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