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!	Conformation	
Breed(s)	Holstein	
Trait definition(s) and unit(s) of measurement2
Attach an appendix if needed	Linear traits (17)
Stature, Chest width, Body depth, Angularity, Rump angle, Rump width, Rear leg set, Rear leg rear view, Foot angle, Fore udder, Rear udder height, Rear udder width, Udder support, Udder depth, Front teat placement, Teat length, Rear teat placement
Score traits (5)
Frame, Feet& Legs, Dairy Character, Udder, Final(overall) score	
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 and SBV (standardized breeding value) for 6 score traits. SBV for 17 linear traits.	
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:	Conformation	
Breed (repeat as necessary):	Holstein
	
Trait	Definition	ITBa	h2b	Genetic
varianceb	official proof
standardisation formulac	
Stature	The measurement of the height at the rump	X	0.53	0.982	a=0, b=0.719, c=1, d=0	
Chest Width	The width of the chest floor	X	0.30	0.203	a=0, b=0.256, c=1, d=0	
Body Depth	Observing the middle of the cow/the depth of rear rib	X	0.38	0.286	a=0, b=0.326, c=1, d=0	
Angularity	Observing the sharpness of and flatness of the bone, openness and slant of the rib, length of the neck, quality of skin.	X	0.25	0.127	a=0, b=0.203, c=1, d=0	
Rump Angle	Observing the slope from hips to pins. A flat rump from hips to pins is scored 3.	X	0.41	0.345	a=0, b=0.360, c=1, d=0	
Rump Width	Distance between pins.	X	0.34	0.331	a=0, b=0.379, c=1, d=0	
Rear Leg Set	Straight leg <-> sickle leg, side view.	X	0.20	0.179	a=0, b=0.215, c=1, d=0	
Rear Leg Rear View	Sickle leg <-> straight leg, rear view.	X	0.11	0.228	a=0, b=0.252, c=1, d=0	
Foot Angle	The angle that the toes of the foot make with the ground.	X	0.05	0.054	a=0, b=0.116, c=1, d=0	
Fore Udder	Strength of the attachment	X	0.21	0.190	a=0, b=0.278, c=1, d=0	
Rear Udder Height	The distance between the bottom of the vulva and the top of the milk secreting tissue of the rear udder.	X	0.26	0.244	a=0, b=0.317, c=1, d=0	
Rear Udder width	The measurement of the width of the rear udder at the point where the lateral ligaments of the udder arrach to the body		0.21	0.124	a=0, b=0.185, c=1, d=0	
Udder Support	The depth of cleft through the bottom of the udder.	X	0.20	0.213	a=0, b=0.262, c=1, d=0	
Udder Depth	The measurement between the lowest point of the udder floor and the point of the hock.	X	0.46	0.369	a=0, b=0.417, c=1, d=0	
Front Teat Placement	Observeing the placement of the front teats on the quarter from behind the cow.	X	0.38	0.408	a=0, b=0.397, c=1, d=0	
Teat Length	Evaluating the length of the extreme teat when length varies.	X	0.40	0.502	a=0, b=0.470, c=1, d=0	
Rear Teat Placement	The placement of  the rear teats at the point of the udder as viewed from the rear.	X	0.31	0.430	a=0, b=0.401, c=1, d=0	
Overall Conformation Score	Frame*0.15
+ Feet& Legs* 0.15
+Dairy Character*0.20
+Body Capacity * 0.10
+Udder * 0.40	X	0.27	0.608		
Overall Udder Score	Udder being strongly attached and fully capacious, and four quarters being well-balanced, fine texture, and indicating heavy production and a long life of production.	X	0.20	0.635		
Dairy Character	Giving an impression of vigorousness, angularity with a stretch as a whole		0.34	0.873		
						
Frame	Revealing femininity, attractive style with harmonious blending of each part for evaluation, full of vigorousness and refinement with gentle temperament		0.27	0.967		
Overall Feet & Leg Score	Length being well proportioned with the depth of body, standing wide apart in a right posture, clean-cut and strong with light and sound walk.	X	0.13	0.471		

						

						

						

						

						

						
						
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.