2007 Paul VanRaden Animal Improvement Programs Laboratory USDA Agricultural Research Service, Beltsville, MD, USA

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Presentation transcript:

2007 Paul VanRaden Animal Improvement Programs Laboratory USDA Agricultural Research Service, Beltsville, MD, USA Genomic History and New Genetic Principles

AIPL Centennial, October (2) Paul VanRaden 2008 Genetic Markers: Changing Goals Past and Future  Determine if major genes exist (few)  Estimate sparse marker effects Only within family analysis  Find causative mutations (DGAT1, ABCG2)  Estimate dense effects across families  Implement routine predictions Increase REL with more genotypes Decrease cost with a selected SNP subset

AIPL Centennial, October (3) Paul VanRaden 2008 Genomic History at Beltsville  174 markers, 1068 bulls, 8 sires Illinois, Israel, and AIPL  367 markers, 1415 bulls, 10 sires GEML, AIPL, Illinois, and Israel  38,416 markers, 16,646 animals BFGL, AIPL, Missouri, Canada, and Illumina Oct Oct 2008

AIPL Centennial, October (4) Paul VanRaden 2008 Experimental Design Holstein, Jersey, and Brown Swiss breeds HOJEBS Predictor: Bulls born <19993, Cows with data202 Predictee: Bulls born >19991, Data from 2003 used to predict independent data from 2008

AIPL Centennial, October (5) Paul VanRaden 2008 Reliability Gain 1 by Breed Yield traits and NM$ TraitHOJEBS Net merit2393 Milk23110 Fat33155 Protein2241 Fat % Protein % Gain above parent average reliability ~35%

AIPL Centennial, October (6) Paul VanRaden 2008 Reliability Gain by Breed Health and type traits TraitHOJEBS Productive life18122 Somatic cell score21116 Dtr pregnancy rate165- Final score186- Udder depth35133 Foot angle1410- Stature2693

AIPL Centennial, October (7) Paul VanRaden 2008 Genetic Progress  Assume 60% REL for net merit 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 genetic SD per year Reduce generation interval more than accuracy

AIPL Centennial, October (8) Paul VanRaden 2008 Genetic Terms  Predicted transmitting ability and parent average 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 (9) Paul VanRaden 2008 Positive or Negative Traits

AIPL Centennial, October (10) Paul VanRaden 2008 Net Merit by Chromosome Planet - high Net Merit bull

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

AIPL Centennial, October (12) Paul VanRaden 2008 Genomic vs. Pedigree Inbreeding BullPedigree FGenomic F O Man Ramos Shottle Planet Earnit Nifty Correlation =.68

AIPL Centennial, October (13) Paul VanRaden 2008 Genomic vs. Expected Future Inbreeding BullEFIGFI Blackstar7.9 Elevation Chief Emory RC Matt Juror7.06.7

AIPL Centennial, October (14) Paul VanRaden 2008 Conclusions  100X more markers allows MAS across rather than within families  5X 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 (15) Paul VanRaden 2008 Acknowledgments  Genotyping and DNA extraction: BFGL, U. Missouri, U. Alberta, GeneSeek, GIFV, and Illumina  Computing: AIPL staff (George Wiggans, Mel Tooker, Leigh Walton)  Funding: National Research Initiative grants – , Agriculture Research Service Contributors to Cooperative Dairy DNA Repository (CDDR)

AIPL Centennial, October (16) Paul VanRaden 2008 CDDR Contributors  National Association of Animal Breeders (NAAB, Columbia, MO) ABS Global (DeForest, 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)