Description
Book SynopsisThis volume provides readers with a collection of the latest protocols used to study plant genome editing and trait engineering. The chapters in this book are organized into five parts: genome engineering systems; machinery design and validation; delivery tools; generation and analysis of engineering materials; and crop genome engineering applications. The chapters cover topics such as methods of applying the popular CRISPR-Cas9 or CRISPR-Cas12 systems for editing genomes in different crop species, the use of small synthetic plastome for potato genome engineering, and the use of CRISPR-Cas9 for algal cell genome engineering. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Cutting-edge and comprehensive, Plant Genome Engin
Table of Contents
Preface…
Table of Contents…
Contributing Authors…
PART I GENOME ENGINEERING SYSTEMS
1 PAM-Less CRISPR-SpRY Genome Editing in Plants
Simon Sretenovic, Xu Tang, Qiurong Ren, Yong Zhang, and Yiping Qi
2 Type I-D CRISPR System-Mediated Genome Editing in Plants
Naoki Wada, Keishi Osakabe, and Yuriko Osakabe
3 CRISPR/LbCas12a-Mediated Genome Editing in Soybean
Dawei Liang, Yubo Liu, Chao Li, Qin Wen, Jianping Xu, Lizhao Geng, Chunxia Liu, Huaibing Jin, Yang Gao, Heng Zhong, John Dawson, Bin Tian, Brenden Barco, Xiujuan Su, Shujie Dong, Changbao Li, Sivamani Elumalai, Qiudeng Que, Ian Jepson, and Liang Shi
4 Base Editing in Poplar through an Agrobacterium-Mediated Transformation Method
Gen Li, Simon Sretenovic, Gary Coleman, and Yiping Qi
5 Genetic Engineering of Potato (Solanum tuberosum) Chloroplasts using the Small Synthetic Plastome “Mini-Synplastome”
Alessandro Occhialini, Alexander C. Pfotenhauer, Henry Daniell, C. Neal Stewart, Jr, and Scott C. Lenaghan
PART II DESIGN AND VALIDATION TOOLS
6 Designing Guide-RNA for Generating Premature Stop Codons for Gene Knockout using CRISPR-BETS
Yuechao Wu and Tao Zhang
7 Construction of CRISPR/Cas9 Multiplex Genome Editing System in Rice
Jie Xiong, Chun Wang, and Kejian Wang
8 Use of Fluorescent Protein Reporters for Assessing and Detecting Genome Editing Reagents and Transgene Expression in Plants
Guoliang Yuan, Gerald A. Tuskan, and Xiaohan Yang
9 Automated, High-Throughput Protoplast Transfection for Gene Editing and Transgene Expression Studies
Stephen B. Rigoulot, Brenden Barco, Yingxiao Zhang, Chengjin Zhang, Kerry A. Meier, Matthew Moore, Jonathan Fabish, Rachel Whinna, Jeongmoo Park, Erin M. Seaberry, Aditya Gopalan, Shujie Dong, Zhongying Chen, and Qiudeng Que
PART III TRANSGENE-FREE DELIVERY OF MACHINERY
10 Delivery of CRISPR-Cas12a Ribonucleoprotein Complex for Genome Editing in an Embryogenic Citrus Cell Line
Hong Fang, James N. Culver, Randall P. Niedz, and Yiping Qi
11 Transgene-Free Genome Editing in Nicotiana benthamiana with CRISPR/Cas9 Delivered by a Rhabdovirus Vector
Xiaonan Ma, Xuemei Li, and Zhenghe Li
12 Ribonucleoprotein (RNP)-Mediated Targeted Mutagenesis in Barley (Hordeum vulgare L.)
Martin Becker and Goetz Hensel
13 Ribonucleoprotein (RNP)-Mediated Allele Replacement in Barley (Hordeum vulgare L.) Leaves
Martin Becker and Goetz Hensel
14 Genome Editing in Chlamydomonas reinhardtii Using Cas9-gRNA Ribonucleoprotein Complex: A Step-by-Step Guide
Dhananjay Dhokane, Nagesh Kancharla, Arockiasamy Savarimuthu, Bhaskar Bhadra, Anindya Bandyopadhyay, and Santanu Dasgupta
PART IV GENERATION AND ANALYSIS OF ENGINEERED LINES
15 Highly Efficient Gene Knockout in Medicago truncatula Genotype R108 using CRISPR-Cas9 System and an Optimized Agrobacterium Transformation Method
Tom Lawrenson, Nicola Atkinson, Macarena Forner, and Wendy Harwood
16 Efficient Targeted Mutagenesis in Brassica Crops using CRISPR/Cas Systems
Tom Lawrenson, Mark Youles, Monika Chhetry, Martha Clarke, Wendy Harwood, and Penny Hundleby
17 Introduction of Genome Editing Reagents and Genotyping of Derived Edited Alleles in Soybean (Glycine max (L.) Merr.)
Truyen Quach, Hanh Nguyen, Olivia Meyer, Shirley J. Sato, Tom Elmo Clemente, and Ming Guo
18 A CRISPR/Cas9 Protocol for Target Gene Editing in Barley
Qiantao Jiang, Qiang Yang, Wendy Harwood, Huaping Tang, Yuming Wei, and Youliang Zheng
19 Targeted Insertion in Nicotiana benthamiana Genomes via Protoplast Regeneration
Fu-Hui Wu, Chen-Tran Hsu, and Choun-Sea Lin
20 Stepwise Optimization of Real-Time RT-PCR Analysis
Nathan A. Maren, James R. Duduit, Debao Huang, Fanghou Zhao, Thomas G. Ranney, and Wusheng Liu
PART V GENOME ENGINEERING FOR CROP IMPROVEMENT
21 CRISPR/Cas9 Technology for Potato Functional Genomics and Breeding
Matías Nicolás González, Gabriela Alejandra Massa, Mariette Andersson, Leonardo Storani, Niklas Olsson, Cecilia Andrea Décima Oneto, Per Hofvander, and Sergio Enrique Feingold
22 Recent Advances in Engineering of In Vivo Haploid Induction Systems
Jian Lv and Timothy Kelliher
Subject Index List…
