Plant Genetics and Genomics: Crops and Models 20 Rebecca Grumet Nurit Katzir Jordi Garcia-Mas Editors Genetics and Genomics of Cucurbitaceae Plant Genetics and Genomics: Crops and Models Volume 20 Series Editor Richard A. Jorgensen More information about this series at http://www.springer.com/series/7397 Rebecca Grumet • Nurit Katzir • Jordi Garcia-Mas Editors Genetics and Genomics of Cucurbitaceae Editors Rebecca Grumet Nurit Katzir Michigan State University Agricultural Research Organization East Lansing, Michigan Newe Ya’ar Research Center USA Ramat Yishay Israel Jordi Garcia-Mas Institut de Recerca i Tecnologia Agroalimentàries (IRTA) Bellaterra, Barcelona Spain ISSN 2363-9601 ISSN 2363-961X (electronic) Plant Genetics and Genomics: Crops and Models ISBN 978-3-319-49330-5 ISBN 978-3-319-49332-9 (eBook) DOI 10.1007/978-3-319-49332-9 Library of Congress Control Number: 2017950169 © Springer International Publishing AG 2017 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer International Publishing AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland Preface The twenty-first century is a golden age for genetics. Massively increasing DNA sequence information and sophisticated bioinformatic capacity at exponentially decreasing cost allow for a world of knowledge that is no longer limited to model species. Members of the Cucurbitaceae family are among the beneficiaries of these technological gains. The Cucurbitaceae, often referred to as “cucurbits,” are proba- bly best known for their large (sometimes extremely large), colorful, and morpho- logically variable fruits. The most economically important crops are watermelon (Citrullus lanatus), melon (Cucumis melo), cucumber (Cucumis sativus), and vari- ous squashes and pumpkins (Cucurbita pepo, maxima, and moschata), which are produced in widely diverse forms throughout the world. Depending on the specific crop and type, they can be consumed as vegetable or dessert, and in some cases, especially for various squashes and pumpkin, can serve as mainstays of the diet. Additional cultivated crops include bitter, bottle, wax, snake sponge, and ridge gourds, which are primarily cultivated in southern and southeastern Asia. Seeds of cucurbit crops also can be an important source of nutrition. In addition, certain cucurbit species are noted for medicinal properties, and gourd shells have historical uses as containers and musical instruments. Several genomic initiatives throughout the world are exploring the genetics and genomics of these crops. Genetic features, including diploid genomes and relatively small genome size (~367, 454, 450, and 400 Mbp for cucumber, melon, water- melon, and squash, respectively), facilitate these efforts, and close genetic relation- ships allow for synergistic approaches. Over the course of the past decade draft genome sequences have been assembled for cucumber, melon, and watermelon; assemblies of Cucurbita species are in progress. As would be expected, a major sec- tion of “Genetics and Genomics of the Cucurbitaceae” is devoted to description of cucurbit genomes and available genomic resources. Of course genomic information does not exist in a vacuum and must be inter- preted within the context of the crop or species and its agronomic, geographic, and evolutionary relationships. The Cucurbitaceae family contains approximately 1000 species, with origins tracing to Southeast Asia prior to subsequent distribution and diversification in Africa and South America. From this great diversity, a small num- v vi Preface ber were domesticated and carried to current crop status. Over the past century, the most extensively cultivated cucurbits have been greatly improved by plant breeders using conventional plant breeding techniques to increase productivity, yield, fruit size, and quality. This volume provides an overview of use of cucurbits and their evolutionary relationships and explores the genetic resources for the cucurbit crops. Much current effort in each of the crops is devoted to incorporation of resistance to critical diseases for which germplasm collections around the world serve as invalu- able, critical resources. Looking forward, molecular breeding approaches facilitated by genomic advances are expected to play an increasing role in facilitating crop improvement, including introgression of novel resistance alleles along with other desirable traits. Finally, the cucurbits are especially noteworthy for several biological features such as unique phloem structure, highly flexible sex expression patterns, extensively diverse fruit size, shape, colors and patterns, and delicious flavors and aromas. Increasing genomic tools and genetic analyses are making major contributions to our understanding of the fundamental bases for these biological phenomena. Thus, collectively, “Genetics and Genomics of the Cucurbitaceae” explores the genetic diversity of cucurbit crops, the current state of knowledge of cucurbit genomics, and evolving applications of genetics and genomics for improvement of cucurbit crops and understanding of cucurbit growth, development, and adaptation to their environments. Contents Cultivation and Uses of Cucurbits ������������������������������������������������������������������ 1 James D. McCreight Phylogeny and Evolution of the Cucurbitaceae �������������������������������������������� 13 Susanne S. Renner and Hanno Schaefer Melon Genetic Resources: Phenotypic Diversity and Horticultural Taxonomy �������������������������������������������������������������������������� 25 Michel Pitrat Genetic Resources of Cucumber . 61 Rachel P. Naegele and Todd C. Wehner Genetic Resources of Watermelon ������������������������������������������������������������������ 87 Amnon Levi, Robert Jarret, Shaker Kousik, W. Patrick Wechter, Padma Nimmakayala, and Umesh K. Reddy Genetic Resources of Pumpkins and Squash, Cucurbita spp. ���������������������� 111 Harry S. Paris Gourds: Bitter, Bottle, Wax, Snake, Sponge and Ridge �������������������������������� 155 Narinder P.S. Dhillon, Supannika Sanguansil, Sheo Pujan Singh, Mohammed Abu Taher Masud, Prashant Kumar, Latchumi Kanthan Bharathi, Halit Yetişir, Rukui Huang, Doan Xuan Canh, and James D. McCreight The Melon Genome ������������������������������������������������������������������������������������������ 173 Josep Casacuberta, Pere Puigdomènech, and Jordi Garcia-Mas The Cucumber Genome ���������������������������������������������������������������������������������� 183 Yiqun Weng The Watermelon Genome �������������������������������������������������������������������������������� 199 Xu Yong and Shaogui Guo Genetics and Genomics of Cucurbita spp.. 211 J. Montero-Pau, C. Esteras, J. Blanca, P. Ziarsolo, J. Cañizares, and B. Picó vii viii Contents Comparative Genomics of the Cucurbitaceae . 229 Padma Nimmakayala, Thangasamy Saminathan, Venkata Lakshmi Abburi, Lav Kumar Yadav, Yan Tomason, Amnon Levi, Yiqun Weng, and Umesh K. Reddy Organellar Genomes of the Cucurbits . 241 Michael J. Havey Databases and Bioinformatics for Cucurbit Species . 253 Yang Bai, Zhonghua Zhang, and Zhangjun Fei Genetic Mapping of Complex Traits in Cucurbits ���������������������������������������� 269 María José Gonzalo and Antonio J. Monforte Phloem Biology of the Cucurbitaceae ������������������������������������������������������������ 291 Robert Turgeon Sex Determination in Cucumis . 307 Natalia Yaneth Rodriguez-Granados, Afef Lemhemdi, Fadi Abou Choucha, David Latrasse, Moussa Benhamed, Adnane Boualem, and Abdelhafid Bendahmane Genomic Analysis of Cucurbit Fruit Growth ������������������������������������������������ 321 Rebecca Grumet and Marivi Colle Fruit Ripening in Melon ���������������������������������������������������������������������������������� 345 Ryoichi Yano and Hiroshi Ezura Genomic Aspects of Melon Fruit Quality ������������������������������������������������������ 377 Amit Gur, Itay Gonda, Vitaly Portnoy, Galil Tzuri, Noam Chayut, Shahar Cohen, Yelena Yeselson, Ayala Meir, Einat Bar, Rachel Davidovitz-Rikanati, Uzi Saar, Harry S. Paris, Joseph Burger, Yaakov Tadmor, Efraim Lewinsohn, Arthur A. Schaffer, and Nurit Katzir Cucurbit Genetics and Genomics: A Look to the Future . 409 Rebecca Grumet, Jordi Garcia-Mas,