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Statistical association of genotype and phenotype
Linkage map
Fig. 3 in Collard et al. Euphytica (2005) 142: 169–196
Fig. 7 in Collard et al. Euphytica (2005) 142: 169–196
Linkage map
Association between genotype and phenotype
Fig. 9 in Collard et al. Euphytica (2005) 142: 169–196
Association between genotype and phenotype
Individual Marker 1 Marker 2 Marker 3 Marker 4 Marker 5 Marker 6 Phenotype
A 1 1 1 1 1 1 1 1 1 1 1 1 0.07
B 1 1 1 1 1 1 1 1 1 1 1 1 0.35
C 2 2 2 2 2 2 2 2 2 2 2 2 0.46
D 2 2 2 2 2 2 2 2 2 2 2 2 0.67
E 1 2 1 2 1 2 1 2 1 2 1 2 0.41
F 1 2 1 2 1 2 1 2 1 2 1 2 0.30
Single marker analysis
• Using e.g., ANOVA, regression• However, can’t distinguish between effect size
and distance between marker and QTL
Interval mapping
• Uses multiple markers at a time• Uses flanking marker genotypess to infer
probability of genotype at intervals between the markers
• Associates probability of genotype with phenotype
Association between genotype and phenotype
Individual Marker 1 Marker 2 Marker 3 Marker 4 Marker 5 Marker 6 Phenotype
A 1 1 1 1 1 1 1 1 1 1 1 1 0.07
B 1 1 1 1 1 1 1 1 1 1 1 1 0.35
C 2 2 2 2 2 2 2 2 2 2 2 2 0.46
D 2 2 2 2 2 2 2 2 2 2 2 2 0.67
E 1 2 1 2 1 2 1 2 1 2 1 2 0.41
F 1 2 1 2 1 2 1 2 1 2 1 2 0.30
• Linear regression
Association between genotype and phenotype
• Maximum likelihood
Association between genotype and phenotype
LOD score = log(maximum likelihood with a QTL) maximum likelihood without a QTL
Selective genotyping• Genotyping is expensive and time consuming• May be more efficient to genotype only the
most phenotypically extreme individuals
Darvasi and Soller 1992, Theor Appl Genet 85: 353-359
Selective genotyping• Genotyping is expensive and time consuming• May be more efficient to genotype only the
most phenotypically extreme individuals• Selective genotyping may reduce power to
resolve linked QTL• Selective genotyping may affect estimates of
QTL effect size
Beavis effect
• Small sample sizes may lead to overestimation of QTL effect sizes
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