Genetics, Genomics and Breeding of Peppers and Eggplants by Byoung-Cheorl Kang and Chittaranjan Kole


4558903559b4c8b-261x361.jpeg Author Byoung-Cheorl Kang and Chittaranjan Kole
Isbn 9781466577459
File size 3MB
Year 2013
Pages 182
Language English
File format PDF
Category biology



 

GENETICS, GENOMICS AND BREEDING OF PEPPERS AND EGGPLANTS 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 • Kristin D. Bilyeu, Milind B. Ratnaparkhe & Chittaranjan Kole: Soybean • Robert Henry & Chittaranjan Kole: Sugarcane • Kevin Folta & Chittaranjan Kole: Berries • Jan Sadowsky & Chittaranjan Kole: Vegetable Brassicas • James M. Bradeen & Chittaranjan Kole: Potato • C.P. Joshi, Stephen DiFazio & Chittaranjan Kole: Poplar • Anne-Françoise Adam-Blondon, José M. Martínez-Zapater & Chittaranjan Kole: Grapes • Christophe Plomion, Jean Bousquet & Chittaranjan Kole: Conifers • Dave Edwards, Jacqueline Batley, Isobel Parkin & Chittaranjan Kole: Oilseed Brassicas • Marcelino Pérez de la Vega, Ana María Torres, José Ignacio Cubero & Chittaranjan Kole: Cool Season Grain Legumes • Yi-Hong Wang, Tusar Kanti Behera & Chittaranjan Kole: Cucurbits • Albert G. Abbott & Chittaranjan Kole: Stone Fruits • Barbara E. Liedl, Joanne A. Labate, John R. Stommel, Ann Slade & Chittaranjan Kole: Tomato • Byoung-Cheorl Kang & Chittaranjan Kole: Peppers and Eggplants GENETICS, GENOMICS AND BREEDING OF PEPPERS AND EGGPLANTS Editors Byoung-Cheorl Kang Dept. of Plant Science College of Agriculture & Life Sciences Seoul National University Seoul Korea Chittaranjan Kole Department of Genetics and Biochemistry Clemson University Clemson, SC USA p, A SCIENCE PUBLISHERS BOOK CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2013 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Version Date: 20130318 International Standard Book Number-13: 978-1-4665-7746-6 (eBook - PDF) This book contains information obtained from authentic and highly regarded sources. Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint. Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, please access www.copyright.com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and registration for a variety of users. For organizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged. Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe. Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com 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 vi Genetics, Genomics and Breeding of Peppers and Eggplants 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 phenotypebased 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, SNPs, etc.; various mapping populations including F2, backcross, 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 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 viii Genetics, Genomics and Breeding of Peppers and Eggplants 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 evolution, 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 delivering 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 metabolites. The enormous amount of information generated on characterization 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 deliberations 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 fields 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 purposewise. We included a section on databases on the gene and genomes, gene expression, 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 finally in the volumes. Preface to the Series ix We are aware of exclusions of some plants for which we have comprehensive compilations on genetics, genomics and breeding in hard copy or digital format and also some other plants which will have enough achievements to claim for individual book volume only in distant future. However, we feel satisfied 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 beneficiaries 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 This page intentionally left blank Preface to the Volume Peppers and eggplants are two leading vegetable crops produced and consumed worldwide. The consumption patterns of peppers are very diverse over cultures and regions. Peppers are the sole source for pungency and contain various functional nutrients such as vitamins and biological compounds. To facilitate the breeding for agronomical traits such as diseases resistance and quality traits, diverse molecular genetic studies have been performed. Although these studies have been hampered by disadvantageous characteristics of peppers such as large genome size and low efficiency of regeneration and transformation, recent achievements on pepper genome sequencing, trait-linked marker development enabled the cloning of genes involved in useful traits. Solanum melongena is an old world species complex that includes weedy and wild relatives as well as primitive cultivars and landraces. As with peppers, the main breeding objectives are yield increase, disease resistance, and fruit quality using parthenocarpy and secondary metabolites. The close relationship between eggplant, tomato, and pepper has facilitated this work as well as made the Solanaceae a model for comparative genomics. In this book, the overall information on agronomical and evolutionary characteristics of peppers and eggplants and results of molecular genetic studies and genome structure are described. Byoung-Cheorl Kang Dept. of Plant Science College of Agriculture & Life Sciences Seoul National University Seoul Korea Chittaranjan Kole Department of Genetics and Biochemistry Clemson University Clemson, SC USA This page intentionally left blank Contents Preface to the Series Preface to the Volume List of Contributors Abbreviations 1. Basic Information on Pepper Wing Yee Liu, Won-Hee Kang and Byoung-Cheorl Kang Abstract 1. Economic Importance 1.1 Yield, Production, Import and Export Values, Top Producing Countries 2. Pepper Consumption and Applications 2.1 Food (Fresh, Dried and Processed) 2.2 Active Ingredients (in Industrial and Medical Products) 3. Nutritional Value of Peppers 3.1 Essential Antioxidant Vitamins 3.2 Biological Pigments 3.3 Minerals and other Nutrients 4. Capsaicinoids and Pungency 4.1 Pungency and the Scoville Scale 4.2 Biosynthesis of Capsaicinoids 4.3 Analytical Technology for Capsaicinoid Compounds 5. Evolution and Domestication of Capsicum 5.1 Evolution of Capsicum 5.2 Domestication of Capsicum 6. Botanical Features 6.1 Botanical Descriptions 6.2 Horticultural Traits of Cultivated Pepper References 2. Classical Genetics and Traditional Breeding in Peppers Wing Yee Liu, Hee-Bum Yang, Yeong Deuk Jo, Hee-Jin Jeong and Byoung-Cheorl Kang Abstract 1. Germplasm v xi xvii xix 1 1 2 2 3 3 3 4 4 4 6 6 6 7 7 8 8 9 10 10 11 13 16 16 17 xiv Genetics, Genomics and Breeding of Peppers and Eggplants 2. Conventional Breeding and Major Breeding Objectives 3. Traits, Classical Genetics and Molecular Markers 4. Other Techniques Used in Pepper Breeding 4.1 Hybrid Seed Production Using Male Sterility 4.2 Doubled Haploid Technology 4.3 Embryo Culture References 18 19 22 22 29 30 31 3. Molecular Linkage Maps of Capsicum Ilan Paran Abstract 1. Early Mapping Studies 2. Evolution of Marker Types 3. Types of Mapping Populations 4. Integrated Maps 5. Comparative Maps 6. Future Perspectives References 40 4. Candidate Gene Approaches in Capsicum Michael Mazourek and Lindsay E. Wyatt Abstract 1. Introduction 2. Map-Based Cloning versus the Candidate Gene Approach 3. Strategies for Compiling Candidate Genes 4. Validation of Candidate Genes in Capsicum 5. Case Studies 5.1 Disease Resistance 5.2 Flavor 5.3 Colors 6. Future Outlook References 56 5. Molecular Mapping of Complex Traits in Capsicum James P. Prince, Davis Cheng and Cristina Fernández Otero Abstract 1. Variation in Capsicum 2. What is a Complex Trait? What are Quantitative Trait Loci (QTL)? 3. Quantitative Traits Analyzed in Pepper 4. How do you Analyze QTLs using Modern Molecular Techniques? 4.1 Phenotypic Issues 77 40 41 42 46 47 49 51 53 56 57 57 58 59 61 61 67 69 71 72 77 77 78 82 82 82 Contents xv 4.2 Molecular Markers 4.3 Populations 4.4 Details on QTL Analyses 5. Mendelization of QTLs and Marker-Assisted Selection (MAS) Acknowledgements References 6. The Structure of Pepper Genome Minkyu Park and Doil Choi Abstract 1. Introduction 2. The Estimated Size of the Pepper Genome 3. The Available Resources of the Pepper Genome 4. The Use of BAC Clones in Marker Development 5. The Comparative Analysis of the Pepper Genome Using Conserved Orthologous Set (COS) Markers 6. Ribosomal Repeats in the Pepper Genome 7. The Structure of the Pepper Genome 8. The Effort to Sequence the Whole Pepper Genome 9. Future Prospects References 7. Eggplant Amy Frary and Sami Doganlar Abstract 1. Economic Importance 2. Nutritional Properties 3. Brief History of the Crop 4. Taxonomy 5. Botanical Description 6. Germplasm 7. Classical Genetics and Traditional Breeding 8. Genetic Engineering 9. Diversity Analysis 10. Molecular Linkage Maps 10.1 A History 10.2 Applications 11. Genomic Resources 12. Future Prospects Acknowledgement References Index Color Plate Section 84 87 90 94 94 95 100 100 100 101 102 105 106 106 108 113 114 114 116 116 117 117 118 119 120 120 121 125 126 128 128 131 135 136 137 137 145 149 This page intentionally left blank List of Contributors Amy Frary Mount Holyoke College, South Hadley, Massachusetts, USA. Email: [email protected] Byoung-Cheorl Kang Department of Plant Science, Seoul National University, Seoul 151-921, Republic of Korea. Email: [email protected] Cristina Fernández Otero Centro de Investigaciones Agrarias de Mabegondo, A Coruña, Spain. Email: [email protected] Davis Cheng Department of Biology, California State University Fresno, Fresno CA 93740 USA. Email: [email protected] Doil Choi Department of Plant Science, Seoul National University, Seoul 151-921, Republic of Korea. Email: [email protected] Hee-Bum Yang Department of Plant Science, Seoul National University, Seoul 151-921, Republic of Korea. Email: [email protected] Hee-Jin Jeong Department of Plant Science, Seoul National University, Seoul 151-921, Republic of Korea. Email: [email protected] Ilan Paran Institute of Plant Sciences, The Volcani Center, Bet Dagan, Israel. Email: [email protected] xviii Genetics, Genomics and Breeding of Peppers and Eggplants James P. Prince Department of Biology, California State University Fresno, Fresno CA 93740, USA. Email: [email protected] Lindsay E. Wyatt Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853. Email: [email protected] Michael Mazourek Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853. Email: [email protected] MinKyu Park Department of Plant Science, Seoul National University, Seoul 151-921, Republic of Korea. Email: [email protected] Sami Doganlar Izmir Institute of Technology, Izmir, Turkey. Email: [email protected] Wing Yee Liu School of Biological Sciences, The University of Hong Kong, 5N01, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong. Email: [email protected] Won-Hee Kang Department of Plant Science, Seoul National University, Seoul 151-921, Republic of Korea. Email: [email protected] Young Deuk Jo Department of Plant Science, Seoul National University, Seoul 151-921, Republic of Korea. Email: [email protected] Abbreviations AFLP AT3 AVRDC BAC BAHD BAP bar BC BLA BSA CaMV CAPS CaSGR CCS CENL CGMS ChiVMV cl cM CMS CMV COS CP cry CS dCAPS DH dhfr DUS EB Amplified fragment length polymorphism Acyltranferase 3 Asian Vegetable Research and Development Center Bacterial artificial chromosome Benzylalcohol acetyltransferase (BEAT), anthocyaninO-hydroxy-cinnamoyltransferase (AHCT), anthranilate N-hydroxycinnamoyl/benzoyltransferase (HCBT), and deacetylvindoline 4-O-acetyltransferase (DAT) Benzyladenine Bialaphos resistance (gene) Backcross Bulked line analysis Bulk segregant analysis Cauliflower mosaic virus Cleaved amplified polymorphic sequences Capsicum stay-green Capsanthin capsorubin synthase Capsicum and Eggplant Newsletter Cytoplasmic-genic male sterility Chilli veinal mottle virus Chlorophyll retainer Centi-Morgan Cytoplasmic male sterility Cucumber mosaic virus Conserved ortholog set Coat protein Cryptochrome (gene) Capsaicin synthase Derived cleaved amplified polymorphic sequences Doubled haploid Dihydrofolate reductase Distinctiveness, uniformity and stability Ethidium bromide

Author Byoung-Cheorl Kang and Chittaranjan Kole Isbn 9781466577459 File size 3MB Year 2013 Pages 182 Language English File format PDF Category Biology Book Description: FacebookTwitterGoogle+TumblrDiggMySpaceShare Peppers and eggplants are two leading vegetable crops produced and consumed worldwide. To facilitate the breeding for agronomical traits such as disease resistance and quality, diverse molecular genetic studies have been carried out. Recent achievements on pepper genome sequencing and trait-linked marker development have enabled the cloning of genes involved in useful traits. This book explores the agronomical and evolutionary characteristics of peppers and eggplants and the results of molecular genetic studies. Topics include molecular linkage maps and candidate gene approaches in capsicum and the structure of the pepper genome.     Download (3MB) Citrus Genetics, Breeding and Biotechnology Cereal Genomics: Methods And Protocols Techniques In Genetic Engineering Obesity: Genomics and Postgenomics Biotechnology Demystified Load more posts

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