Plant Cytogenetics and Cytogenomics: Methods and Protocols

ISBN-13: 9781071632253 / Angielski

Tony Heitkam; Sònia Garcia

Opis

This book provides an up-to-date account of the most widespread methods used by specialists in the field of plant cytogenetics and the emerging field of cytogenomics that will likely soon be adapted by more labs. From the classical basic karyological approaches to the most recent genomics-informed and computational methods, the volume explores genome size and ploidy level estimation, chromosome fixation, preparation, and manipulation, banding and staining techniques, in situ hybridization, as well as numerous methods that integrate cytogenetics with bioinformatics and computational genomics. 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, as well as tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Plant Cytogenetics and Cytogenomics: Methods and Protocols serves as an ideal resource for plant scientists interested in molecular and evolutionary biology, breeding, systematics, and plant -omics in general.

Spis treści

Part I: Introduction

 

1. Plant Cytogenetics: From Chromosomes to Cytogenomics

            Trude Schwarzacher, Qing Liu, and J.S. (Pat) Heslop-Harrison

 

Part II: Sizing the Nucleus: Methods for Genome Size and Ploidy Level Estimation

 

2. The Use of Flow Cytometry for Estimating Genome Sizes and DNA Ploidy Levels in Plants

            João Loureiro, Martin Čertner, Magdalena Lučanová, Elwira Sliwinska, Filip Kolář, Jaroslav Doležel, Sònia Garcia, Sílvia Castro, and David W. Galbraith

 

3. Nuclear DNA Content Estimation of Seaweed by Fluorimetry Analysis

            Rafael P. Martín-Martín, Noemí Salvador-Soler, Jordi Rull Lluch, and Amelia Gómez Garreta

 

4. K-Mer-Based Genome Size Estimation in Theory and Practice

            Uljana Hesse

 

5. A Bioinformatic Pipeline to Estimate Ploidy Level from Target Capture Sequence Data Obtained from Herbarium Specimens

            Juan Viruel, Oriane Hidalgo, Lisa Pokorny, Félix Forest, Barbara Gravendeel, Paul Wilkin, and Ilia J. Leitch

 

Part III: Getting to the Chromosomes: Methods for Chromosome Fixation, Preparation, and Manipulation

 

6. Nitrous Oxide-Induced Metaphase Arrest: A Technique for Somatic Chromosome Analysis

            Patrice S. Albert and James A. Birchler

 

7. Preparation of Mitotic Chromosomes with the Squash Technique

            Alexis J. Maravilla, Marcela Rosato, and Josep A. Rosselló

 

8. Preparation of Mitotic Chromosomes with the Dropping Technique

            Nicola Schmidt, Beatrice Weber, Jessica Klekar, Susan Liedtke, Sarah Breitenbach, and Tony Heitkam

 

9. Laser Capture Microdissection: From Genomes to Chromosomes, from Complex Tissue to Single-Cell Analysis

            Tomáš Janíček, Roman Hobza, and Vojtěch Hudzieczek

 

10. Flow Cytometric Analysis and Sorting of Plant Chromosomes

            Petr Cápal, Mahmoud Said, István Molnár, and Jaroslav Doležel

 

Part IV: Putting on Color: Banding and Staining Techniques

 

11. C-Banding of Plant Chromosomes

            Adam J. Lukaszewski

 

12. CMA/DAPI Banding of Plant Chromosomes

            Ana Emília Barros e Silva and Marcelo Guerra

 

13. Silver Nitrate Staining of Nucleolar Organizer Regions (Ag-NORs) in Plant Chromosomes

            Claudio Palma-Rojas, Pedro Jara-Seguel, and Cristian Araya-Jaime

 

14. Chromatin Immunostaining of Plant Nuclei

            Nobuko Ohmido and Aqwin Polosoro

 

Part V: Labeling DNA: In Situ Hybridization and Other Methods Using Fluorescent Labels

 

15. Critical Steps in DAPI and FISH Imaging of Chromosome Spread Preparations

            Hans de Jong, José van de Belt, and Paul Fransz

 

16. Formamide-Free Genomic In Situ Hybridization (ff-GISH)

            Hanna Weiss-Schneeweiss and Tae-Soo Jang

 

17. The Use of Ribosomal DNA for Comparative Cytogenetics

            Gülru Yücel, Magdalena Senderowicz, and Bożena Kolano

 

18. Identification of the Sequence and the Length of Telomere DNA

            Martin Lyčka, Petr Fajkus, Leon P. Jenner, Eva Sykorová, Miloslava Fojtová, and Vratislav Peska

 

19. Chromosome Painting Using Chromosome-Specific BAC Clones

            Terezie M. Mandáková and Martin A. Lysak

 

20. CRISPR-FISH: A CRISPR/Cas9-Based In Situ Labeling Method

            Bhanu Prakash Potlapalli, Takayoshi Ishii, Kiyotaka Nagaki, Saravanakumar Somasundaram, and Andreas Houben

 

21. Preparation of Male Meiotic Chromosomes for Fluorescence In Situ Hybridization and Immunodetection with Major Focus on Dogroses

            Jana Lunerová and Radka Vozárová

 

22. Extended DNA Fibers for High-Resolution Mapping

            Paul Fransz, José van de Belt, and Hans de Jong

 

23. Visualizing Chromosome Territories and Nuclear Architecture of Large Plant Genomes Using Alien Introgressions

            Kateřina Perničková and David Kopecký

 

24. Visualization of the Nucleolus Using 5´Ethynyl Uridine

            Martina Dvořáčková and Jiří Fajkus

 

Part VI: Leveraging Data onto Nuclei: Genomics-Informed Methods

 

25. Bioinformatics Prediction of Bulked Oligonucleotide Probes for FISH Using Chorus2

            Guanqing Liu and Tao Zhang

 

26. Visualization of Oligonucleotide-Based Probes along Pseudochromosomes Using RIdeogram, KaryoploteR, and Circlize (Circos)

            Ludwig Mann and Sophie Maiwald

 

27. Bulked Oligo-FISH for Chromosome Painting and Chromosome Barcoding

            Denisa Beránková and Eva Hřibová

 

28. Flow Sorting-Assisted Optical Mapping

            Hana Šimková, Zuzana Tulpová, and Petr Cápal

 

29. Chromosome Conformation Capture of Mitotic Chromosomes

            Petr Cápal

 

30. Analysis of 5S rDNA Genomic Organization through the RepeatExplorer2 Pipeline: A Simplified Protocol

            Sònia Garcia, Joan Pere Pascual-Díaz, Alice Krumpolcová, and Ales Kovarík

 

Part VII: Software and Online Plant Cytogenetics & Genomics Resources

 

31. Tools for Drawing Informative Idiograms

            Shoaeib Mahmoudi and Ghader Mirzaghaderi

 

32. Using ChromEvol to Determine the Mode of Chromosomal Evolution

            Marcial Escudero, Enrique Maguilla, José Ignacio Márquez-Corro, Santiago Martín-Bravo, Itay Mayrose, Anat Shafir, Lu Tan, Carrie Tribble, and Rosana Zenil-Ferguson

 

33. Online Resources Useful for Plant Cytogenetics and Cytogenomics Research

            María Luisa Gutiérrez, Roi Rodríguez-González, Joan Pere Pascual-Díaz, Inés Fuentes, and Sònia Garcia