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
