2. F2 population x 2

3. Progeny testing x 3

4. QTL
Can look within families 4

5. QTL
Can look within families 5

6. QTL
Can look within families 6

7. QTL Effect of genotype Location of recombination
Can look within families
Location of recombination 7

8. QTL
Can look within families 8

9. QTL
Can look within families 9

10. QTL
Can look within families 10

11. QTL Effect of genotype Location of recombination
Can look within families
Location of recombination 11

12. Are ones without overlap with zero the significant ones?
Pooling families at the same location, min family size of 10.
Reference line is the estimated effect at the highest peak, combining all data. 12

13. Another QTL off to left, but not segregating in all families
Reference line is the estimated effect at the highest peak, combining all data. 13

14. Progeny testing x 14

15. Single QTL
Oliver et al. 2005
PLoS Biol 3(5): e135

16. Multiple QTL
Christians et al Genetics 173: 1547–1553

17. Alternative approaches
Recombinant inbred lines (RIL)

18. Recombinant inbred lines (by sibling mating)
From

19. Recombinant inbred lines (by selfing)
From

20. Recombinant inbred lines
Only have to genotype each line once
Can phenotype multiple individuals per genotype
Can measure multiple phenotypes
Different environments
A number of RILs already available, e.g., WebQTL

21. The “Collaborative Cross”
From

22. Genome of an 8-way RI
From

23. Alternative approaches
Recombinant inbred lines
Collaborative cross
Heterogeneous stocks – like collaborative cross, but not inbred
Microarrays combined with QTL
Expression QTL

24. Expression QTL
How often is regulation cis vs. trans?, e.g., Ronald et al PLoS Genet 1(2): e25.
Mapping “cluster regulators”
Yvert et al. 2003, Nature Genetics 35: 57-64

25. How often is regulation cis vs. trans?
Mapping “cluster regulators”/ networks
Chesler et al. 2005, Nature Genetics 37:

26. Mapping expression networks and behaviour
Chesler et al. 2005,
Nature Genetics 37:

27. Alternative approaches
Recombinant inbred lines
Collaborative cross
Heterogeneous stocks – like collaborative cross, but not inbred
Microarrays combined with QTL
Expression QTL
In silico methods

28. In silico methods
Use already-available phenotypes from many inbred lines
Associate with marker data, e.g., Pletcher et al. (2004 PLoS Biol 2(12): e393) typed many new SNPs
Associate with haplotypes, not individual marker genotypes
Strain
Marker A
Marker B
Marker C
Marker D
Marker E
Marker F 1 A T G 2 3 C 4 5

29. In silico methods
Use already-available phenotypes from many inbred lines
Associate with marker data, e.g., Pletcher et al. (2004 PLoS Biol 2(12): e393) typed many new SNPs
Associate with haplotypes, not individual marker genotypes
Strain
Marker A
Marker B
Marker C
Marker D
Marker E
Marker F 1 A T G 2 3 C 4 5

30. In silico methods
Use already-available phenotypes from many inbred lines
Associate with marker data, e.g., Pletcher et al. (2004 PLoS Biol 2(12): e393) typed many new SNPs
Associate with haplotypes, not individual marker genotypes
In addition, can look for concordance of QTL location between different crosses, different species (!) (Burgess-Herbert 2008; Genetics 180: 2227–2235)