Status as of: 2019-04-02

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!	Conformation	
Breed(s)	Holstein (Black & White and Red & White)	
Trait definition(s) and unit(s) of measurement2
Attach an appendix if needed	 See appendix	
Source of genotypes (chips used)	Illumina Chip BovineSNP50 and >26 low, middle or high 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) and USA and Canada are included in reference population. Genotyped females with qualified phenotype records in Germany are considered in the training set as well. The total number of Holstein reference bulls reached 37,737 and reference cows 109,857 by April 2019 based on phenotypic information of stature.	
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. For cows, national EBV are deregressed following the same procedure as for bulls. The deregressed EBV of cows are used as phenotypes for genomic evaluation.	
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 daughters in < 10 herds are not considered. Cows must have own phenotype records in order for their deregressed EBV to be qualified as phenotypes for genomic evaluation.	
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 from 5% to 40% total genetic variance for the conformation traits. Deregressed bull or cow proofs are weighted using daughter EDC or own effective record contribution. DGV of second or third generation candidates are multiplied with 0.95 or 0.90, respectively, 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 parental average (PA) to derive GEBV using the selection index theory. The PA or DGV are weighted using corresponding reliabilities.	
Environmental effects in the genetic evaluation model	A general mean in both the SNP BLUP 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 EuroGenomics or other 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	Weekly official genomic evaluations. 
Publication of official top lists on a weekly basis	
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., Z. Liu, F. Reinhardt, and R. Reents. 2017. Impact of adding cows to the uurrent EuroGenomics bull reference population on genomic prediction. Interbull Bulletin 51:86-90.
Liu, Z., Alkhoder, H., Reinhard, F., and Reents R. 2016. Accuracy and bias of genomic prediction for second-generation candidates. Interbull Bulletin 50:17-23.  
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:	Conformation	
Breed (repeat as necessary):	Holstein (Black & White and Red & White)	

Trait	   Definition	ITBa	  h2b	genetic
varianceb	official proof
standardisation formulac	
Stature	WHFF definition	X	.39	144		
Chest width	WHFF definition	X	.18	144		
Body depth	WHFF definition	X	.22	144		
Angularity	WHFF definition	X	.24	144		
Rump angle	WHFF definition	X	.29	144		
Rump width	WHFF definition	X	.29	144		
Rear leg set	WHFF definition	X	.17	144		
Rear leg rear view	WHFF definition	X	.12	144		
Foot angle	WHFF definition	X	.09	144		
Fore udder	WHFF definition	X	.23	144		
Rear udder height	WHFF definition	X	.21	144		
Udder support	WHFF definition	X	.16	144		
Udder depth	WHFF definition	X	.33	144		
Front teat placement	WHFF definition	X	.26	144		
Teat length	WHFF definition	X	.31	144		
Rear teat placement	WHFF definition	X	.23	144		
Overall udder score	WHFF definition	X	.23	144		
Overall feet&leg score	WHFF definition	X	.11	144		
Locomotion	WHFF definition	X	.08	144		
Body condition score	WHFF definition	X	.23	144		
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.