Effect of increasing accuracy of genomic evaluations on economic efficiency of dairy cattle breeding programmes

Figures & data

Table 1. Breeding and productive parameters.

Population parameters	Number of productive cows	502,400
	Percentage of herd book population	33
Biological variables	Heritability of milk production^a	0.18–0.36
	Genetic variance of milk production	477, kg
	Proportion of captured genetic variance	0.875
	Twining rate	5.34, %
	Abortion rate	6.28, %
	Number of needed mothers for producing one YB	6.07
	Alive daughters per cow	40, %
	Young cows under milk recording as DS	30, %
	Death birth rate	2.93, %
	Death rate at 3 months	2.78, %
	Insemination number per pregnancy	2.22
Technical variables	Years of using a proved bull	4
	Quarantine time	6, month
	Time interval between two recalculating haplotype effects	2
	Number of individual in training set^b	500–10,000
	Number of daughters per bulls in training set	100
	Age at first calving	2.13
	open days	397.8
	Sperm production per bull	18,000, dose
Economic variables	Insemination cost	7, US$
	Cost of buying a YB	1429, US$
	Maintenance and feeding cost in Quarantine/month/YB	157, US$
	Cost of testing for diseases in Quarantine/YB	28, US$
	Cost of collecting each Vial of Sperm	2, US$
	Cost of recording/daughter	2, US$
	Feeding cost/year/YB	1543, US$
	Maintenance cost/year/YB	343, US$
	Price of culled bull	2000, US$
	Genotyping cost^c	50–400, US$
	Discount rate of costs	0.06
	Discount rate of returns	0.08
	Economic value of milk production (US$)	0.23

^a In the basic scenario, the number of individuals in training set was 1000, in the first scenario varied from 500 to 3500 and in order to produce the figure 1 varied from 500 to 10,000.

^b In the basic scenario the assumed heritability was 0.29 and in the second scenario varied from 0.18 to 0.36.

^c In the basic scenario genotyping, cost was 100 US$ and in the third scenario varied from 50 to 400 US$.

Figure 1. The general structure of genomic selection simulation.

Table 2. Effect of the size of training set on economic efficiency, accuracy, genetic gain and cost (h²=0.29 and genotyping cost = US$100).

NP	AGSE	CG	TDC	DB	EE
500	0.62	0.0053	85.94	1085.01	13.63
1000	0.72	0.0061	96.81	1241.70	13.83
1500	0.76	0.0064	107.69	1306.59	13.13
2000	0.78	0.0066	118.57	1339.13	12.29
2500	0.80	0.0068	129.45	1355.43	11.48
3000	0.81	0.0068	140.32	1356.33	10.73
3500	0.82	0.0069	151.20	1369.11	10.06

N_P is the number of individuals in training set. AGSE: accuracy of genomic selection; EE: economic efficiency; CG: cumulative genetic gain of continuous selection per dairy cow; TDC: cumulative discounted cost of continuous selection per dairy cow (US$); DB: discounted benefit corresponding to maximum economic efficiency (US$).

Figure 2. Effect of varying the number of individuals in training set (Np), on economic efficiency (EE), accuracy of genomic selection evaluation (AGSE), continuous selections genetic gain (CSGG) and total discounted cost (TDC).

Table 3. Effect of genotyping cost on the maximum efficiency and optimum number of training set, accuracy and genetic gain.

Gc	AGSEopt	NpOpt	CGopt	TDCopt	DBopt	EEmax
50	0.63	500	0.0053	70.86	1100.09	16.53
100	0.72	1000	0.0061	96.81	1241.70	13.83
150	0.72	1000	0.0061	112.18	1226.33	11.93
200	0.72	1000	0.0061	127.55	1210.97	10.49
250	0.72	1000	0.0061	142.91	1195.60	9.37
300	0.72	1000	0.0061	158.28	1180.24	8.46
350	0.72	1000	0.0061	173.64	1164.87	7.71
400	0.72	1000	0.0061	189.01	1149.50	7.08

G_c: genotyping cost; N_pOpt: optimum number of individuals in the training set; AGSE_opt: optimum accuracy of genomic selection; EE_max: maximum economic efficiency; CG_opt: optimum cumulative genetic gain of continuous selection per dairy cow; TDC_opt: optimum cumulative discounted cost of continuous selection per dairy cow (US$); DB_opt: discounted benefit which leads to maximum economic efficiency (US$).

Table 4. Effect of heritability on the maximum economic efficiency and optimal number of training set, accuracy and genetic gain.

h^2	rs	AGSEopt	NpOpt	CGopt	TDCopt	DBopt	Emax
0.18	0.825	0.71	1000	0.0060	96.81	120.96	13.49
0.21	0.847	0.71	1000	0.0060	96.81	122.03	13.60
0.24	0.865	0.71	1000	0.0060	96.81	122.93	13.70
0.27	0.879	0.71	1000	0.0030	62.12	287.96	15.63
0.30	0.890	0.72	1000	0.0030	62.12	289.94	15.67
0.33	0.900	0.72	1000	0.0030	62.12	291.74	15.69
0.36	0.908	0.72	1000	0.0030	62.12	293.38	15.72

r_s: the accuracy of breeding values in sires of training set; N_pOpt: optimum number of individuals in training set; AGSE_opt: optimum accuracy of genomic selection; EE_max: maximum economic efficiency; CG_opt: optimum cumulative genetic gain of continuous selection per dairy cow; TDC_opt: cumulative discounted cost of continuous selection perdairy cow (US$); DB_opt: discounted benefit which leads to maximum economic efficiency (US$).