Comparative chromosome painting (Brassicaceae)

Knowledge graph centered on Comparative chromosome painting (Brassicaceae) with 37 nodes and 127 connections. Top connected: Pekania pennanti, Asteraceae, Boechera stricta, Bacteria, Young inversion with multiple linked QTLs under se.

Method synopsis

Chromosome-specific BAC contigs of Arabidopsis thaliana were used as painting probes to analyze mitotic and meiotic chromosomes of C. cordifolia. Fluorescent signals were detected and analyzed to determine chromosome structure and evolutionary relationships.

Synthesized from method descriptions across 2 papers using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — Young inversion with multiple linked QTLs under selection in a hybrid zone (2017), Nature Ecology and Evolution. Implementations in other papers (listed below) may differ.

1. Chromosome preparation and painting
   Chromosome spreads were prepared according to a previously published protocol with minor modifications. Slides were fixed overnight in ethanolacetic acid (3:1) and then stored in 70% ethanol at 20°C until further use. Before chromosome spreading, the chromosome suspensions were treated with citrate buffer (4 mM sodium chloride, pH 4.8) and digested using a pectolytic enzyme mixture. An individual flower bud was put on a microscope slide and dissected using needles. A drop of citrate buffer at 37°C for 3-6 h was applied, and a fine suspension was made. Slides were pipetted with 100 μl of ethanolacetic acid (3:1) to fixative, then placed in hot formaldehdye at 50°C in a humid chamber. Chromosomes and nuclei were then fixed by pipetting 100 μl of ethanolacetic acid (3:1) to fixative the slide was titled, dried using a hairdryer and postfixed with 4% formaldehyde in distilled water and then left on air dry.
   Quantities: Individual flower bud per slide, 100 μl ethanolacetic acid, 4 mM sodium chloride citrate bufferDuration: Fixed overnight, 3-6 h citrate buffer treatment, 50°C humid chamberConditions: 20°C storage in 70% ethanol, 37°C citrate buffer treatment, 50°C humid chamber, air drying
   Equipment: microscope slides, ethanolacetic acid, ethanol, citrate buffer, sodium chloride, pectolytic enzyme mixture, needles, hairdryer, formaldehyde

Typical Equipment

• RNase
• pepsin
• biotin-dUTP
• digoxigenin-dUTP
• Cy3-dUTP
• DAPI
• Olympus BX-51 microscope

Output Measurements

• chromosome structure
• translocation events
• karyotype composition

Papers Using This Protocol (2)

Species Studied With This Protocol

Places Where Used