Rice Genome Engineering and Gene Editing: Methods and Protocols

ISBN-13: 9781071610701 / Angielski / Miękka / 2022

Bandyopadhyay, Anindya

Opis

This detailed volume explores rice molecular biology, genetic engineering, and genome editing technologies. Dividing into three parts, the book covers subjects such as genetic engineering and tissue culture of rice, including efficient methods for rice transformation and regeneration, genome editing, targeted integration, and gene stacking in rice, including multiple methods utilizing CRISPR systems for targeted gene knock-out or genome modification via base editing, and diverse methods describing bioinformatic, molecular, and cellular analyses in rice. Written for the highly successful Methods in Molecular Biology series, 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. 

Authoritative and practical, Rice Genome Engineering and Gene Editing: Methods and Protocols serves as a valuable resource for researchers worldwide striving to further their efforts on advancing research and producing genetically improved rice varieties.

Spis treści

Part I: Genetic Engineering and Tissue Culture of Rice

 

1. Gene Assembly in Agrobacterium via Nucleic Acid Transfer Using Recombinase Technology (GAANTRY)

            Leyla T. Hathwaik, James G. Thomson, and Roger Thilmony

 

2. TransGene Stacking II Vector System for Plant Metabolic Engineering and Synthetic Biology

            Qinlong Zhu and Yao-Guang Liu

 

3. Morphogenic Regulators and Their Application in Improving Plant Transformation

            Samson Nalapalli, Meral Tunc Ozdemir, Yuejin Sun, Sivamani Elumalai, and Qiudeng Que

 

4. A Rapid Method for Stably Transforming Rice Seeds

            Sudheer Kumar and Neeti Sanan-Mishra

 

5. Agrobacterium tumefaciens-Mediated Transformation of Rice by Hygromycin Phosphotransferase (hptII) Gene Containing CRISPR/Cas9 Vector

            Shuvobrata Majumder, Karabi Datta, and Swapan Kumar Datta

 

6. Genotype Independent Regeneration and Transformation Protocol for Rice Cultivars

            Tanushri Kaul, Sonia Khan Sony, Nitya Meenakshi Raman, Khaled Fathy Motelb, and Jyotsna Bharti

 

Part II: Genome Editing and Targeted Integration in Rice

 

7. Rapid Vector Construction and Assessment of BE3 and Target-AID C to T Base Editing Systems in Rice Protoplasts

            Simon Sretenovic, Changtian Pan, Xu Tang, Yong Zhang, and Yiping Qi

 

8. Genome Editing of Rice by CRISPR-Cas: End-to-End Pipeline for Crop Improvement

            Amit Das, Pallavi Ghana, Bhojaraja Rudrappa, Rita Gandhi, Sresty Tavva Venkata, and Amitabh Mohanty

 

9. Single Base Editing Using Cytidine Deaminase to Change Grain Size and Seed Coat Color in Rice

            My Vo Thi Tra, Xiaojia Yin, Ishita Bajal, Christian Paolo Balahadia, William Paul Quick, and Anindya Bandyopadhyay

 

10. Analysis of Off-Target Mutations in CRISPR-Edited Rice Plants Using Whole Genome Sequencing

            Guanqing Liu, Yiping Qi, and Tao Zhang

 

11. Efficient Genome Editing in Rice Protoplasts Using CRISPR/CAS9 Construct

            Martine Bes, Leo Herbert, Thibault Mounier, Anne-Cécile Meunier, Franz Durandet, Emmanuel Guiderdoni, and Christophe Périn

 

12. Single Transcript Unit CRISPR 2.0 Systems for Genome Editing in Rice

            Xu Tang, Yiping Qi, and Yong Zhang

 

13. Improving a Quantitative Trait in Rice by Multigene Editing with CRISPR-Cas9

            Yesuf Teslim Yimam, Jianping Zhou, Sayed Abdul Akher , Xuelian Zheng,

Yiping Qi, and Yong Zhang

 

14. Rice Haploid Inducer Development by Genome Editing

            Juntao Liu, Dawei Liang, Li Yao, Ya Zhang, Chunxia Liu, Yubo Liu, Yanli Wang, Hongju Zhou, Timothy Kelliher, Xingping Zhang, and Anindya Bandyopadhyay

 

15. FLP-Mediated Site-Specific Gene Integration in Rice

            Vibha Srivastava

 

16. Rice Gene Targeting by Homologous Recombination with Positive Negative Selection Strategy

            Rie Terada and Zenpei Shimatani

 

Part III: Bioinformatics, Cellular, and Molecular Analysis of Rice

 

17. Prediction of Rice Transcription Start Sites Using TransPrise: A Novel Machine Learning Approach

            Stepan Pachganov, Khalimat Murtazalieva, Alexei Zarubin, Tatiana Taran, Duane Chartier, and Tatiana V. Tatarinova

 

18. Single Cell Type Specific RNA Isolation and Gene Expression Analysis in Rice Using Laser Capture Microdissection (LCM)-Based Method

            Vibhav Gautam, Sourav Chatterjee, and Ananda K. Sarkar

 

19. Immunolocalization Analysis of C4 Proteins in the Leaf Tissue of Rice

            Hsiang-Chun Lin, Joanne Jerenice Añonuevo, Paul Quick, and Anindya Bandyopadhyay

 

20. Selection of Suitable Reference Genes for qRT-PCR Gene Expression Studies in Rice

            Meng Wang and Navreet K. Bhullar

 

21. Rice Protoplast Isolation and Transfection for Transient Gene Expression Analysis

            Jennylyn L. Trinidad, Toshisangba Longkumer, and Ajay Kohli

 

22. Identification and Analysis of Steroidogenic Acute Regulatory (StAR) Protein-Related Lipid Transfer (START) Domains in Rice

            Sanjeet Kumar Mahtha, Ravikiran Purama, Renu Kumari, and Gitanjali Yadav

 

23. Assessing Rice Salinity Tolerance: From Phenomics to Association Mapping

            Nadia Al-Tamimi, Helena Oakey, Mark Tester, and Sónia Negrão