, 3N4W87 Taylor & Francis Group 270 Madison Avenue an informa business New York, NY 10016 2 Park Square, Milton Park www.crcpress.com Abingdon, Oxon OX 14 4RN, UK Copyright reserved © 2010 Cover illustration reproduced by courtesy of Dale Rehder ISBN 978-1-57808-676-4 Library of Congress Cataloging-in-Publication Data Genetics, genomics and breeding of sunflower / editors, Jinguo Hu, Gerald Seiler. p. cm. -- (Genetics, genomics and breeding of crop plants) Includes bibliographical references and index. ISBN 978-1-57808-676-4 (hardcover) 1. Sunflowers--Genetics. 2. Sunflowers--Genome mapping. 3. Sunflowers--Breeding. I. Hu, Jinguo. II. Seiler, Gerald J., 1949- III. Series. QK495.C74G445 2009 635.9'3399--dc22 2009039713 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 or otherwise, without the prior permission of the publisher, in writing. The exception to this is when a reasonable part of the text is quoted for purpose of book review, abstracting etc. This book is sold subject to the condition that it shall not, by way of trade or otherwise be lent, re-sold, hired out, or otherwise circulated without the publisher’s prior consent in any form of binding or cover other than that in which it is published and without a similar condition including this condition being imposed on the subsequent purchaser. Printed in the United States of America Dedication Professor Loren Rieseberg This book is dedicated to Professor Loren Rieseberg, Canadian Research Chair in Plant Evolutionary Genomics, University of British Columbia, and Distinguished Professor, Department of Biology, Indiana University for his early and innovative research on plant evolutionary genomics of sunflower (Helianthus annuus L.) and its wild relatives. His pioneering research on hybridization and speciation in the genus have raised sunflower to the level of Darwin’s finches and stickleback fishes as natural paradigms for the study of adaptive evolution and speciation. This work, in combination with Prof. Rieseberg’s studies of the domestication process and habitat diversification, has furthered our understanding of the potential value of the wild sunflower species and their related traits for the expansion of sunflower production in diverse environments. Prof. Rieseberg was one of the first to document the very high levels of gene flow between cultivated and wild sunflowers, implying that transgene escape is likely. He also directs the Compositae Genome Project, a multiple collaborator project, vi Genetics, Genomics and Breeding of Sunflower which has developed over 250,000 ESTs for sunflower. More recently, he is leading an effort to sequence the sunflower genome. He has been recognized for his numerous significant accomplishments receiving several awards such as the MacArthur and Guggenheim Fellowships, Class of ’54 Endowed Professorship, Fellow of the American Academy of Arts and Sciences, and the American Association for the Advancement of Science, Stebbins Medal, David Starr Jordan Prize, and the Teaching Excellence Recognition Award, Indiana University. During more than 20 years of teaching and research many national and international undergraduate, graduate, and postgraduate students have been beneficiaries of his teaching, expertise, philosophy, and passion for seeking out the how and why of science. Preface to the Series Genetics, genomics and breeding has emerged as three overlapping and complimentary disciplines for comprehensive and fine-scale analysis of plant genomes and their precise and rapid improvement. While genetics and plant breeding have contributed enormously towards several new concepts and strategies for elucidation of plant genes and genomes as well as development of a huge number of crop varieties with desirable traits, genomics has depicted the chemical nature of genes, gene products and genomes and also provided additional resources for crop improvement. In today’s world, teaching, research, funding, regulation and utilization of plant genetics, genomics and breeding essentially require thorough understanding of their components including classical, biochemical, cytological and molecular genetics; and traditional, molecular, transgenic and genomics-assisted breeding. There are several book volumes and reviews available that cover individually or in combination of a few of these components for the major plants or plant groups; and also on the concepts and strategies for these individual components with examples drawn mainly from the major plants. Therefore, we planned to fill an existing gap with individual book volumes dedicated to the leading crop and model plants with comprehensive deliberations on all the classical, advanced and modern concepts of depiction and improvement of genomes. The success stories and limitations in the different plant species, crop or model, must vary; however, we have tried to include a more or less general outline of the contents of the chapters of the volumes to maintain uniformity as far as possible. Often genetics, genomics and plant breeding and particularly their complimentary and supplementary disciplines are studied and practiced by people who do not have, and reasonably so, the basic understanding of biology of the plants for which they are contributing. A general description of the plants and their botany would surely instill more interest among them on the plant species they are working for and therefore we presented lucid details on the economic and/or academic importance of the plant(s); historical information on geographical origin and distribution; botanical origin and evolution; available germplasms and gene pools, and genetic and cytogenetic stocks as genetic, genomic and breeding resources; and viii Genetics, Genomics and Breeding of Sunflower basic information on taxonomy, habit, habitat, morphology, karyotype, ploidy level and genome size, etc. Classical genetics and traditional breeding have contributed enormously even by employing the phenotype-to-genotype approach. We included detailed descriptions on these classical efforts such as genetic mapping using morphological, cytological and isozyme markers; and achievements of conventional breeding for desirable and against undesirable traits. Employment of the in vitro culture techniques such as micro- and megaspore culture, and somatic mutation and hybridization, has also been enumerated. In addition, an assessment of the achievements and limitations of the basic genetics and conventional breeding efforts has been presented. It is a hard truth that in many instances we depend too much on a few advanced technologies, we are trained in, for creating and using novel or alien genes but forget the infinite wealth of desirable genes in the indigenous cultivars and wild allied species besides the available germplasms in national and international institutes or centers. Exploring as broad as possible natural genetic diversity not only provides information on availability of target donor genes but also on genetically divergent genotypes, botanical varieties, subspecies, species and even genera to be used as potential parents in crosses to realize optimum genetic polymorphism required for mapping and breeding. Genetic divergence has been evaluated using the available tools at a particular point of time. We included discussions on phenotype-based strategies employing morphological markers, genotype-based strategies employing molecular markers; the statistical procedures utilized; their utilities for evaluation of genetic divergence among genotypes, local landraces, species and genera; and also on the effects of breeding pedigrees and geographical locations on the degree of genetic diversity. Association mapping using molecular markers is a recent strategy to utilize the natural genetic variability to detect marker-trait association and to validate the genomic locations of genes, particularly those controlling the quantitative traits. Association mapping has been employed effectively in genetic studies in human and other animal models and those have inspired the plant scientists to take advantage of this tool. We included examples of its use and implication in some of the volumes that devote to the plants for which this technique has been successfully employed for assessment of the degree of linkage disequilibrium related to a particular gene or genome, and for germplasm enhancement. Genetic linkage mapping using molecular markers have been discussed in many books, reviews and book series. However, in this series, genetic mapping has been discussed at length with more elaborations and examples on diverse markers including the anonymous type 2 markers such as RFLPs, RAPDs, AFLPs, etc. and the gene-specific type 1 markers such as EST-SSRs, Preface to the Series ix SNPs, etc.; various mapping populations including F , backcross, 2 recombinant inbred, doubled haploid, near-isogenic and pseudotestcross; computer software including MapMaker, JoinMap, etc. used; and different types of genetic maps including preliminary, high-resolution, high-density, saturated, reference, consensus and integrated developed so far. Mapping of simply inherited traits and quantitative traits controlled by oligogenes and polygenes, respectively has been deliberated in the earlier literature crop-wise or crop group-wise. However, more detailed information on mapping or tagging oligogenes by linkage mapping or bulked segregant analysis, mapping polygenes by QTL analysis, and different computer software employed such as MapMaker, JoinMap, QTL Cartographer, Map Manager, etc. for these purposes have been discussed at more depth in the present volumes. The strategies and achievements of marker-assisted or molecular breeding have been discussed in a few books and reviews earlier. However, those mostly deliberated on the general aspects with examples drawn mainly from major plants. In this series, we included comprehensive descriptions on the use of molecular markers for germplasm characterization, detection and maintenance of distinctiveness, uniformity and stability of genotypes, introgression and pyramiding of genes. We have also included elucidations on the strategies and achievements of transgenic breeding for developing genotypes particularly with resistance to herbicide, biotic and abiotic stresses; for biofuel production, biopharming, phytoremediation; and also for producing resources for functional genomics. A number of desirable genes and QTLs have been cloned in plants since 1992 and 2000, respectively using different strategies, mainly positional cloning and transposon tagging. We included enumeration of these and other strategies for isolation of genes and QTLs, testing of their expression and their effective utilization in the relevant volumes. Physical maps and integrated physical-genetic maps are now available in most of the leading crop and model plants owing mainly to the BAC, YAC, EST and cDNA libraries. Similar libraries and other required genomic resources have also been developed for the remaining crops. We have devoted a section on the library development and sequencing of these resources; detection, validation and utilization of gene-based molecular markers; and impact of new generation sequencing technologies on structural genomics. As mentioned earlier, whole genome sequencing has been completed in one model plant (Arabidopsis) and seven economic plants (rice, poplar, peach, papaya, grapes, soybean and sorghum) and is progressing in an array of model and economic plants. Advent of massively parallel DNA sequencing using 454-pyrosequencing, Solexa Genome Analyzer, SOLiD system, Heliscope and SMRT have facilitated whole genome sequencing in many other plants more rapidly, cheaply and precisely. We have included