Plant Genotyping: Methods and Protocols

ISBN-13: 9781493943678 / Angielski / Miękka / 2016 / 315 str.

Jacqueline Batley

Opis

The ability to produce vast amounts of DNA sequence data has enabled the discovery of molecular markers in model organisms, crops, as well as orphan species making genotyping the rate limiting factor, and this volume focuses on the different markers available and the low to high throughput genotyping of these markers. Given the diverse nature of some of these systems, an overview is provided on the identification of markers from sequence data, as well as data analysis with example applications once the genotyping data has been generated. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Plant Genotyping: Methods and Protocols is aimed at plant molecular biologists, geneticists, plant breeders and ecologists who have a target question and need to know the most suitable markers and genotyping system to use.

Spis treści

1. Advances in Plant Genotyping – Where the Future Will Take Us

                Dhwani A. Patel, Manuel Zander, Jessica Dalton-Morgan, and Jacqueline Batley

 

2. Molecular Marker Applications in Plants

                Alice C. Hayward, Reece Tollenaere, Jessica Dalton-Morgan, and Jacqueline Batley

 

3. Bioinformatics: Identification of Markers from Next Generation Sequence Data

                Pradeep Ruperao and David Edwards

 

4. Molecular Marker Databases

                Kaitao Lai, Michal Lorenc, and David Edwards

 

5. Plant Genotyping Using Fluorescently Tagged Inter Simple Sequence Repeats (ISSRs): Basic Principles and Methodology

Linda M. Prince

 

6. SSR Genotyping

                Annaliese S. Mason

 

7. Genotyping Analysis Using an RFLP Assay

                Shutao Dai and Yan Long

 

8. DNA Barcoding for Plants

        &

nbsp;       Natasha de Vere, Tim C.G. Rich, Sarah A. Trinder and Charlotte Long

 

9. Multiplexed Digital Gene Expression Analysis for Genetical Genomics in Large Plant Populations

Christian Obermeier, Bertha M. Salazar-Colqui, Viola Spamer, and Rod Snowdon

 

10. SNP Genotyping by Heteroduplex Analysis

                Norma Paniego, Corina Fusari, Verónica Lia, and Andrea Puebla

 

11. Application of the High-Resolution Melting Technique for Gene Mapping and SNP Detection in Plants

David Chagne

 

12. Challenges of Genotyping Polyploid Species

                Annaliese S. Mason

 

13. Genomic Reduction Assisted Single Nucleotide Polymorphism Discovery using 454-Pyrosequencing

Peter J. Maughan, Joshua A. Udall, and Eric N. Jellen

 

14. Inter-SINE Amplified Polymorphism (ISAP) for Rapid and Robust Plant Genotyping

Torsten Wenke, Kathrin M. Seibt, Thomas Döbel, Katja Muders, and Thomas Schmidt

 

15. Screening of Mutations by TILLING in Plants

Nian Wang and Lei Shi

 

16. Gene Analysis Using Mass Spectrometric Cleaved Amplified Polymorphic Sequence (MS-CAPS) with Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectro

metry (MALSI-TOF)

                Hideyuki Kajiwara

 

17. Quantitative SNP Genotyping of Polyploids with MassARRAY and Other Platforms

                Marcelo Mollinari and Oliver Serang

 

18. SNP Genotyping using KASPar Assays

                Scott M. Smith and Peter J. Maughan

 

19. Skim Based Genotyping by Sequencing

                Agnieszka A. Golicz, Philipp E. Bayer, and David Edwards

 

20. The Restriction Enzyme Target Approach to Genotyping by Sequencing (GBS)

                Elena Hilario

 

21. Methods for the Design, Implementation and Analysis of Illumina Infinium™ SNP Assays in Plants

David Chagné, Luca Bianco, Cindy Lawley, Diego Micheletti, and Jeanne M.E. Jacobs

 

22. Use of the Illumina GoldenGate Assay for Single Nucleotide Polymorphism (SNP) Genotyping in Cereal Crops

Shiaoman Chao and Cindy Lawley