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Title: Genomic inbreeding and relationships among Holsteins, Jerseys, and Brown Swiss

Author
item Vanraden, Paul
item OLSON, K - National Association Of Animal Breeders
item Wiggans, George
item Cole, John
item Tooker, Melvin

Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/20/2011
Publication Date: 11/1/2011
Citation: Van Raden, P.M., Olson, K.M., Wiggans, G.R., Cole, J.B., Tooker, M.E. 2011. Genomic inbreeding and relationships among Holsteins, Jerseys, and Brown Swiss. Journal of Dairy Science. 94(11):5673-5682.

Interpretive Summary: Genomic and pedigree relationships were compared using genotypes of 25,219 Holsteins, 3,068 Jerseys, and 872 Brown Swiss. Adjustment factors were estimated for means and regressions of genomic on pedigree relationships, for allele frequencies in the base population, and for pedigree relationships to make those match genomic relationships more closely in multibreed populations. Genomic inbreeding accurately detected pedigree inbreeding, and use of genomic relationships accurately determined breed differences. Correlations of genomic with pedigree inbreeding were higher within each breed when 0.5 rather than allele frequencies in the base population were used. The results provide a basis for multibreed genomic evaluation.

Technical Abstract: Genomic measures of relationship and inbreeding within and across breeds were compared with pedigree measures using genotypes for 43,385 loci of 25,219 Holsteins, 3,068 Jerseys, and 872 Brown Swiss. Adjustment factors were estimated for means and regressions of genomic on pedigree relationships, for allele frequencies in the base populations, and for pedigree relationships to make those match genomic relationships more closely in multibreed populations. Correlations of genomic with pedigree inbreeding were higher within each breed when an allele frequency of 0.5 rather than base population frequencies were used. Allele frequencies differed in the 3 breeds and were correlated by 0.65 to 0.67 when estimated from genotyped animals compared with 0.72 to 0.74 when estimated from the breed base populations. The largest difference was between Holstein and the other breeds on chromosome BTA4 near a gene affecting the appearance of white skin patches (vitiligo) in humans. Each animal’s breed was predicted very accurately using regressions on genotypes at all loci or somewhat less accurately using subsets of loci. Genomic future inbreeding, which was defined as half an animal’s mean genomic relationship to current animals of the same breed, was compared with expected future inbreeding defined as half the mean pedigree relationship. For net merit of young Holstein bulls, correlations of both were slightly higher with parent averages than with genomic evaluations (0.02 for genomic future inbreeding and 0.10 for expected future inbreeding). Thus, selection using genomic rather than traditional evaluations has only small effects on average relationships among selected animals. New methods to adjust and compare pedigree and genomic relationship matrices may provide an improved basis for multibreed genomic evaluation.