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

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.

Rapid DNA-FISH in Arabidopsis thaliana Somatic Cells.

Fluorescence in situ hybridization (FISH) technique has been widely used to detect and localize specific DNA and RNA sequences in interphase nuclei and chromosomes in animals and plants. Here, we present a protocol for localization of genomic loci in nuclei of the model plant Arabidopsis thaliana. This protocol includes several advances and adaptations to A. thaliana, including preparation of nuclei and chromosomes without the use of liquid nitrogen, and an in situ hybridization procedure that preserves chromatin structure without the use of paraformaldehyde and formamide. Simultaneous denaturation of the BAC (bacterial artificial chromosome) probe and nuclei followed by annealing at high temperature allows hybridization in less than an hour. These hybridization conditions also provide high signal to noise ratio by a small number of washes. Thus, this simplified in situ hybridization procedure is completed in one working day.

Preparation of Mitotic Chromosomes with the Dropping Technique.

The quality of chromosome preparation influences all downstream analyses and is therefore crucial. Hence, numerous protocols exist to produce microscopic slides with mitotic chromosomes. Nevertheless, due to the high content of fibers in and around a plant cell, preparation of plant chromosomes is still far from trivial and needs to be fine-tuned for each species and tissue type. Here, we outline the "dropping method," a straightforward and efficient protocol to prepare multiple slides with uniform quality from a single chromosome preparation. In this method, nuclei are extracted and cleaned to produce a nuclei suspension. In a drop-by-drop manner, this suspension is then applied from a certain height onto the slides, causing the nuclei to rupture and the chromosomes to spread. Due to the physical forces that accompany the dropping and spreading process, this method is best suited for species with small- to medium-sized chromosomes.

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

Meiosis is a very essential cell division resulting in the formation of four haploid gametes in plants. The preparation of meiotic chromosomes is a key step in plant meiotic research. Well-spread chromosomes, low background signal, and effective cell wall elimination give the best hybridization results. Dogroses (Rosa, section Caninae) are allopolyploids and frequently pentaploids (2n = 5x = 35) with asymmetrical meiosis. Their cytoplasm is enriched with organic compounds such as vitamins, tannins, phenols, essential oils, and many more. The cytoplasm is often a huge problem, avoiding successful cytogenetic experiments using fluorescence staining techniques. Here, we present a protocol with modifications for the preparation of male meiotic chromosomes suitable for fluorescence in situ hybridization (FISH) and immunolabeling with a major focus on dogroses.

A Basic and Simple Chromosome Preparation Protocol.

Chromosome preparation for chromosome analysis is basic and indispensable for wide area of biology such as genetics, medicine, molecular biology, or other many fields. However, it seems that the many artisans in that fields feel hard to get start chromosome preparation technique, as it is something technically demanding or troublesome, or it needs something secret manner to prepare good quality of chromosome spreads. Actually many technical variations among individual laboratories exist. The aims of this chapter is to describe concise and minimal fundamental protocols specifically focused on human chromosome preparation, as step-by-step guiding with instructing essential points.

An efficient protocol for chromosome isolation from sterlet (A. ruthenus) embryos and larvae.

In the present manuscript an efficient and feasible protocol for chromosome preparation from sterlet (A. ruthenus) embryos and larvae was developed that can be used as routine molecular diagnostic tool of the species genome manipulation procedures verification. For this end, a multi-dimensional experimental system was conceived that enabled for the establishment of chromosome preparation protocol, which characterized the mean efficiency of chromosome extraction ranged from 70% to 100% and the average number of recorded metaphases per slide ranged between 9 and 15. The developed under the current study protocol can be used as a fast and reliable tool, alternative for flow cytometry techniques that enable for the molecular verification of genome manipulations effectiveness. As genome engineering is presently the fundamental biotechnology tool that enables for effective and sustainable aquaculture of fish, including sturgeons that are known as one of the most valuable economically and ecologically fish group, the development of easy and fast methods for the verification of genome manipulation effects is especially important. Thus, the established chromosome preparation protocol contributes to genome and reproduction studies of sturgeons, including taxonomy, inter-species hybridization, genome aberrations, sex determination system and selection. Moreover, the application of cytogenetic techniques also contributes to the development of new or improvement existing techniques of genome engineering utilized in sturgeon aquaculture.

Methods for Cytogenetic Chromosome Barcoding and Chromosome Painting in Brachypodium distachyon and Its Relative Species.

Brachypodium distachyon provides a particularly appealing object for molecular cytogenetic analysis due to its compact genome and low repetitive DNA content, as well as low (x = 5) basic number of chromosomes easily identifiable on the basis of their morphometric features. Some of these features, such as genome compactness, are shared by the other members of the genus, thus making them amenable for comparative cytogenetic mapping. Cytogenetic infrastructure established for B. distachyon was initially based on fluorescence in situ hybridization with various tandemly repeated sequences as probes. The molecular cytogenetic studies advanced greatly with the development of B. distachyon large DNA insert genomic libraries. These resources coupled with the access to the fully sequenced genome of B. distachyon enabled chromosome painting in monocots for the first time. This pioneering work was subsequently extended to other Brachypodium species, allowing insight into grass karyotype evolution. In this protocol we describe the methods of making somatic and meiotic chromosome preparations, probe labeling, FISH with BAC clones, a strategy for chromosome barcoding and chromosome painting in B. distachyon, and comparative chromosome painting in the other Brachypodium species.

Chromosome Preparation for Myeloid Malignancies.

Many cases of myeloid malignancies are associated with recurring cytogenetic aberrations. Chromosomal analysis can aid in diagnosis, predict prognosis, and disclose subsequent clonal evolution. Three different cell culture methods: direct harvest, nonsynchronized culture, and synchronized culture are usually prepared if the nucleated cell counts in marrow blood are sufficient. Synchronized culture is the first choice of method in myeloid malignancies, whereas the direct method can be omitted if the cell count is low. The aseptic culture technique is strictly followed until harvesting procedure. For synchronized culture, uridine and fluorodeoxyuridine are added as blocking reagents and released by thymidine on the following day. Harvesting steps of the cultures involved colcemid exposure, hypotonic treatment, and Carnoy's fixation. The cells are then ready for slide making and banding for chromosomal analysis.

Pachytene Chromosome Preparation in Populus deltoides Marsh.

A technique that produces large numbers of good quality pachytene chromosome preparations has been developed for Populus. Anthers at the pachytene stage of meiosis are used as materials. There are two main modifications in our method relative to the traditional squashing method that address the challenges the thick cytoplasm observed during the pachytene phase of meiosis presents. One is the temperature during squashing, i.e., the slide is placed on a 52°C heater for squashing. The other is the removal of the cover slip using 45% acetic acid. © 2016 by John Wiley & Sons, Inc.

Application of improved chromosome short-term culture method in the chromosome karyotype analysis of leukemia patients / 西安交通大学学报(医学版)

Objective To make the chromosome karyotype analysis of 130 patients with leukemia by using the improved chromosome short-term culture method.Methods We optimized the main factors with a single factor gradient experiment in short-term culture of bone marrow chromosome, including colchicines concentration, duration of action of colchicines,and hypotonic time.On this basis,we conducted the three-factors and three-level orthogonal experiment to achieve improved bone marrow chromosome preparation system,which was later applied in 130 patients with leukemia in our hospital.Results The orthogonal experiment results showed that the optimum conditions were colchicines concentration of 0.07 μg/mL,colchicines action time of 80 min,and hypotonic time of 35 min during the preparation of the bone marrow chromosome.Using this method,the chromosome preparation success rate reached 97.69% and the detection rate of abnormal karyotype reached 82.3% in the chromosome karyotype analysis.Conclusion Bone marrow chromosome preparation system with colchicines concentration of 0.07 μg/mL and colchicines action time of 80 min,and hypotonic time of 35 min is worthy of clinical promotion.