Status as of: 2015-09-14) 
Form GENO
DESCRIPTION OF NATIONAL GENOMIC EVALUATION SYSTEMS
Country (or countries) 	Czech Republic	
Main trait groupa. 
NOTE. Only one trait group per form! 	Production	
Breed(s) 	Holstein	
Trait definition(s) and unit(s) of measurement
Attach an appendix if needed 	As conventional – Test day measured in Kg
Milk, Fat, and Protein yield
	
Source of genotypes (chips used) 	Illumina 54K v1 or v2,	
Imputation method for missing genotypes 	none	
Propagation of genomic information to non-genotyped descendants and ancestors 	Via changed relationship matrix. More accurate relationship is spread to all animals related to the genotyped-ones. 	
Animals included in reference population (males, females, countries included, total number) 	All genotyped animals. Include:
-
-	
Source of phenotypic data (DYD, de-regressed proofs, national EBVs and/or MACE evaluations) 	Test day records like in conventional evaluation.
Lactations(TD records) with calving since January 1st 1995.	
Other criteria (data edits) for inclusion of records 	None - no difference from conventional run.	
Criteria for extension of records (if applicable) 	Not applicable	
Sire categories 	All sires	
Genomic model (linear, Bayesian, polygenic effect, genotypes or haplotypes) 	Single-step GBLUP – test-day - animal model with random regression
TD records are the imputed phenotypes	
Blending of direct genomic value (DGV) with traditional EBV 	Not possible to answer for single step. The conventional pedigree matrix “corrected” by genotype based relationship	
Environmental effects in the genetic evaluation model 	Same like conventional model
Herd-test day-parity (F) Regressions on DIM within parity-season-year-service period-age at first calving or calving interval for later lactations (F)	
Adjustment for heterogeneous variance in evaluation model 	none	
Computation of genomic reliability 	The procedure calculates reliability of genomic breeding values on the basis of effective number of records resulting from test-day records and information about related animals described by pedigree- and genomic relationship matrix in single-step genomic BLUP method (Misztal et al., 1993 and 2013).
	
Blending of foreign/Interbull information in evaluation 	none	
Genetic parameters in the evaluation 	Use Appendix GENO for heritability/genetic variance estimates; 	
Expression of genetic evaluations
If standardized (e.g. RBV), give standardization formula in the appendix 	Same like conventional. 
EBVlact is calculated as sum of test day EBV from 5th day to day 305. 
EBVtot is calculated as average of all three lactations without weights. EBVtot is published as EBV standardized to equal variance with previous subtraction of the base.	
Definition of genetic reference base 	All cows born 2000 (will change soon)	
Labeling of genomic evaluations 	Published separately, will be labeled with ”g”	
Criteria for official publication of evaluations 	Daughters in less than 6 herds, no official MACE released. 	
Number of evaluations / publications per year 	6 times per year, all official.	
Use in total merit index 	Planned - when all genomic traits available. Probably same weights like in current conventional index, only labeled “g”	
Anticipated changes in the near future 	-	Genetic reference base – in-line with conventional
-	Significant amount of genotyped cows added.	
Key reference on methodology applied 	Misztal, I., Legarra, A., Short, T. H. 1993. Implementation of single- and multiple-trait Animal models for genetic evaluation of Holstein type traits. Journal of Dairy Science. 76 (5). 1421–1432.
Misztal, I., Tsuruta, S., Aguilar, I., Leggara, A., Van Raden, P. M., Lawlor, T. J.. 2013. Methods to approximate reliabilities in single-step genomic evaluation. Journal of Dairy Science. 96 (1). 647 – 654.
Přibyl, J., Haman, J., Kott, T., Přibylová, J., Šimečková, M., Vostrý, L., Zavadilová, L., Čermák, V., Růžička, Z., Šplíchal, J., Verner, M., Motyčka, J., Vondrášek, L., 2012. Single-step prediction of genomic breeding value in a small dairy cattle population with strong import of foreign genes. Czech Journal of Animal Science. 57  (4). 151–159.
Přibyl, J., Madsen P., Bauer J., Přibylová, J., Šimečková M., Vostrý, L., Zavadilová, L. 2013. Contribution of domestic production records, Interbull estimated breeding values, and single nucleotide polymorphism genetic markers to the single-step genomic evaluation of milk production. Journal of Dairy Science. 96 (2). 1865-1873. 
Bauer J., Vostrý L., Přibyl J., Svitáková A., Zavadilová L. 2014. Approximation of reliability of single-step genomic breeding values for dairy cattle in the Czech Republic. Animal Science Papers and Reports. 32, (4), 301-306.
Bauer J., Přibyl, J., Vostrý, L. 2015. Reliability of single-step genomic BLUP breeding values in multi-trait test-day model analysis. Journal of Dairy Science. 98(7):4999-5003.
	
Key organization: name, address, phone, fax, e-mail, web site 	Plemdat sro, Benesovska 123, Hradisto, Czech Rep.
splichal@plemdat.cz, www.plemdat.cz, +420257896444	
aEither: Production (e.g. milk, fat, protein), Conformation, Health (e.g. mastitis resistance, milk somatic cell, resistance to diseases other than mastitis), Longevity, Calving (e.g. stillbirth, calving ease), Female fertility (e.g. non-return rate, interval between reproductive events, number of AI’s, heat strength), Workability (e.g. milking speed, temperament), Beef production, Efficiency (e.g. body weight, energy balance, body conditioning score), or Other traits. 

System Validation
Approximate number of test bulls for this trait group:	370	
If including foreign reference bulls:
4-yr old de-regressed MACE EBVs, OR
Current de-regressed MACE EBVs
If including foreign test bulls (type of proof 21 or 22), provide the reason.	none	
If using a truncation ≠ 4 years, provide the reason.		
If applying an age cutoff for test bulls ≠ (YYYY-8), provide the reason		

Appendix GENO
Parameters used in genetic/genomic evaluation 
Country (or countries): 		
Main trait group: 		
Breed (repeat as necessary): 		
Trait 	Definition 	ITBa 	h2b 	Genetic varianceb 	Official proof standardisation formulac 	
Milk	Milk yield for 6-306 days in kg		0.39	367 291	See appendix PR of conventional form GE	
Fat	Milk yield for 6-306 days in kg		0.38	574.48		
Protein	Milk yield for 6-306 days in kg		0.37	349.64		
aIndicate, with X, traits that are submitted to Interbull for international genetic evaluations.
bIf repeated records are treated as separate traits, provide heritability estimates and genetic variances separately for each trait, as well as for all traits pooled, i.e. for the trait submitted to Interbull.
cExpressed as follows: StandEval=((eval-a)/b)*c+d where a=mean of the base adjustment, b=standard deviation of the base, c=standard deviation of expression (include sign if scale is reversed), and d=base of expression.