Next Article in Journal
Impact of SGLT2 Inhibitors on Heart Failure: From Pathophysiology to Clinical Effects
Next Article in Special Issue
Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus
Previous Article in Journal
Tumor Extracellular Matrix Stiffness Promptly Modulates the Phenotype and Gene Expression of Infiltrating T Lymphocytes
Previous Article in Special Issue
Epigenetic Distribution of Recombinant Plant Chromosome Fragments in a Human–Arabidopsis Hybrid Cell Line
Article

A Dual-Color Tyr-FISH Method for Visualizing Genes/Markers on Plant Chromosomes to Create Integrated Genetic and Cytogenetic Maps

1
Laboratory of Plant Cell Engineering, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia
2
Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 127550 Moscow, Russia
3
Laboratory of Applied Genomics and Crop Breeding, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
4
Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
5
Kurchatov Genomics Center of ARRIAB, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
6
Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan
7
Graduate School of Life Science, Tohoku University, Miyagi 980-8577, Japan
8
Department of Botany, Breeding and Seed Production of Garden Plants, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskay 49 Str., 127550 Moscow, Russia
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editors: Robert Hasterok, Natalia Borowska-Zuchowska and Ewa Robaszkiewicz
Int. J. Mol. Sci. 2021, 22(11), 5860; https://doi.org/10.3390/ijms22115860
Received: 21 April 2021 / Revised: 19 May 2021 / Accepted: 25 May 2021 / Published: 30 May 2021
(This article belongs to the Special Issue Cytomolecular Organisation of the Nuclear Genome)
In situ imaging of molecular markers on a physical chromosome is an indispensable tool for refining genetic maps and validation genome assembly at the chromosomal level. Despite the tremendous progress in genome sequencing, the plant genome assembly at the chromosome level remains a challenge. Recently developed optical and Hi-C mapping are aimed at assistance in genome assembly. For high confidence in the genome assembly at chromosome level, more independent approaches are required. The present study is aimed at refining an ultrasensitive Tyr-FISH technique and developing a reliable and simple method of in situ mapping of a short unique DNA sequences on plant chromosomes. We have carefully analyzed the critical steps of the Tyr-FISH to find out the reasons behind the flaws of this technique. The accurate visualization of markers/genes appeared to be significantly dependent on the means of chromosome slide preparation, probe design and labeling, and high stringency washing. Appropriate adjustment of these steps allowed us to detect a short DNA sequence of 1.6 Kb with a frequency of 51.6%. Based on our results, we developed a more reliable and simple protocol for dual-color Tyr-FISH visualization of unique short DNA sequences on plant chromosomes. This new protocol can allow for more accurate determination of the physical distance between markers and can be applied for faster integration of genetic and cytogenetic maps. View Full-Text
Keywords: Tyr-FISH; plant chromosome preparation; recombinant and cytogenetic maps; transcript-based markers; genome assembly; Allium cepa Tyr-FISH; plant chromosome preparation; recombinant and cytogenetic maps; transcript-based markers; genome assembly; Allium cepa
Show Figures

Figure 1

MDPI and ACS Style

Kudryavtseva, N.; Ermolaev, A.; Karlov, G.; Kirov, I.; Shigyo, M.; Sato, S.; Khrustaleva, L. A Dual-Color Tyr-FISH Method for Visualizing Genes/Markers on Plant Chromosomes to Create Integrated Genetic and Cytogenetic Maps. Int. J. Mol. Sci. 2021, 22, 5860. https://doi.org/10.3390/ijms22115860

AMA Style

Kudryavtseva N, Ermolaev A, Karlov G, Kirov I, Shigyo M, Sato S, Khrustaleva L. A Dual-Color Tyr-FISH Method for Visualizing Genes/Markers on Plant Chromosomes to Create Integrated Genetic and Cytogenetic Maps. International Journal of Molecular Sciences. 2021; 22(11):5860. https://doi.org/10.3390/ijms22115860

Chicago/Turabian Style

Kudryavtseva, Natalya, Aleksey Ermolaev, Gennady Karlov, Ilya Kirov, Masayoshi Shigyo, Shusei Sato, and Ludmila Khrustaleva. 2021. "A Dual-Color Tyr-FISH Method for Visualizing Genes/Markers on Plant Chromosomes to Create Integrated Genetic and Cytogenetic Maps" International Journal of Molecular Sciences 22, no. 11: 5860. https://doi.org/10.3390/ijms22115860

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop