Multibreed genomic evaluations in purebred dairy cattle
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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 katie.olson@ars.usda.gov. Background. Multibreed methods are currently used in traditional evaluations

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Multibreed Genomic Evaluations in Purebred Dairy Cattle

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Multibreed Genomic Evaluations in Purebred Dairy Cattle

K. M. Olson1 and P. M. VanRaden2

1National Association of Animal Breeders

2AIPL, ARS, USDA

Beltsville, MD

katie.olson@ars.usda.gov


Background

  • Multibreed methods are currently used in traditional evaluations

  • Only within breed methods are used for genomic evaluations

  • Previous research has shown little improvement in accuracy from combining breeds for genomic evaluations however, little research has been done using multi-trait methodology


Background

  • Smaller breeds are interested in genomic evaluations

  • Genomic evaluations on crossbreds

    • 1999 2,236 1st lactation crossbreds, 2009 there were 23,209

    • With the 3k might be more demand

      • Currently, system not set up to handle crossbred data


Objectives

  • To investigate different methods of multibreed genomic evaluations using purebred Holsteins, Jerseys, and Brown Swiss genotypes


Materials & Methods – Animals

  • Animals genotype Illumina BovineSNP50

    • 43,385 SNP

  • The training data set - animals were proven by Nov. 2004

    • Holsteins – 5,331

    • Jerseys – 1,361

    • Brown Swiss – 506

  • The validation data set - animals were unproven as of Nov. 2004 and proven by Aug. 2009

    • Holsteins – 2,507

    • Jerseys – 413

    • Brown Swiss - 185


Overview - Methods

  • Method 1 estimated SNP effects within breed then applied those effects to the other breeds

  • Method 2 (across-breed) used a common set of SNP effects from the combined breed genotypes and phenotypes

  • Method 3 (multi-breed) used a correlated SNP effects using a multi-trait method


Method 1 (breed SNP effects)

  • Estimated SNP effects within breed

  • Applied those SNP effects to the other breeds

  • Multiple regressions were used to test the GPTA using other breeds SNP effects along with PA


Method 2 - (across-breed)

  • All breeds were treated as one population

    • Base allele frequency assumed to be 0.33 for each breed

  • Breed PTAs were converted to the Holstein 2004 Base

  • Multiple regressions were used to test across breed GPTA along with PA


Method 3 – (multi-breed)

  • Used a multi-trait genomic method as explained by VanRaden and Sullivan, 2010

    • Breeds instead of countries

    • Animals were purebreds

      • Their information only used for their respective breed

      • Assumption of independent residuals

  • Three levels of correlation were tested

    • 0.20, 0.30, and 0.55 for Protein yield


Results – prediction of protein yield P-Values


0.8

0.7

0.6

HO SNP

0.5

JE SNP

2

0.4

R

BS SNP

0.3

PA Only

0.2

0.1

0

Holstein

Jersey

Brown Swiss

R2 adjusted for Method 1


Correlation GPTAs and other Breeds’ GPTAs


Results – prediction of protein yield P-Values


Results – R2 for protein yield


Correlation with traditional GPTA


R2 of different correlation levels for multi-breed

The correlation yielding best results was 0.30 - results in

0.09 sharing between breeds

Denser SNP panels would likely result in a higher correlation,

therefore greater gains across breeds


Conclusions

  • Using another breeds SNP estimates did not help

  • Across-breed method increased the predictive ability, however the traditional GPTA accounted for more variation than the across-breed GPTA

  • Multi-breed increased the predictive ability and the multi-breed GPTA accounted for more variation than the traditional GPTA


Implications

  • The multi-breed does slightly increase the accuracy, but may not warrant the increased computational demands

  • Higher density SNP chips would most likely increase the gains in accuracy for multi-breed genomic evaluations

  • Across-breed or multi-breed would be needed for genomic selection in crossbred herds

    • Not much demand for that yet


Questions


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