Plant Genotyping: Methods and Protocols

ISBN-13: 9781071630235 / Angielski / Twarda / 2023 / 428 str.

Yuri Shavrukov

Opis

This thorough volume presents a wide range of existing methods, from the very popular to the more exotic, in the area of plant genotyping. Many methods of plant genotyping were initially developed for medical research, but all genotyping methods, if they are to be successful, should be suitable for application across the full range of studies within plant biology, as seen in this collection. Plant genotyping methods herein are based on a variety of assessments, including DNA microarray, with its hundreds of thousands of simultaneous reactions, or separate individual studies of DNA sequencing and fragment analysis, PCR and qPCR, allele-specific molecular probes and primers, digestion with restriction endonucleases, microscopy and many others. 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 and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Plant Genotyping: Methods and Protocols offers researchers the opportunity to update their knowledge and choose the most suitable method of plant genotyping for their chosen application.

Spis treści

1. Genotyping by Sequencing (GBS) for Genome-Wide SNP Identification in Plants

            Wirulda Pootakham

 

2. Genotyping by Multiplexed Sequencing (GMS) Using SNP Markers

            Travis M. Ruff, Karol Marlowe, Marcus A. Hooker, Yan Liu, and Deven R. See

 

3. Computational Protocol for DNA Methylation Profiling in Plants Using Restriction Enzyme-Based Genome Reduction

            Wendell Jacinto Pereira, Marília de Castro Rodrigues Pappas, and Georgios Joannis Pappas Jr.

 

4. Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq) Technology

            Natalia Cristina Aguirre, Carla Valeria Filippi, Pablo Alfredo Vera, Andrea Fabiana Puebla, Giusi Zaina, Verónica Viviana Lia, Susana Noemí Marcucci Poltri, and Norma Beatriz Paniego

 

5. Whole Genome Wide SSR Markers Identification Based on ddRAD-Seq Data

            Gitanjali Tandon, Sarika Jaiswal, Mir Asif Iquebal, Anil Rai, and Dinesh Kumar

 

6. High-Throughput Association Mapping in Brassica napus L.: Methods and Applications

            Rafaqat Ali Gill, Md Mostofa Uddin Helal, Minqiang Tang, Ming Hu, Chaobo Tong, and Shengyi Liu

 

7. Polyploid SNP Genotyping Using the MassARRAY System

            Aline da Costa Lima Moraes, Danilo Augusto Sforça, Melina Cristina Mancini, Bianca Baccili Zanotto Vigna, and Anete Pereira de Souza

 

8. qPCR Genotyping of Polyploid Species

            Haiyan Wang, Jiangbo Dang, Qigao Guo, and Guolu Liang

 

9. Genome-Wide Association Studies (GWAS)

            Jianbo He and Junyi Gai

 

10. Transcriptomic Approach for Global Distribution of SNP/Indel and Plant Genotyping

            Claudia Muñoz-Espinoza, Marco Meneses, and Patricio Hinrichsen

 

11. Specific-Locus Amplified Fragment Sequencing (SLAF-Seq)

            Yang Zhou and Huitang Pan

 

12. Modifications of Kompetitive Allele-Specific PCR (KASP) Genotyping for Detection of Rare Alleles

            Anthony Brusa, Eric Patterson, and Margaret Fleming

 

13. Amplifluor-Based SNP Genotyping

            Manmode Darpan Mohanrao, Senapathy Senthilvel, Yarabapani Rushwanth Reddy, Chippa Anil Kumar, and Palchamy Kadirvel

 

14. SNP Genotyping with Amplifluor-Like Method

            Gulmira Khassanova, Sholpan Khalbayeva, Dauren Serikbay, Shynar Mazkirat, Kulpash Bulatova, Maral Utebayev, and Yuri Shavrukov

 

15. Semi-Thermal Asymmetric Reverse PCR (STARP) Genotyping

            Awais Rasheed

 

16. Modified Allele-Specific qPCR (ASQ) Genotyping

            Aigul Amangeldiyeva, Akmaral Baidyussen, Marzhan Kuzbakova, Raushan Yerzhebayeva, Satyvaldy Jatayev, and Yuri Shavrukov

 

17. Allele-Specific Mutation Genotyping with Mismatches in Primer Design

            Yutaro Saito, Fumito Tada, Tadashi Takashina, and Hidetoshi Ikegami

 

18. PCR Allele Competitive Extension (PACE)

            Daniel von Maydell

 

19. Molecular Beacon Probe (MBP)-Based Real Time PCR

            Gopal Kumar Prajapati, Ashutosh Kumar, Aakanksha Wany, and Dev Mani Pandey

 

20. Molecular Beacons – Loop-Mediated Amplification (MB-LAMP)

            Patrick Hardinge

 

21. TaqMan Probes for Plant Species Identification and Quantification in Food and Feed Traceability

            Maria Doroteia Campos, Catarina Campos, and Hélia Cardoso

 

22. Tetra-Primer Amplification Refractory Mutation System (T-ARMS)

            Arnab Mukherjee and Tirthartha Chattopadhyay

 

23. Penta-Primer Amplification Refractory Mutation System (PARMS) with Direct PCR-Based SNP Marker-Assisted Selection (D-MAS)

            Chao Tan and Yanyu Yang

 

24. High-Resolution Melting (HRM) Genotyping

            Nayoung Kim, Ji-Su Kwon, Won-Hee Kang, and Seon-In Yeom

 

25. Modified High-Resolution Melting (HRM) Marker Systems Increasing Discriminability Between Homozygous Alleles

            Satoshi Watanabe, Yoshiyuki Yamagata, and Nobuhiro Kotoda

 

26. A New SNP Genotyping Technology by Target SNP-Seq

            Jian Zhang, Jingjing Yang, and Changlong Wen

 

27. Derived Polymorphic Amplified Cleaved Sequence (dPACS) Assay

            Shiv Shankhar Kaundun, Sarah-Jane Hutchings, Joe Downes, and Ken Baker

 

28. Tubulin-Based Polymorphism (TBP) in Plant Genotyping

            Luca Braglia, Floriana Gavazzi, Silvia Gianì, Laura Morello, and Diego Breviario

 

29. Multiplexed ISSR Genotyping by Sequencing (MIG-Seq)

            Satoshi Nanami

 

30. Application of SolCAP Genotyping in Potato (Solanum tuberosum l.) Association Mapping

            Muhammad Farhan Yousaf, Muhammad Abu Bakar Zia, and Muhammad Naeem

 

31. Fluorescence In Situ Hybridization (FISH) for Genotyping of Triticeae Tribe Species and Hybrids

            Irina Adonina

 

32. Innovative Advances in Plant Genotyping

            William J.W. Thomas, Yueqi Zhang, Junrey C. Amas, Aldrin Y. Cantila, Jaco D. Zandberg, Samantha L. Harvie, and Jacqueline Batley