Genomic History and New Genetic Principles Paul Van

Genomic History and New Genetic Principles Paul Van. Raden Animal Improvement Programs Laboratory USDA Agricultural Research Service, Beltsville, MD, USA Paul. Van. Raden@ars. usda. gov 2008 2007

Genetic Markers: Changing Goals Past and Future Ø Determine if major genes exist (few) Ø Estimate sparse marker effects • Only within family analysis Ø Find causative mutations (DGAT 1, ABCG 2) Ø Estimate dense effects across families Ø Implement routine predictions • • Increase REL with more genotypes Decrease cost with a selected SNP subset AIPL Centennial, October 28 2008 (2) Paul Van. Raden 2008

Genomic History at Beltsville Ø 174 markers, 1068 bulls, 8 sires • • Ø 367 markers, 1415 bulls, 10 sires • • Ø Illinois, Israel, and AIPL 1991 -1999 GEML, AIPL, Illinois, and Israel 1995 -2004 38, 416 markers, 16, 646 animals • • BFGL, AIPL, Missouri, Canada, and Illumina Oct 2007 - Oct 2008 AIPL Centennial, October 28 2008 (3) Paul Van. Raden 2008

Experimental Design Holstein, Jersey, and Brown Swiss breeds Predictor: Bulls born <1999 Cows with data Predictee: Bulls born >1999 HO JE BS 3, 576 743 202 225 1, 759 425 118 Data from 2003 used to predict independent data from 2008 AIPL Centennial, October 28 2008 (4) Paul Van. Raden 2008

Reliability Gain 1 by Breed Yield traits and NM$ Trait Net merit Milk Fat Protein Fat % Protein % 1 Gain HO 23 23 33 22 43 34 JE 9 11 15 4 41 29 BS 3 0 5 1 10 5 above parent average reliability ~35% AIPL Centennial, October 28 2008 (5) Paul Van. Raden 2008

Reliability Gain by Breed Health and type traits Trait Productive life Somatic cell score Dtr pregnancy rate Final score Udder depth Foot angle Stature AIPL Centennial, October 28 2008 (6) HO 18 21 16 18 35 14 26 JE 12 1 5 6 13 10 9 BS 2 16 3 3 Paul Van. Raden 2008

Genetic Progress Ø Assume 60% REL for net merit • • Ø Sires mostly 2 instead of 6 years old Dams of sons mostly heifers with 60% REL instead of cows with phenotype and genotype (66% REL) Progress could increase by >50% • • 0. 37 vs. 0. 23 genetic SD per year Reduce generation interval more than accuracy AIPL Centennial, October 28 2008 (7) Paul Van. Raden 2008

Genetic Terms Ø Predicted transmitting ability and parent average • • • Ø PTA required progeny or own records PA included only parent data Genomics blurs the distinction Reliability • • • REL of PA could not exceed 50% Genomics can predict the other 50% REL limit for calves theoretically 99% AIPL Centennial, October 28 2008 (8) Paul Van. Raden 2008

Positive or Negative Traits AIPL Centennial, October 28 2008 (9) Paul Van. Raden 2008

Net Merit by Chromosome Planet - high Net Merit bull AIPL Centennial, October 28 2008 (10) Paul Van. Raden 2008

New Genetic Terms Ø Actual vs. expected genetic similarity • • Genomic relationships and inbreeding Genomic future inbreeding (GFI) vs. EFI Ø Daughter merit vs. son merit Ø Haplotyping and imputation • • • Which allele is from sire vs. dam? Which alleles are linked together? Can missing genotypes be predicted? AIPL Centennial, October 28 2008 (11) Paul Van. Raden 2008

Genomic vs. Pedigree Inbreeding Bull O Man Ramos Shottle Planet Earnit Nifty Pedigree F 4. 5 2. 3 5. 6 6. 7 6. 2 3. 1 Genomic F 15. 8 11. 5 11. 9 18. 8 12. 8 11. 7 Correlation =. 68 AIPL Centennial, October 28 2008 (12) Paul Van. Raden 2008

Genomic vs. Expected Future Inbreeding Bull Blackstar Elevation Chief Emory RC Matt Juror AIPL Centennial, October 28 2008 (13) EFI 7. 9 7. 6 7. 1 7. 0 GFI 7. 9 7. 4 6. 8 6. 9 6. 7 Paul Van. Raden 2008

Conclusions Ø Ø Ø 100 X more markers allows MAS across rather than within families 5 X more bulls allows estimation of much smaller QTL effects (HO) Reliability increases by tracing actual genes inherited instead of expected average from parents AIPL Centennial, October 28 2008 (14) Paul Van. Raden 2008

Acknowledgments Ø Genotyping and DNA extraction: • Ø Computing: • Ø BFGL, U. Missouri, U. Alberta, Gene. Seek, GIFV, and Illumina AIPL staff (George Wiggans, Mel Tooker, Leigh Walton) Funding: • National Research Initiative grants – • • 2006 -35205 -16888, 2006 -35205 -16701 Agriculture Research Service Contributors to Cooperative Dairy DNA Repository (CDDR) AIPL Centennial, October 28 2008 (15) Paul Van. Raden 2008

CDDR Contributors Ø National Association of Animal Breeders (NAAB, Columbia, MO) • ABS Global (De. Forest, WI) Accelerated Genetics (Baraboo, WI) Alta (Balzac, AB) Genex (Shawano, WI) New Generation Genetics (Fort Atkinson, WI) • Select Sires (Plain City, OH) • Semex Alliance (Guelph, ON) • Taurus-Service (Mehoopany, PA) • • AIPL Centennial, October 28 2008 (16) Paul Van. Raden 2008