Status as of: 2016-04-01

Form GENO

DESCRIPTION OF NATIONAL GENOMIC EVALUATION SYSTEMS

Country (or countries)	JAPAN	
Main trait group1
NOTE! Only one trait group per form!	Health	
Breed(s)	Holstein	
Trait definition(s) and unit(s) of measurement2
Attach an appendix if needed	Milk Somatic Cell Score (SCS) = log2(Somatic Cell Count(SCC) /100,000) +3; where SCC is somatic cells per milliliter	
Source of genotypes (chips used)	Illumina’s 54K SNP Chip	
Imputation method for missing genotypes	No	
Propagation of genomic information to non-genotyped descendants and ancestors	No	
Animals included in reference population (males, females, countries included, total number)	3906 males 	
Source of phenotypic data (DYD, deregressed proofs, national EBVs and/or MACE evaluations)	Deregressed MACE EBVs or deregressed national EBVs if MACE not available.	
Other criteria (data edits) for inclusion of records		
Criteria for extension of records (if applicable)		
Sire categories	All genotyped bulls	
Genomic model (linear, Bayesian, polygenic effect, genotypes or haplotypes)	Linear Model with genotypes including polygenic effect	
Blending of direct genomic value (DGV) with traditional EBV	Selection index	
Environmental effects in the genetic evaluation model	Overall mean	
Adjustment for heterogeneous variance in evaluation model	No	
Computation of genomic reliability	PEV using MCMC	
Blending of foreign/Interbull information in evaluation	PI of young bulls	
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	Comparison 692 young bulls between deregressed EBVs(2015) and GEBVs(2011) estimated using 3211 reference bulls.	
Expression of genetic evaluations
If standardised (e.g. RBV), give standardisation formula in the appendix	EBV 	
Definition of genetic reference base	5-year stepwise, average EBV of cows born in 2010
August/2020	
Labeling of genomic evaluations		
Criteria for official publication of evaluations		
Number of evaluations / publications per year		
Use in total merit index	NTP: Nippon Total Profit Index
NTP = 4.5×PC + 1.5×(15×EBV feet & legs/0.386+85×UC/0.302)
PC( Production Composite ) = 27×EBV fat yield/16.07 + 73×EBV protein yield/12.38
UC(Udder Composite) = 0.32×EBV udder (score) + 0.68×{0.16×EBV fore udder attachment + 0.10×EBV rear udder height + 0.28×EBV udder cleft +0.35×EBV udder depth + 0.11×EBV teat placement}	
Anticipated changes in the near future		
Key reference on methodology applied		
Key organisation: name, address, phone, fax, e-mail, web site	Member organization: Livestock Improvement Association of Japan, Inc
Ohno-building, 1-19-8, Kyobashi, Chuo-ku, Tokyo, 104-0031, JAPAN
Tel: +81-3-3561-8561
Fax: +81-3-3561-8165
Web: http://liaj.lin.go.jp/
E-mail: webmaster@liaj.lin.go.jp
National evaluation center: National Livestock Breeding Center, IAI
1 Odakurahara, Nishigo, Nishi-Shirakawa, Fukushima, 961-8511, JAPAN
Tel: +81-248-25-4904
Fax: +81-248-25-3982
Web: http://www.nlbc.go.jp/
Contact: data analysis div. to: k0hagiya@nlbc.go.jp	
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):	Japan	
Main trait group:	Health	
Breed (repeat as necessary):	Holstein	

Trait	Definition	ITBa	h2b	genetic
varianceb	official proof
standardisation formulac	
Milk Somatic Cell:		X	0.082	0.188	A=0, b= 1, c=1, d = 2.23	

						

						

						

						

						
						
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.