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Rice Genome Engineering and Gene Editing
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Table of Contents

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-Cecile Meunier, Franz Durandet, Emmanuel Guiderdoni, and Christophe Perin

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 Anonuevo, 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 Sonia Negrao

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