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Chromosome and Genomic Engineering in Plants Methods in Molecular Biology 1469

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Methods in Molecular Biology 1469

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Transformation or transfection is an indispensable tool in basic and applied studies in biological sciences. In plants, a number of species can be transformed by an Agrobacteriummediated system, particle bombardment, and/or protoplast fusion. Compared to other organisms, however, these three techn...

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methods in molecular biology 1469

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Methods in
Molecular Biology 1469

Minoru Murata Editor

Chromosome
and Genomic
Engineering in
Plants
Methods and Protocols

,METHODS IN MOLECULAR BIOLOGY

Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB, UK

For further volumes:
http://www.springer.com/series/7651

,
,Chromosome and Genomic
Engineering in Plants

Methods and Protocols

Edited by

Minoru Murata
Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan

,Editor
Minoru Murata
Institute of Plant Science and Resources
Okayama University
Kurashiki, Japan

ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-4929-8 ISBN 978-1-4939-4931-1 (eBook)
DOI 10.1007/978-1-4939-4931-1

Library of Congress Control Number: 2016946367

© Springer Science+Business Media New York 2016
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.
Cover illustration: Arabidopsis transgenic plants in plate, expressing Ac transposase

Printed on acid-free paper

This Humana Press imprint is published by Springer Nature
The registered company is Springer Science+Business Media LLC New York

,Preface

Transformation or transfection is an indispensable tool in basic and applied studies in bio-
logical sciences. In plants, a number of species can be transformed by an Agrobacterium-
mediated system, particle bombardment, and/or protoplast fusion. Compared to other
organisms, however, these three techniques are uncontrollable with regard to the insertion
of exogenous genes or DNA because the insertion into the genome or chromosome is quite
random, and multiple-copy insertion frequently occurs. This random and multiple-copy
insertion increases the risk of disrupting essential genes. To avoid such risk, gene targeting
via homologous recombination is most desirable, as has been shown in yeast and mice.
However, the occurrence of homologous recombination is quite limited in plants, except
for in some lower plants (i.e., Physcomitrella patens and Chlamydomonas reinhardtii).
To overcome such difficulties in controlling exogenous DNA insertion, at least two
approaches have recently been developed. The first approach is a “plant chromosome vec-
tor” system that allows us to introduce desired genes or DNA into target sites on the chro-
mosome vector. Although these systems are not completely established, plant artificial
chromosomes, which could be used as platforms for introducing exogenous genes, have
been successfully generated in some plant species. This approach requires various tech-
niques, such as telomere DNA-induced chromosome truncation, sequence-specific recom-
bination (i.e., Cre/LoxP), and transposon (i.e., Ac/DS) systems, in addition to knowledge
of chromosome functional elements (centromere, telomere, and origin of replication). The
second approach is “genome editing,” which makes it possible to introduce mutations into
any of the genes or DNA that we wish to change. This technique has been used since the
discovery of zinc finger nucleases in 1996. To date, more efficient and mature techniques
have been developed such as TALEN and CRISPR/Cas9. These two approaches are not
independent from each other and can be applied cooperatively. Hence, this volume assem-
bles protocols for chromosome engineering and genome editing that are needed when
using the two aforementioned approaches to manipulate chromosomal and genomic DNA
in plants. In addition, other related techniques supporting these two approaches are used
to accelerate progress in plant chromosome and genome engineering.
Finally, I would like to extend my heartfelt thanks to all of the authors who contributed
their excellent and interesting research results to this volume. I am also grateful to the series
editor, John Walker, for encouraging me to edit one part of the series, “Methods in
Molecular Biology”.

Kurashiki, Japan Minoru Murata

v

,
,Contents

Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix

1 Production of Engineered Minichromosome Vectors via the Introduction
of Telomere Sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Nathaniel Graham, Nathan Swyers, Jon Cody, Morgan McCaw,
Changzeng Zhao, and James A. Birchler
2 Method for Biolistic Site-Specific Integration in Plants Catalyzed
by Bxb1 Integrase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Ruyu Li, Zhiguo Han, Lili Hou, Gurminder Kaur, Qian Yin,
and David W. Ow
3 Protocol for In Vitro Stacked Molecules Compatible
with In Vivo Recombinase-Mediated Gene Stacking . . . . . . . . . . . . . . . . . . . . 31
Weiqiang Chen and David W. Ow
4 Generation and Analysis of Transposon Ac/Ds-Induced
Chromosomal Rearrangements in Rice Plants . . . . . . . . . . . . . . . . . . . . . . . . . 49
Yuan Hu Xuan, Thomas Peterson, and Chang-deok Han
5 One-Step Generation of Chromosomal Rearrangements in Rice . . . . . . . . . . . 63
Minoru Murata, Asaka Kanatani, and Kazunari Kashihara
6 Genome Elimination by Tailswap CenH3: In Vivo Haploid Production
in Arabidopsis thaliana . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Maruthachalam Ravi and Ramesh Bondada
7 Gametocidal System for Dissecting Wheat Chromosomes . . . . . . . . . . . . . . . . 101
Hisashi Tsujimoto
8 CRISPR/Cas-Mediated Site-Specific Mutagenesis in Arabidopsis
thaliana Using Cas9 Nucleases and Paired Nickases . . . . . . . . . . . . . . . . . . . . 111
Simon Schiml, Friedrich Fauser, and Holger Puchta
9 Targeted Mutagenesis in Rice Using TALENs and the CRISPR/
Cas9 System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Masaki Endo, Ayako Nishizawa-Yokoi, and Seiichi Toki
10 Seamless Genome Editing in Rice via Gene Targeting
and Precise Marker Elimination. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Ayako Nishizawa-Yokoi, Hiroaki Saika, and Seiichi Toki
11 Development of Genome Engineering Tools from Plant-Specific
PPR Proteins Using Animal Cultured Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Takehito Kobayashi, Yusuke Yagi, and Takahiro Nakamura

vii

,viii Contents

12 Chromosomal Allocation of DNA Sequences in Wheat
Using Flow-Sorted Chromosomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
Petr Cápal, Jan Vrána, Marie Kubaláková, Takashi R. Endo,
and Jaroslav Doležel
13 Image Analysis of DNA Fiber and Nucleus in Plants . . . . . . . . . . . . . . . . . . . . 171
Nobuko Ohmido, Toshiyuki Wako, Seiji Kato, and Kiichi Fukui
14 Detection of Transgenes on DNA Fibers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Fukashi Shibata
15 Three-Dimensional, Live-Cell Imaging of Chromatin Dynamics
in Plant Nuclei Using Chromatin Tagging Systems . . . . . . . . . . . . . . . . . . . . . 189
Takeshi Hirakawa and Sachihiro Matsunaga
16 Chromatin Immunoprecipitation for Detecting Epigenetic Marks
on Plant Nucleosomes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Kiyotaka Nagaki
17 Mapping of T-DNA and Ac/Ds by TAIL-PCR to Analyze
Chromosomal Rearrangements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
Satoru Fujimoto, Sachihiro Matsunaga, and Minoru Murata

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217

, Contributors

JAMES A. BIRCHLER • Division of Biological Sciences, University of Missouri, Columbia,
MO, USA
RAMESH BONDADA • School of Biology, Indian Institute of Science Education
and Research (IISER)-Thiruvananthapuram, Thiruvananthapuram, Kerala, India
PETR CÁPAL • Institute of Experimental Botany, Centre of the Region Haná
for Biotechnological and Agricultural Research, Olomouc, Czech Republic
WEIQIANG CHEN • Plant Gene Engineering Center, South China Botanical Garden,
Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of
Sciences, Beijing, China
JON CODY • Division of Biological Sciences, University of Missouri, Columbia,
MO, USA
JAROSLAV DOLEŽEL • Institute of Experimental Botany, Centre of the Region Haná
for Biotechnological and Agricultural Research, Olomouc, Czech Republic
MASAKI ENDO • Plant Genome Engineering Research Unit, National Institute
of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
TAKASHI R. ENDO • Institute of Experimental Botany, Centre of the Region Haná
for Biotechnological and Agricultural Research, Olomouc, Czech Republic; Faculty of
Agriculture, Department of Plant Life Science, Ryukoku University, Otsu,
Shiga, Japan
FRIEDRICH FAUSER • Department of Plant Biology, Carnegie Institution for Science,
Stanford, CA, USA
SATORU FUJIMOTO • Institute of Plant Science and Resources, Okayama University,
Kurashiki, Japan; Department of Applied Biological Science, Faculty of Science
and Technology, Tokyo University of Science, Noda, Chiba, Japan
KIICHI FUKUI • Department of Biotechnology, Graduate School of Engineering,
Osaka University, Suita, Osaka, Japan
NATHANIEL GRAHAM • Division of Biological Sciences, University of Missouri, Columbia,
MO, USA
CHANG-DEOK HAN • Division of Applied Life Science (BK21 program),
Plant Molecular Biology & Biotechnology Research Center (PMBBRC),
Gyeongsang National University, Jinju, South Korea
ZHIGUO HAN • Plant Gene Engineering Center, South China Botanical Garden,
Chinese Academy of Sciences, Guangzhou, China
TAKESHI HIRAKAWA • Department of Applied Biological Science, Faculty of Science
and Technology, Tokyo; University of Science, Noda, Chiba, Japan
LILI HOU • Plant Gene Engineering Center, South China Botanical Garden,
Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy
of Sciences, Beijing, China
ASAKA KANATANI • Institute of Plant Science and Resources, Okayama University,
Kurashiki, Japan

ix

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