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 1Marker 2Marker 3Marker 4Marker 5Marker 6Phenotype A B C D E F

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 1Marker 2Marker 3Marker 4Marker 5Marker 6Phenotype A B C D E F

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:

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