QTL Interval Mapping

About QTL Mapping

Quantitative Trait Locus (QTL) mapping is a statistical method to identify genomic regions associated with variation in quantitative (continuous) traits. Interval mapping scans along chromosomes to find the most likely position of genes affecting traits like height, yield, or disease resistance.

LOD Score Profile

The LOD (logarithm of odds) score measures the statistical evidence for a QTL at each chromosomal position:

• LOD score: log₁₀(likelihood with QTL / likelihood without QTL)
• Peak location: Estimated position of the QTL
• LOD threshold: Typically 3.0 for single chromosome, higher for genome-wide tests
• Confidence interval: Region where LOD drops by 1.5 from peak (support interval)

Interval Mapping Method

At each position between markers, interval mapping:

• Imputes genotypes: Uses flanking markers to infer QTL genotype probabilities
• Tests association: Regresses phenotype on genotype probabilities
• Calculates LOD: Compares model with vs without QTL effect
• Scans genome: Repeats at dense grid of positions

Effect Size and Power

Detection power depends on:

• Effect size: Larger allelic effects are easier to detect
• Sample size: More individuals increase statistical power
• Heritability: Proportion of variance explained (h² = σ²ₐ / (σ²ₐ + σ²ₑ))
• Marker density: Closer markers improve position resolution

Cross Types

• F₂ intercross: (AA × BB) → F₁(AB) → F₂(AA, AB, BB in 1:2:1 ratio)
• Backcross: F₁(AB) × parent(AA) → (AA, AB in 1:1 ratio)

Variance Explained (R²)

The QTL's contribution to phenotypic variance:

• F₂ cross: R² = 2a²/(2a² + σ²ₑ), where a = allele substitution effect
• Detection threshold: Larger R² means easier detection at given sample size

Historical Context

QTL mapping was pioneered by Eric Lander and David Botstein in 1989, building on earlier linkage analysis methods. The interval mapping approach uses maximum likelihood to localize QTL between markers. Modern GWAS (genome-wide association studies) extend these principles to high-density SNP markers in natural populations, while QTL mapping remains essential for experimental crosses in model organisms and agriculture.