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Takuji Sasaki · Motoyuki Ashikari Editors Rice Genomics, Genetics and Breeding Rice Genomics, Genetics and Breeding Takuji Sasaki • Motoyuki Ashikari Editors

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Takuji Sasaki · Motoyuki Ashikari Editors Rice Genomics, Genetics and Breeding Rice Genomics, Genetics and Breeding Takuji Sasaki • Motoyuki Ashikari Editors Takuji Sasaki · Motoyuki Ashikari Editors Rice Genomics, Genetics and Breeding Rice Genomics, Genetics and Breeding Takuji Sasaki • Motoyuki Ashikari Editors Rice Genomics, Genetics and Breeding Editors Takuji Sasaki Motoyuki Ashikari NODAI Research Institute Bioscience and Biotechnology Center Tokyo University of Agriculture Nagoya University Setagaya, Tokyo, Japan Nagoya, Aichi, Japan ISBN 978-981-10-7460-8 ISBN 978-981-10-7461-5 (eBook) https://doi.org/10.1007/978-981-10-7461-5 Library of Congress Control Number: 2018930351 © Springer Nature Singapore Pte Ltd. 2018 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 Nature Singapore Pte Ltd. The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore Preface Rice is a staple food for about half of the world population and has sustained mankind since the dawn of agriculture. As the mid-twenty first century approaches, the world is faced with the monumental task of feeding 9 billion people. To address this challenge, sustainable increases in cereal grain production has to be met. Increasing rice production would require significant improvements in two key aspects: (1) crop management strategies including soil, water, and pest and disease management and (2) development of cultivars with better characteristics including higher yield and improved grain quality. Both these factors would be critical in realizing sustainable rice cultivation. This book focuses on the body of genetics, genomics, and breeding researches that have been carried out to characterize the rice plant itself towards the purposeful development of better rice cultivars. Existing rice varieties that are being grown in localities worldwide are results of breeding efforts in response to demands by farmers for cultivars that are adapted to specific regional environments and by consumers with established quality preferences. For a long time, breeding for improved cultivars relied on visual observations and selection of recombinants with favorable phenotypes. With the discovery of Mendel’s law, however, it has been shown that many important phenotypes or traits are too complex to be explained by mere visual observations. As in the case of many other organisms, advancement in molecular genetics has revolutionized our understanding of rice as a plant. The map-based, genome sequence of a standard rice variety that was released in 2004 via an international collaboration has facilitated the identification and cloning of genes and quantitative trait locus (QTL) controlling various traits. This sequence information also opened the doors to the field of genomics which aims to understand genome-wide variation in rice in terms of gene expression, metabolite profile, and hormonal level during development. These information are in turn used to elucidate genetic networks that make up the rice plant. v vi Preface Combined with the fast pace of technological advancements, the mega-volume of genomic information has allowed targeted genetic manipulations to induce variations in a given allele using genome-editing technologies such as TALENS or CRISPR/Cas9 system. To this day, genome editing has found applications not only in validating gene function but also in generating new alleles that can give more favorable phenotypes. This book is composed of 28 chapters that describe the recent progress and future perspectives in Rice Genomics, Genetics and Breeding. Each chapter, written by established rice researchers who are experts in their field, is a comprehensive look at the genetics and genomics machineries underlying various traits in rice that can be used to address issues on food security. This is especially intended for rice scientists, breeders, post-docs, and graduate and undergraduate students as a stan- dard reference that can be used to device strategies towards solving the 9 billion people challenge. The editors would like to gratefully acknowledge the respective authors for their outstanding contributions towards the realization of this wonderful book. Special thanks go to Ms. Yoko Niimi of Nagoya University for carefully checking all the citations in each chapter and to Ms. Sowmya Ramalingam of Springer for the final editing of this book. Tokyo, Japan Takuji Sasaki Aichi, Japan Motoyuki Ashikari Contents 1 Genome Sequences of Oryza Species ........................ 1 Masahiko Kumagai, Tsuyoshi Tanaka, Hajime Ohyanagi, Yue-Ie C. Hsing, and Takeshi Itoh 2 Small RNAs in Rice: Molecular Species and Their Functions ..... 21 Yutaka Sato, Misuzu Nosaka-Takahashi, Toshiya Suzuki, and Sae Shimizu-Sato 3 Composition and Structure of Rice Centromeres and Telomeres ......................................... 37 Hiroshi Mizuno, Takashi Matsumoto, and Jianzhong Wu 4 Rice Organelle Genomics: Approaches to Genetic Engineering and Breeding .......................................... 53 Tomohiko Kazama, Asuka Nishimura, and Shin-ichi Arimura 5 Genetic and Epigenetic Regulation of Meiotic Fate Decision and Gametophyte Specification in Rice ...................... 69 Ken-Ichi Nonomura, Seijiro Ono, and Kenji Ueda 6 Transcriptome Dynamics in Rice Leaves Under Natural Field Conditions ....................................... 97 Takeshi Izawa 7 Plant Hormone Cross Talk with a Focus on Strigolactone and Its Chemical Dissection in Rice ........................ 113 Shinsaku Ito, Kai Jiang, and Tadao Asami 8 Rice Plant Architecture: Molecular Basis and Application in Breeding ........................................... 129 Shiwei Bai, Steven M. Smith, and Jiayang Li vii viii Contents 9 Breeding Applications and Molecular Basis of Semi-dwarfism in Rice .................................. 155 Keisuke Nagai, Ko Hirano, Rosalyn B. Angeles-Shim, and Motoyuki Ashikari 10 Genetic and Molecular Dissection of Flowering Time Control in Rice ........................................ 177 Kazuki Matsubara and Masahiro Yano 11 Gene Network of Grain Size and Number in Rice ............. 191 Qian Qian 12 Domestication Loci Controlling Panicle Shape, Seed Shattering, and Seed Awning ............................. 207 Takashige Ishii and Ryo Ishikawa 13 Transport System of Mineral Elements in Rice ................ 223 Namiki Mitani-Ueno, Naoki Yamaji, and Jian Feng Ma 14 Genetic Mechanisms Involved in the Formation of Root System Architecture ................................ 241 Yuka Kitomi, Jun-Ichi Itoh, and Yusaku Uga 15 Genetics and Breeding of Flooding Tolerance in Rice ........... 275 Endang M. Septiningsih and David J. Mackill 16 The Gene Network That Regulates Salt Tolerance in Rice ....... 297 Dai-Yin Chao and Hong-Xuan Lin 17 Cold and Water-Deficit Regulatory Mechanisms in Rice: Optimizing Stress Tolerance Potential by Pathway Integration and Network Engineering ............... 317 Benildo G. de los Reyes, Yong Sig Kim, Bijayalaxmi Mohanty, Arvind Kumar, Ai Kitazumi, Isaiah Catalino M. Pabuayon, Nitika Sandhu, and Dong-Yup Lee 18 Pathogen Recognition and Immune Signaling ................. 361 Tsutomu Kawasaki 19 Interaction of Rice and Xanthomonas TAL Effectors ........... 375 Si Nian Char, Sangryeol Park, and Bing Yang 20 Marker-Assisted Gene Pyramiding for Durable Resistance to Blast .............................................. 393 Shuichi Fukuoka 21 Genes Affecting Eating and Processing Qualities .............. 417 Takayuki Umemoto Contents ix 22 Genetic Dissection and Breeding for Grain Appearance Quality in Rice ........................................ 435 Kiyosumi Hori 23 Rice Epigenomes: Characteristics, Regulatory Functions, and Reprogramming Mechanisms ......................... 453 Yongfeng Hu and Dao-Xiu Zhou 24 Genomic Selection in Rice Breeding ........................ 473 Jennifer Spindel and Hiroyoshi Iwata 25 Genome-Wide Association Mapping of Complex Traits in Rice ............................................... 497 Xuehui Huang and Bin Han 26 Next-Generation Breeding of Rice by Whole-Genome Approaches ........................................... 511 Akira Abe, Hiroki Takagi, Hiroki Yaegashi, Satoshi Natsume, Hiroe Utsushi, Muluneh Tamiru, and Ryohei Terauchi 27 Rice Genome Editing ................................... 523 Masaki Endo, Ayako Nishizawa-Yokoi, and Seiichi Toki 28 Databases for Rice Omics Studies .......................... 541 Takeshi Itoh,
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