Status as of: 2016-05-02

Form GENO

DESCRIPTION OF NATIONAL GENOMIC EVALUATION SYSTEMS

Country (or countries)	Germany, Austria and Luxembourg	
Main trait group1
NOTE! Only one trait group per form!	Female fertility	
Breed(s)	Holstein (Black & White and Red & White)	
Trait definition(s) and unit(s) of measurement2
Attach an appendix if needed	Trait 1: non-return rate 56 days of virgin heifer (NRh), in %
Trait 2: interval from first to successful inseminations virgin heifer (FSh), in days 
Trait 3: interval from calving to first insemination of cow (CFc), in days
Trait 4: non-return rate 56 days of cow (NRc), in %
Trait 5: interval from first to successful inseminations of cow (FSc), in days
Days open (DO) of cow is derived as sum of CFc and FSc.	
Source of genotypes (chips used)	Illumina Chip BovineSNP50 and various lower density chips  	
Imputation method for missing genotypes	Using the software FImpute  	
Propagation of genomic information to non-genotyped descendants and ancestors	No propagation of genomic information to non-genotyped relatives done yet in routine genomic evaluation	
Animals included in reference population (males, females, countries included, total number)	Genotyped Holstein bulls with daughter information from EuroGenomics countries (Germany, France, The Netherlands, Nordic countries, Spain and Poland) are included in reference population. No genotyped females are considered yet in the training set. The total number of Holstein reference bulls reached 30,577 by April 2016 based on phenotypic information of Non-Return rate cow.	
Source of phenotypic data (DYD, deregressed proofs, national EBVs and/or MACE evaluations)	Deregressed MACE proofs for bulls with daughters are used as phenotype for genomic evaluation. In case of traits not evaluated by Interbull or bulls missing MACE EBV, deregressed national proofs of bulls are chosen.	
Other criteria (data edits) for inclusion of records	Animals having genotypes inconsistent with their parents are excluded from genomic evaluation. Deregressed EBV of bulls with EDC < 10 or daughters in < 10 herds are not considered.	
Criteria for extension of records (if applicable)	N/A	
Sire categories	All categories of genotyped bulls	
Genomic model (linear, Bayesian, polygenic effect, genotypes or haplotypes)	A linear SNP BLUP genomic model including a residual polygenic effect and 45,613 random SNP effects with equal variance. Residual polygenic variance is set to 20% total genetic variance for the five fertility traits. Deregressed bull proofs are weighted using daughter EDC. DGV of second or third generation candidates are multiplied with a factor, 0.95, in order to account for the loss in genomic variance caused by the breakup of linkage disequilibrium between SNP markers and genes/mutations.	
Blending of direct genomic value (DGV) with traditional EBV	Estimated DGV is combined with conventional EBV or male pedigree index (PI) to derive GEBV using the selection index theory. The male PI or DGV are weighted using corresponding reliabilities.	
Environmental effects in the genetic evaluation model	A general mean in both the SNP genomic model and the selection index method for combining genomic and phenotypic information	
Adjustment for heterogeneous variance in evaluation model	N/A	
Computation of genomic reliability	Reliability of DGV is set to realised genomic reliability obtained from a genomic validation study. Reliability of combined GEBV is approximated using both genomic and phenotypic information with the selection index theory.	
Blending of foreign/Interbull information in evaluation	MACE EBVs on DEU scale are used as phenotypic data for genomic evaluation. Genotyped reference bulls from the other EuroGenomics countries are added to the German national genomic reference population for estimating SNP effects and calculating combined GEBV.	
Genetic parameters in the evaluation	Use Appendix GENO for heritability/genetic variance estimates; for multiple-trait genetic evaluations, provide genetic correlation estimates between traits separately.
Use also appendices PR, CO, BCO, SM, LO, CA, as applicable, if you participate in the international genetic evaluations of Interbull	
System validation	Routine checks on genotype and phenotype data: mean, standard deviation and correlation of DGV, EBV or GEBV within and between genomic evaluations. 
Interbull genomic validation method via GEBVtest software is applied on a regular basis.	
Expression of genetic evaluations
If standardised (e.g. RBV), give standardisation formula in the appendix	Same as in conventional genetic evaluation	
Definition of genetic reference base	Same as conventional genetic evaluation	
Labeling of genomic evaluations	Direct genomic values receive the label dGW and combined GEBV the label gZW 	
Criteria for official publication of evaluations	All genotyped bulls selected for artificial insemination and reliability of production trait GEBV  ≥ 50%	
Number of evaluations / publications per year	Monthly official and weekly non-official genomic evaluations. For animals genotyped with the standard Illumina chip 50K, a non-official genomic evaluation is performed just-in-time. 
Publication of official top lists three times a year	
Use in total merit index	Same as for conventional genetic evaluation	
Anticipated changes in the near future	A single-step SNP BLUP model for joint conventional and genomic evaluations  	
Key reference on methodology applied	Alkhoder, H., Liu, Z., Bach, Th., Pasman, E., and Reinhardt, F. 2014. A continuous genomic evaluation system for German Holsteins. Interbull Bulletin: 48:100-104. 
Liu, Z., Seefried, F., Reinhardt, F, Rensing, S., Thaller, G., and Reents, R. 2011. Impacts of both reference population size and inclusion of a residual polygenic effect on the accuracy of genomic prediction. Genet. Sel. Evol. 43:19. 
Liu, Z., Seefried, F., Reinhardt, F, and Reents, R. 2010. Approximating reliabilities of direct genomic values. Interbull Bulletin: 41:29-32.
Reinhardt, F., Z. Liu, F. Seefried, and G. Thaller. 2009. Implementation of genomic evaluation in German Holsteins. Interbull Bulletin 40:219-226.	
Key organisation: name, address, phone, fax, e-mail, web site	vit, Department of Genetic Evaluation and Biometrics 
Heinrich-Schröder-Weg 1, D-27283 Verden/Aller, GERMANY
Telefon: 0049 - 4231 - 955 10
Fax: 0049 - 4231 - 955 166
e-mail: zws@vit.de or info@vit.de,  web site: http://www.vit.de	
1) Either: 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.

Form GENO	Appendix GENO

Parameters used in genetic evaluation

Country (or countries):	Germany, Austria and Luxembourg	
Main trait group:	Female fertility	
Breed (repeat as necessary):	Holstein (Black & White and Red & White)	

Trait	Definition	ITBa	h2b	genetic
varianceb	official proof
standardisation formulac	
Non-Return rate to 56 days, virgin heifer (NRh)	Interbull trait 1 (HCO)	X	.012	21.08 (%2)		
Interval first to successful inseminations virgin heifer (FSh)			.014	55.35		
Interval from calving to first insemination (CFc)	Interbull trait 2 (CRC)	X	.039	33.36		
Non-Return rate to 56 days, cow (NRc)	Interbull trait 3 (CC1)	X	.015	34.34 (%2)		
Interval from first to successful insemination, cow (FSc)	Interbull trait 4 (CC2)	X	.010	28.99		
Days open (DO)	Interbull trait 5 (INT)	X	.026	67.04		

						
						
a	Indicate, with X, traits that are submitted to Interbull for international genetic evaluations.
b	If 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.
c	Expressed 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.