1. 04/01/10University of North Carolina Techniques for Accelerating Inbreeding in the Collaborative Cross 1 Department of Computer Science, University of North Carolina at Chapel Hill 2 Department of Genetics, University of North Carolina at Chapel Hill Catie Welsh 1, Ryan J. Buus 2, Jennifer Shockley 2, Stephanie Hansen 2, Darla Miller 2, Fernando Pardo-Manuel de Villena 2, Leonard McMillan 1

2. Motivation 2 Figures Courtesy of Karl Broman

3. Motivation 3

4. Observations 4 Large difference between selfing and random sibling mating. Randomization was an important design decision in the CC. Attempt to accelerate inbreeding using marker-assisted techniques. Study impact of marker-assisted inbreeding on the genetic structure of the CC.

5. Backcross Sib-Mating Pedigree Diagram Parent-Child Backcross Pedigree Diagram 5 Change breeding scheme after 10 generations of random sib-matings to cross offspring with their parent; alternating sex of parent at each generation. G2:F10

6. Backcross 6 100,000 Simulations were done. No genotyping necessary. 33.5 38.2 141.2 145.1

7. Marker-Assisted Inbreeding (MAI) 7 Random sib-matings for 10 generations Starting at generation 11: – Generate 4 female and 4 male offspring – Consider all 16 pair matings – Choose the “best” breeding pair

8. MAI DD Ss DS Each of the marked regions is some form of heterozygosity between the 2 animals. 8 SS Choosing the “Best” Breeding Pair Consider all heterozygous regions Calculate fraction of the genome that segregates in each pair of mice. Take into account the different types of heterozygosity SS Ss = Opposite Homozygous DD = Both Heterozygous DS = One Heterozygous, One Homozygous SS = Same Homozygous

9. MAI Metrics 9 Ss = Opposite Homozygous DD = Both Heterozygous DS = One Heterozygous, One Homozygous SS = Inbred Relationship between a potential breeding pair at 1 allele Interval123Probability Breeding Pair 1DDDSDD= 1/8 x ¼ x 1/8 = 1/256 Breeding Pair 2SsDSDD= 0 x ¼ x 1/8 = 0

10. MAI 10 Model is very conservative; assume every location fully informative 100,000 simulations 10 23.5 33.5 38.2 137.5 141.2 145.1

11. 99% Fixation 11 25.7 generations to reach 99% inbred with a regular 8-way cross 23.5 generations to be 99% inbred using Backcrosses 17.5 generations to be 99% inbred using MAI 17.6 23.5 25.7

12. MAI Impact 12 Regular 8-wayMAI 8-way

13. Starting Earlier 13 Impact on Number of Generations Impact on Number of Segments

14. Maximizing Mapping Power 14 Advanced Intercross – Maximize # of segments for x generations, thereafter minimize heterozygosity until inbred. Impact on Number of Segments Impact on Number of Generations

15. Conclusion 2 approaches to accelerating inbreeding Backcrosses – slight speedup MAI – dramatic acceleration Both have small impact on # of segments (slight decrease) Use of advanced intercross will increase # of segments MAI techniques are currently being used at UNC with CC lines 8 lines in various stages Considering the use of backcrosses in more lines 15

16. Acknowledgements 16 UNC Computer Science  Wei Wang  Yi Liu  Jeremy Wang FPMV Lab  David Aylor  Tim Bell  John Calaway  Mark Calaway  John Didion  Justin Gooch  Ginger Shaw  Jason Spence Churchill Lab  Gary Churchill  Hyuna Yang UNC Genetics  Will Valdar Funding Sources  NIH U01 CA105417 “Integrative Genetics of Cancer Susceptibility”  NSF IIS 0534580 “Visualizing and Exploring High-dimensional Data”  NIH GM 076468 “The Center for Genome Dynamics at Jackson Laboratory: An NIGMS National Center of Systems Biology”