Genetic Linkage Map Builder

About Linkage Mapping

Linkage mapping uses recombination frequencies between genetic markers to estimate their relative positions on chromosomes. The closer two loci are, the less likely recombination will occur between them, and the more their alleles will be inherited together (genetic linkage).

Cross Designs

• Backcross (testcross): Heterozygous F1 (AaBb) × homozygous recessive (aabb). Produces four offspring classes with expected 1:1:1:1 ratio when genes are unlinked, but deviates when linked. This is the simplest design for mapping.
• F2 Intercross: F1 (AaBb) × F1 (AaBb). Produces nine genotypic classes with expected 9:3:3:1 phenotypic ratio when genes are unlinked. More complex but provides additional information about dominance.

Recombinant Classes

In a backcross between AaBb × aabb, if A and B are on the same chromosome:

• Parental types: AB/ab and ab/ab (non-recombinant gametes from F1)
• Recombinant types: Ab/ab and aB/ab (recombinant gametes from F1)

The recombination fraction r is estimated as: r = (# recombinants) / (total offspring)

Map Distance and Mapping Functions

Recombination frequency underestimates true genetic distance when multiple crossovers occur. Mapping functions correct for this:

• Haldane function: d = -50 ln(1 - 2r) centiMorgans (cM). Assumes no crossover interference (crossovers are independent Poisson events).
• Kosambi function: d = 25 ln[(1 + 2r)/(1 - 2r)] cM. Accounts for positive crossover interference (one crossover reduces probability of nearby crossovers).

Testing for Independent Assortment

A chi-square test can assess whether observed genotype frequencies deviate significantly from expectations under independent assortment. For a backcross, we expect 1:1:1:1 if unlinked.

• χ² statistic: χ² = Σ[(observed - expected)² / expected]
• Degrees of freedom: (number of classes - 1)
• p < 0.05: Reject independence hypothesis (genes are linked)

Historical Context

Thomas Hunt Morgan and his students developed linkage mapping in the 1910s using Drosophila, establishing that genes are arranged linearly on chromosomes. Alfred Sturtevant, as an undergraduate in Morgan's lab, created the first genetic map in 1913. One centiMorgan (1 cM) represents a 1% recombination frequency and is named after Morgan.