GENETICS, GENOMICS AND BREEDING OF BERRIES 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: (cid:129) Jinguo Hu, Gerald Seiler & Chittaranjan Kole: Sunfl ower (cid:129) Kristin D. Bilyeu, Milind B. Ratnaparkhe & Chittaranjan Kole: Soybean (cid:129) Robert Henry & Chittaranjan Kole: Sugarcane (cid:129) Kevin Folta & Chittaranjan Kole: Berries (cid:129) Jan Sadowsky & Chittaranjan Kole: Vegetable Brassicas (cid:129) James M. Bradeen & Chittaranjan Kole: Potato (cid:129) C.P. Joshi, Stephen DiFazio & Chittaranjan Kole: Poplar (cid:129) Anne-Françoise Adam-Blondon, José M. Martínez- Zapater & Chittaranjan Kole: Grapes (cid:129) Christophe Plomion, Jean Bousquet & Chittaranjan Kole: Conifers (cid:129) Dave Edwards, Jacqueline Batley, Isobel Parkin & Chittaranjan Kole: Oilseed Brassicas (cid:129) Marcelino Pérez de la Vega, Ana María Torres, José Ignacio Cubero & Chittaranjan Kole: Cool Season Grain Legumes GENETICS, GENOMICS AND BREEDING OF BERRIES Editors Kevin M. Folta Horticultural Sciences Department Institute for Food and Agriculture Sciences (IFAS) University of Florida 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 Published by Science Publishers, P.O. Box 699, Enfi eld, 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 © 2011 ISBN 978-1-57808-707-5 Library of Congress Cataloging-in-Publication Data Genetics, genomics and breeding of berries / editors: Kevin M. Folta, Chittaranjan Kole. -- 1st. ed. p. cm. Includes bibliographical references and index. ISBN 978-1-57808-707-5 (hardcover) 1. Berries--Genetics. 2. Berries--Genome mapping. 3. Berries--Breeding. I. Folta, Kevin M. II. Kole, Chittaranjan. SB381.G464 2011 634’.7--dc22 2010035715 The views expressed in this book are those of the author(s) and the publisher does not assume responsibility for the authenticity of the fi ndings/conclusions drawn by the author(s). Also no responsibility is assumed by the publishers for any damage to the property or persons as a result of operation or use of this publication and/or the information contained herein. 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, mechani- cal, 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 oth- erwise 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 pub- lished and without a similar condition including this condition being imposed on the subsequent purchaser. Printed in the United States of America Preface to the Series Genetics, genomics and breeding has emerged as three overlapping and complimentary disciplines for comprehensive and fi ne-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 utiliza- tion of plant genetics, genomics and breeding essentially require thorough understanding of their components including classical, biochemical, cyto- logical 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 com- ponents 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 fi ll 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 vi Genetics, Genomics and Breeding of Berries basic information on taxonomy, habit, habitat, morphology, karyotype, ploidy level and genome size, etc. Classical genetics and traditional breeding have contributed enormous- ly 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. Em- ployment 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 infi nite wealth of desirable genes in the indigenous cultivars and wild allied species besides the available germplasms in na- tional 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 exam- ples on diverse markers including the anonymous type 2 markers such as RFLPs, RAPDs, AFLPs, etc. and the gene-specifi c type 1 markers such as EST-SSRs, SNPs, etc.; various mapping populations including F, backcross, 2 Preface to the Series vii 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 dif- ferent 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 breed- ing 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 develop- ing 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 avail- able 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 struc- tural 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 viii Genetics, Genomics and Breeding of Berries extensive coverage on the level (national or international) of collaboration and the strategies and status of whole genome sequencing in plants for which sequencing efforts have been completed or are progressing currently. We have also included critical assessment of the impact of these genome initiatives in the respective volumes. Comparative genome mapping based on molecular markers and map positions of genes and QTLs practiced during the last two decades of the last century provided answers to many basic questions related to evolu- tion, origin and phylogenetic relationship of close plant taxa. Enrichment of genomic resources has reinforced the study of genome homology and synteny of genes among plants not only in the same family but also of taxonomically distant families. Comparative genomics is not only deliver- ing answers to the questions of academic interest but also providing many candidate genes for plant genetic improvement. The ‘central dogma’ enunciated in 1958 provided a simple picture of gene function—gene to mRNA to transcripts to proteins (enzymes) to me- tabolites. The enormous amount of information generated on characteriza- tion of transcripts, proteins and metabolites now have led to the emergence of individual disciplines including functional genomics, transcriptomics, proteomics and metabolomics. Although all of them ultimately strengthen the analysis and improvement of a genome, they deserve individual de- liberations for each plant species. For example, microarrays, SAGE, MPSS for transcriptome analysis; and 2D gel electrophoresis, MALDI, NMR, MS for proteomics and metabolomics studies require elaboration. Besides transcriptome, proteome or metabolome QTL mapping and application of transcriptomics, proteomics and metabolomics in genomics-assisted breeding are frontier fi elds now. We included discussions on them in the relevant volumes. The databases for storage, search and utilization on the genomes, genes, gene products and their sequences are growing enormously in each second and they require robust bioinformatics tools plant-wise and purpose-wise. We included a section on databases on the gene and genomes, gene expres- sion, comparative genomes, molecular marker and genetic maps, protein and metabolomes, and their integration. Notwithstanding the progress made so far, each crop or model plant species requires more pragmatic retrospect. For the model plants we need to answer how much they have been utilized to answer the basic questions of genetics and genomics as compared to other wild and domesticated species. For the economic plants we need to answer as to whether they have been genetically tailored perfectly for expanded geographical regions and current requirements for green fuel, plant-based bioproducts and for improvements of ecology and environment. These futuristic explanations have been addressed fi nally in the volumes. Preface to the Series ix We are aware of exclusions of some plants for which we have compre- hensive compilations on genetics, genomics and breeding in hard copy or digital format and also some other plants which will have enough achieve- ments to claim for individual book volume only in distant future. However, we feel satisfi ed that we could present comprehensive deliberations on genetics, genomics and breeding of 30 model and economic plants, and their groups in a few cases, in this series. I personally feel also happy that I could work with many internationally celebrated scientists who edited the book volumes on the leading plants and plant groups and included chapters authored by many scientists reputed globally for their contributions on the concerned plant or plant group. We paid serious attention to reviewing, revising and updating of the manuscripts of all the chapters of this book series, but some technical and formatting mistakes will remain for sure. As the series editor, I take complete responsibility for all these mistakes and will look forward to the readers for corrections of these mistakes and also for their suggestions for further improvement of the volumes and the series so that future editions can serve better the purposes of the students, scientists, industries, and the society of this and future generations. Science publishers, Inc. has been serving the requirements of science and society for a long time with publications of books devoted to advanced concepts, strategies, tools, methodologies and achievements of various science disciplines. Myself as the editor and also on behalf of the volume editors, chapter authors and the ultimate benefi ciaries of the volumes take this opportunity to acknowledge the publisher for presenting these books that could be useful for teaching, research and extension of genetics, genomics and breeding. Chittaranjan Kole Preface to the Volume The commercial berry has enjoyed a resurgence of interest over the last decade, mostly due to the promotion of its potentially positive health benefits. Recent discussions have implicated berries in the possible mitigation of aging, cancer, brain function, cardiovascular disease and metabolic disorders. Colorful and fl avorful berries are capsules fi lled with antioxidants, anthocyanins, polyphenols and ellagic acid—all compounds with possible roles in disease prevention or enhanced quality of life. Berries occupy a distinct dietary role in highly industrialized nations. As mundane causes of mortality are overcome with new medical technology humans are living longer, and the trends predict higher likelihoods of long-term degenerative disease leading to death. Diets rich in fruits and vegetables will have a central role in limiting or preventing these illnesses, if not for their inherent compounds then for their intense fl avors and colors with few accompanying calories. In the developing world berries might deliver nutritious compounds to those who desperately need them- possibly via plants that will be adapted to local conditions. The popularity and demand for berries continues to increase. At the same time the production of all fruits, nuts and vegetables is limited by a series of challenges. Once potent soil fumigants have been banned, no longer presenting an affordable and effective way to curb soil pests, pathogens and weedy competitors. The price of labor, fuel, and fertilizers continues to rise, while prime land and fresh water become increasingly scarce. Farmers have to do more with less, and then do so in a market where prices are depressed by a limited number of competitive wholesalers. The current slate of commercial cultivars meets the berry de- mand, but as consumption grows in concert with production threats, new cultivars will need to be developed to meet the challenges of production and distribution. Today, the challenge is to enhance varietal performance and produce perfect products with fewer agricultural inputs. These accomplishments must be performed with high sensitivity to environmental stewardship yet be fl exible in an ever-changing climate. Traditional crop breeding offers the potential to greatly improve the capacity of cultivars. Coupled with modern genomics-enabled breeding techniques, the likelihood for breeding