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CODA (crossover distribution analyzer): quantitative characterization of crossover position patterns along
Franck Gauthier1, Olivier C Martin, Matthieu Falque
1UMR de Génétique Végétale, INRA, Univ Paris-Sud, CNRS, AgroParisTech, Ferme du Moulon, F-91190 Gif-sur-Yvette, France.
BMC Bioinformatics
|January 22, 2011
Summary
A new software, CODA (CrossOver Distribution Analyzer), quantifies crossover patterns during meiosis. It analyzes interference models and extends analysis to gametic data, aiding research into crossover formation mechanisms.
Area of Science:
- Genetics
- Molecular Biology
- Computational Biology
Background:
- Meiosis involves homologous chromosome crossovers, a process exhibiting interference where crossovers are unevenly distributed.
- Understanding crossover patterns provides insights into their formation mechanisms.
- Evidence suggests crossovers form via at least two pathways: one interfering and one non-interfering.
Purpose of the Study:
- To develop a software tool for quantitative analysis of crossover distribution patterns.
- To enable the fitting of interference models to experimental crossover data.
- To advance the study of crossover formation by analyzing complex datasets.
Main Methods:
- Development of the CrossOver Distribution Analyzer (CODA) software package.
- Implementation of two families of interference models: gamma and beam-film.
- Inference of model parameters and confidence intervals for single or two-pathway modeling.
Main Results:
- CODA allows quantitative characterization of crossover patterns using interference models.
- The software handles diverse data types, including continuous positions and marker genotyping from bivalents or gametes.
- Illustrative analyses were performed on data from wheat, corn, and mouse.
Conclusions:
- CODA expands the scope of analyzable crossover data to include gametic data with two-pathway modeling.
- The software facilitates analyses using the beam-film model by implementing its complex physics and mathematics.
- CODA overcomes previous limitations by employing a summary statistic, enabling the use of the beam-film model.
Related Concept Videos
01:30Crossing Over
Crossing over is the exchange of genetic information between homologous chromosomes during prophase I of meiosis I. Genetic recombination gives rise to allelic diversity in the newly formed daughter cells. In humans, crossing over produces genetically distinct haploid egg and sperm cells that undergo fertilization to produce unique offspring. Before cell division starts, the germ cell’s chromosome(s) undergo duplication in the S phase of the cell cycle. As the cells enter prophase I, duplicated...
01:34Crossing Over
Unlike mitosis, meiosis aims for genetic diversity in its creation of haploid gametes. Dividing germ cells first begin this process in prophase I, where each chromosome—replicated in S phase—is now composed of two sister chromatids (identical copies) joined centrally.
The homologous pairs of sister chromosomes—one from the maternal and one from the paternal genome—then begin to align alongside each other lengthwise, matching corresponding DNA positions in a process called synapsis.
In order to...
The homologous pairs of sister chromosomes—one from the maternal and one from the paternal genome—then begin to align alongside each other lengthwise, matching corresponding DNA positions in a process called synapsis.
In order to...
01:34Crossing over
Unlike mitosis, meiosis aims for genetic diversity in its creation of haploid gametes. Dividing germ cells first begin this process in prophase I, where each chromosome—replicated in S phase—is now composed of two sister chromatids (identical copies) joined centrally.
The homologous pairs of sister chromosomes—one from the maternal and one from the paternal genome—then begin to align alongside each other lengthwise, matching corresponding DNA positions in a process called synapsis.
In order to...
The homologous pairs of sister chromosomes—one from the maternal and one from the paternal genome—then begin to align alongside each other lengthwise, matching corresponding DNA positions in a process called synapsis.
In order to...
01:16Crossover Experiments
Crossover experiments, also called the repeated-measurements design, is a study design in which all experimental units are exposed to all treatments in different periods. Crossover experiments are generally used in psychology, the pharmaceutical industry, agriculture, and medicine.
Crossover designs are performed even with smaller sample sizes since the samples can act as their controls. These are better than simple randomized trials since patients are exposed to all the treatments.
Crossover designs are performed even with smaller sample sizes since the samples can act as their controls. These are better than simple randomized trials since patients are exposed to all the treatments.
01:17Karyotyping
Describing the number and physical features of chromosomes can reveal abnormalities that underlie genetic diseases. This description is facilitated by special staining techniques that produce a particular banding pattern on each chromosome. State-of-the-art techniques make this approach even more powerful, enabling the detection of individual genes that cause disease.A Simple Chromosome Staining Technique Provides Valuable Scientific InsightSome genetic diseases can be detected by looking at...
01:17Karyotyping
Describing the number and physical features of chromosomes can reveal abnormalities that underlie genetic diseases. This description is facilitated by special staining techniques that produce a particular banding pattern on each chromosome. State-of-the-art techniques make this approach even more powerful, enabling the detection of individual genes that cause disease.A Simple Chromosome Staining Technique Provides Valuable Scientific InsightSome genetic diseases can be detected by looking at...