Status as of: 2017-04-01
Form GENO

DESCRIPTION OF NATIONAL GENETIC EVALUATION SYSTEMS

Country (or countries)	United States of America	
Main trait group	Production (milk, fat, protein)	
Breed(s)	BSW, HOL, JER, GUR, RDC	
Trait definition(s) and unit(s) of measurement	Same as regular genetic evaluation	
Source of genotypes	Illumina Bovine SNP50 3K HD, LD, LD2; 
GeneSeek Genomic Profiler, GGP, GHD, GP2, GP3, GH2, G7K GP4; Zoetis ZLD, ZMD, ZL2, ZM2, ZL4	
Imputation method for missing genotypes	Missing genotypes filled using a combination of population and pedigree haplotyping in findhap.f90; additionally, imputed genotypes of non-genotyped dams included if >90% of haplotypes can be determined from progeny genotypes (usually ≥4 progeny)	
Propagation of genomic information to non-genotyped descendants and ancestors	Evaluations of non-genotyped progeny recomputed to include genomic information from parents if reliability gain is ≥1% based on methods developed previously for foreign information; genotypes for non-genotyped dams imputed using methods described above	
Animals included in reference population	Reference animals included as of April 2017:
BSW: 2,423 U.S. females and 5 CAN females; 1,048 U.S. males as well as 5,589 males provided by Interbull from 10 other countries
GUR: 692 U.S. females as well as 1CAN and 1 GBR female; 346 U.S. males as well as 97 GBR and 26 CAN males.   
HOL: 358,630 U.S. females as well as 2,206 females from 27 other countries; 19,034 U.S. males as well as 17,117 males from 22 other countries.
JER: 70,342 U.S. females and 102 females from 5 other countries; 3,562 U.S. males as well as 1,581 from 6 other countries.
RDC: 234 U.S. females, 21 CAN females and 1 DNK female; 208 U.S. males, 509 CAN males, and 312 males from 5 other countries.	
Source of phenotypic data	Deregressed proofs (DPs) calculated from PTA and parent average (PA) by the simple formula DP = PA + (PTA − PA)/RELdau, where RELdau is REL from daughters; traditional cow PTAs first adjusted (yield traits only) to provide means and variances comparable to those of bull PTAs before deregression; DP in genomic model weighted by RELdau/(1 − RELdau)	
Other criteria (data edits) for inclusion of records	The 60,671selected SNP were selected considering minor genotype frequency, parent–progeny conflicts and call rate.	
Criteria for extension of records	Not applicable	
Sire categories	None	
Genomic model	Iterative, nonlinear model with heavy-tailed prior for marker effects analogous to Bayes A used; base population allele frequencies subtracted from genotypes, and polygenic effect  (poly) with 10% of additive variance fit in the model: DP = mean + Σgenotypes(effects) + poly + error	
Blending of direct genomic value (DGV) with traditional EBV	For animals with non-genotyped ancestors such as sire, dam, or maternal grandsire, selection index with 3 terms used to combine direct genomic effect, traditional evaluation, and genotyped subset evaluation if REL gain is ≥1%; to reduce bias, coefficients adjusted by trait group to assign more weight to traditional evaluation and less weight to direct genomic effect	
Environmental effects in the genetic evaluation model	Not applicable	
Adjustment for heterogeneous variance in evaluation model	Not applicable	
Computation of genomic reliability	DGV REL computed from traditional daughter equivalents plus genomic daughter equivalents, which differ for each animal depending on its average genomic relationship to reference population; final REL computed by selection index using RELs of DGV, traditional PTA, and subset PTA	
Blending of foreign/Interbull information in evaluation	Calculation of DGV includes foreign information from previous Interbull evaluation; current Interbull evaluation used in 3-term selection index step	
Genetic parameters in the evaluation	Not applicable	
System validation	BSW: DPs for bulls evaluated after August 2012 predicted from evaluations available in August 2016	
Expression of genetic evaluations	PTA: Yield (lb), yield components (%),
	
Definition of genetic reference base
	Cows born in 2010 (stepwise, 5 years)	
Labeling of genomic evaluations	Genomic indicator code (0 = no genomic information, 1 = genotyped, 2 = non-genotyped progeny of genotyped parent, and 3 = imputed dam genotype); industry reports often use G prefix to indicate genotyped (e.g., GPTA, GTPI)	
Criteria for official publication of evaluations	All genomic evaluations (young, old, domestic, foreign, male, female) released as official; official distribution is controlled by Council on Dairy Cattle Breeding	
Number of evaluations/ publications per year	3 full releases (April, August, December) plus monthly updates for newly genotyped animals between full releases	
Use in total merit index	Net merit is sum of genomic PTAs times economic values for each trait [yield (milk, fat, protein), PL, SCS (minus phenotypic mean of 3), udder composite, feet & legs composite, DPR, calving ability (includes service-sire and daughter CE and SB as available)]	
Anticipated changes in the near future	Evaluation of crossbreds via blending of purebred evaluations	
Key reference on methodology applied	VanRaden, P.M. 2008. Efficient methods to compute genomic predictions. J. Dairy Sci. 91:4414–4423.
VanRaden, P.M., C.P. Van Tassell, G.R., Wiggans, T.S. Sonstegard, R.D. Schnabel, J.F. Taylor, and F.S. Schenkel. 2009. Invited review: Reliability of genomic predictions for North American Holstein bulls. J. Dairy Sci. 92:16–24.
Wiggans, G.R., P.M. VanRaden, L.R. Bacheller, M.E. Tooker, J.L. Hutchison, T.A. Cooper, and T.S. Sonstegard. 2010. Selection and management of DNA markers for use in genomic evaluation . J. Dairy Sci. 93:2287–2292.
VanRaden, P.M., J.R. O'Connell, G.R. Wiggans, and K.A. Weigel. 2011. Genomic evaluations with many more genotypes. Genet. Sel. Evol. 43:10.
Wiggans, G.R., P.M. VanRaden, and T.A. Cooper. 2011. The genomic evaluation system in the United States: Past, present, future. J. Dairy Sci. 94:3202–3211.
Boichard, D., H. Chung, R. Dassonneville, X. David, A. Eggen, S. Fritz, K.J. Gietzen, B.J. Hayes, C.T. Lawley, T.S. Sonstegard, C.P. Van Tassell, P.M. VanRaden, K.A. Viaud-Martinez, and G.R. Wiggans. 2012. Design of a bovine low-density SNP array optimized for imputation. PLoS ONE 7:e34130.
Wiggans, G.R., T.A. Cooper, C.P. Van Tassell, T.S. Sonstegard, and E.B. Simpson. 2013. Technical note: Characteristics and use of the Illumina BovineLD and GeneSeek Genomic Profiler low-density bead chips for genomic evaluation. J. Dairy Sci. 96:1258–1263.	
Key organisation: name, address, phone, fax, e-mail, web site	Animal Genomics and Improvement Laboratory
Agricultural Research Service, U.S. Dept. of Agriculture 
Bldg. 005, Room 306, BARC-West 
10300 Baltimore Ave.
Beltsville, Maryland 20705-2350, USA
Voice: 301-504-8334; Fax: 301-504-8092 
web site: http://aipl.arsusda.gov

Council on Dairy Cattle Breeding 
One Town Center
4201 Northview Drive,
Suite 302
Bowie, MD 20716
Ph: 240 334 4164
Web site: https://www.uscdcb.com/