Multibreed Genomic Evaluations in Purebred Dairy Cattle K. M. Olson 1 and P. M. VanRaden 2 1 National Association of Animal Breeders 2 AIPL, ARS, USDA.

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Presentation transcript:

Multibreed Genomic Evaluations in Purebred Dairy Cattle K. M. Olson 1 and P. M. VanRaden 2 1 National Association of Animal Breeders 2 AIPL, ARS, USDA Beltsville, MD

July 2010 ADSA (2) K. M. Olson Background l Multibreed methods are currently used in traditional evaluations l Only within breed methods are used for genomic evaluations l Previous research has shown little improvement in accuracy from combining breeds for genomic evaluations however, little research has been done using multi-trait methodology

July 2010 ADSA (3) K. M. Olson Background l Smaller breeds are interested in genomic evaluations l Genomic evaluations on crossbreds w ,236 1 st lactation crossbreds, 2009 there were 23,209 w With the 3k might be more demand − Currently, system not set up to handle crossbred data

July 2010 ADSA (4) K. M. Olson Objectives l To investigate different methods of multibreed genomic evaluations using purebred Holsteins, Jerseys, and Brown Swiss genotypes

July 2010 ADSA (5) K. M. Olson Materials & Methods – Animals l Animals genotype Illumina BovineSNP50 w 43,385 SNP l The training data set - animals were proven by Nov w Holsteins – 5,331 w Jerseys – 1,361 w Brown Swiss – 506 l The validation data set - animals were unproven as of Nov and proven by Aug w Holsteins – 2,507 w Jerseys – 413 w Brown Swiss - 185

July 2010 ADSA (6) K. M. Olson Overview - Methods l Method 1 estimated SNP effects within breed then applied those effects to the other breeds l Method 2 (across-breed) used a common set of SNP effects from the combined breed genotypes and phenotypes l Method 3 (multi-breed) used a correlated SNP effects using a multi-trait method

July 2010 ADSA (7) K. M. Olson Method 1 (breed SNP effects) l Estimated SNP effects within breed l Applied those SNP effects to the other breeds l Multiple regressions were used to test the GPTA using other breeds SNP effects along with PA

July 2010 ADSA (8) K. M. Olson Method 2 - (across-breed) l All breeds were treated as one population w Base allele frequency assumed to be 0.33 for each breed l Breed PTAs were converted to the Holstein 2004 Base l Multiple regressions were used to test across breed GPTA along with PA

July 2010 ADSA (9) K. M. Olson Method 3 – (multi-breed) l Used a multi-trait genomic method as explained by VanRaden and Sullivan, 2010 w Breeds instead of countries w Animals were purebreds − Their information only used for their respective breed − Assumption of independent residuals l Three levels of correlation were tested w 0.20, 0.30, and 0.55 for Protein yield

July 2010 ADSA (10) K. M. Olson Results – prediction of protein yield P -Values HolsteinJerseyBrown Swiss Traditional PA< GPTA< Method 1 HO GPTA JE GPTA BS GPTA

July 2010 ADSA (11) K. M. Olson R 2 adjusted for Method HolsteinJersey Brown Swiss R 2 HO SNP JE SNP BS SNP PA Only

July 2010 ADSA (12) K. M. Olson Correlation GPTAs and other Breeds’ GPTAs

July 2010 ADSA (13) K. M. Olson Results – prediction of protein yield P -Values HolsteinJerseyBrown Swiss Across-breed PA< ABGPTA< Multi-breed PA< MBGPTA<

July 2010 ADSA (14) K. M. Olson Results – R 2 for protein yield HolsteinJerseyBrown Swiss PA only Traditional Across-breed Multi-breed

July 2010 ADSA (15) K. M. Olson Correlation with traditional GPTA

July 2010 ADSA (16) K. M. Olson R 2 of different correlation levels for multi-breed Correlation Level/ Breed Holstein Jersey Brown Swiss The correlation yielding best results was results in 0.09 sharing between breeds Denser SNP panels would likely result in a higher correlation, therefore greater gains across breeds

July 2010 ADSA (17) K. M. Olson Conclusions l Using another breeds SNP estimates did not help l Across-breed method increased the predictive ability, however the traditional GPTA accounted for more variation than the across- breed GPTA l Multi-breed increased the predictive ability and the multi-breed GPTA accounted for more variation than the traditional GPTA

July 2010 ADSA (18) K. M. Olson Implications l The multi-breed does slightly increase the accuracy, but may not warrant the increased computational demands l Higher density SNP chips would most likely increase the gains in accuracy for multi-breed genomic evaluations l Across-breed or multi-breed would be needed for genomic selection in crossbred herds w Not much demand for that yet

July 2010 ADSA (19) K. M. Olson Questions