statistical association of genotype and phenotype
TRANSCRIPT
![Page 1: Statistical association of genotype and phenotype](https://reader035.vdocuments.mx/reader035/viewer/2022062320/56649d125503460f949e5a40/html5/thumbnails/1.jpg)
Statistical association of genotype and phenotype
![Page 2: Statistical association of genotype and phenotype](https://reader035.vdocuments.mx/reader035/viewer/2022062320/56649d125503460f949e5a40/html5/thumbnails/2.jpg)
Linkage map
Fig. 3 in Collard et al. Euphytica (2005) 142: 169–196
![Page 3: Statistical association of genotype and phenotype](https://reader035.vdocuments.mx/reader035/viewer/2022062320/56649d125503460f949e5a40/html5/thumbnails/3.jpg)
Fig. 7 in Collard et al. Euphytica (2005) 142: 169–196
Linkage map
![Page 4: Statistical association of genotype and phenotype](https://reader035.vdocuments.mx/reader035/viewer/2022062320/56649d125503460f949e5a40/html5/thumbnails/4.jpg)
Association between genotype and phenotype
Fig. 9 in Collard et al. Euphytica (2005) 142: 169–196
![Page 5: Statistical association of genotype and phenotype](https://reader035.vdocuments.mx/reader035/viewer/2022062320/56649d125503460f949e5a40/html5/thumbnails/5.jpg)
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
![Page 6: Statistical association of genotype and phenotype](https://reader035.vdocuments.mx/reader035/viewer/2022062320/56649d125503460f949e5a40/html5/thumbnails/6.jpg)
Single marker analysis
• Using e.g., ANOVA, regression• However, can’t distinguish between effect size
and distance between marker and QTL
![Page 7: Statistical association of genotype and phenotype](https://reader035.vdocuments.mx/reader035/viewer/2022062320/56649d125503460f949e5a40/html5/thumbnails/7.jpg)
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
![Page 8: Statistical association of genotype and phenotype](https://reader035.vdocuments.mx/reader035/viewer/2022062320/56649d125503460f949e5a40/html5/thumbnails/8.jpg)
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
![Page 9: Statistical association of genotype and phenotype](https://reader035.vdocuments.mx/reader035/viewer/2022062320/56649d125503460f949e5a40/html5/thumbnails/9.jpg)
![Page 10: Statistical association of genotype and phenotype](https://reader035.vdocuments.mx/reader035/viewer/2022062320/56649d125503460f949e5a40/html5/thumbnails/10.jpg)
• Linear regression
Association between genotype and phenotype
![Page 11: Statistical association of genotype and phenotype](https://reader035.vdocuments.mx/reader035/viewer/2022062320/56649d125503460f949e5a40/html5/thumbnails/11.jpg)
• Maximum likelihood
Association between genotype and phenotype
LOD score = log(maximum likelihood with a QTL) maximum likelihood without a QTL
![Page 12: Statistical association of genotype and phenotype](https://reader035.vdocuments.mx/reader035/viewer/2022062320/56649d125503460f949e5a40/html5/thumbnails/12.jpg)
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
![Page 13: Statistical association of genotype and phenotype](https://reader035.vdocuments.mx/reader035/viewer/2022062320/56649d125503460f949e5a40/html5/thumbnails/13.jpg)
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
![Page 14: Statistical association of genotype and phenotype](https://reader035.vdocuments.mx/reader035/viewer/2022062320/56649d125503460f949e5a40/html5/thumbnails/14.jpg)
Beavis effect
• Small sample sizes may lead to overestimation of QTL effect sizes