linkage map
Definition
A linkage map is a genetic map that shows the relative positions and distances of genetic markers or genes along chromosomes based on recombination frequencies during meiosis. Unlike physical maps that measure actual DNA base pair distances, linkage maps use centiMorgans (cM) as units, where 1 cM represents a 1% chance of recombination between two loci per generation. These maps are constructed by analyzing inheritance patterns in families or breeding populations, tracking how frequently genetic markers are inherited together. Linkage maps are fundamental for identifying disease-causing genes through positional cloning, marker-assisted selection in breeding programs, and understanding genome organization and evolution across species.
Visualize linkage map in Nodes Bio
Researchers can visualize linkage relationships as network graphs where nodes represent genetic markers or loci and edges represent linkage strength based on recombination frequencies. This network approach reveals clustering patterns of tightly linked markers, identifies recombination hotspots, and maps quantitative trait loci (QTL) relationships. Users can overlay phenotypic data onto linkage networks to identify genomic regions associated with specific traits or diseases.
Visualization Ideas:
- Chromosome-based network showing marker positions with edge weights representing recombination frequencies
- QTL network connecting phenotypic traits to genomic regions with linkage evidence
- Comparative linkage maps across species showing synteny and chromosomal rearrangements
Example Use Case
A plant breeding team studying drought resistance in wheat constructs a linkage map using 500 SNP markers across 200 F2 progeny. By visualizing the linkage network, they identify three major QTL clusters on chromosomes 2, 5, and 7 that strongly associate with water-use efficiency traits. The network reveals that markers within 5 cM show tight co-inheritance patterns, helping prioritize candidate genes for functional validation. This linkage map guides marker-assisted selection to accelerate breeding of drought-tolerant cultivars.