Using a very low-density SNP panel for genomic selection in a breeding program for sheep

Table 2 Genetic gain, inbreeding rate, (G)EBV accuracies, and imputation concordance rates for six scenarios^a with VLD panels of 1000 SNPs (standard deviations for 50 replicates shown in brackets)

Scenarios^a	CS^b	GSsc^c	GSs_Ic^c	GSscd^c	GSs_Icd^c	GSs_Icd_pop^c
Genetic gain^d (σ_a/year)	0.162 (0.015)	0.205 (0.019)	0.197 (0.021)	0.249 (0.016)	0.230 (0.014)	0.179 (0.020)
Inbreeding rate/year^e	0.0043 (0.0011)	0.0034 (0.0006)	0.0033 (0.0006)	0.0028 (0.0005)	0.0031 (0.0006)	0.0040 (0.0008)
(G)EBV accuracy^f
Dams^g	0.71 (0.02)	0.76 (0.02)	0.75 (0.02)	0.87 (0.01)	0.83 (0.02)	0.74 (0.03)
Male candidates	0.36 (0.07)	0.53 (0.06)	0.51 (0.06)	0.71 (0.05)	0.63 (0.05)	0.43 (0.07)
Imputation concordance rate^h
Dams^g					96.1 (0.1)	91.1 (0.2)
Old femalesⁱ					93.3 (0.1)	88.3 (0.2)
Male candidates			94.7 (0.2)		96.5 (0.1)	92.3 (0.2)

^aScenarios based on imputation were performed with a very low-density 1000-SNP panel
^bCS = classical selection design
^cGS = genomic selection design; GSsc, sires and candidates had medium-density genotypes; GSs_Ic, sires had medium-density genotypes and candidates had medium-density genotypes imputed from very low-density genotypes; GSscd, sires, candidates and dams had medium-density genotypes; GSs_Icd, sires had medium-density genotypes and candidates and dams had medium-density genotypes imputed from very low-density genotypes; GSs_Icd_pop, sires had medium-density genotypes and candidates and dams had medium-density genotypes imputed from very low-density genotypes without using the pedigree information
^dComputed as the slope of the average true breeding value of females in first parity between time10 and time25
^eComputed as the slope of the average inbreeding coefficient of females in first parity between time10 and time25
^fComputed as the average Pearson correlation between the true breeding value and (genomic) estimated breeding values of animals at time25
^gDams mated at time 25
^hComputed as the average of number of correctly imputed SNP divided by the number of imputed SNP obtained for the imputation realized at time 25
ⁱDams not present anymore at time 25

ISSN: 1297-9686