TABLE 4

Loss of accuracy of GEBVs with genotyping of selected low-density (SLD) SNPs as a percentage of the accuracy obtained by high-density BayesB in generations after training and with 100, 500, and 1000 simulated QTL

No. of simulated QTLGeneration
Method234
SLD-BB-1101.1 (±3.2)0.8 (±3.2)0.7 (±4.2)
100SLD-BB-403.1 (±3.1)2.0 (±3.2)1.7 (±4.2)
SLD-FSS-0.019.0 (±2.4)8.1 (±3.3)8.7 (±4.0)
SLD-FSS-11018.2 (±3.2)23.1 (±3.2)24.9 (±4.2)
SLD-BB-1102.5 (±3.2)1.9 (±4.8)1.5 (±5.4)
500SLD-BB-407.8 (±3.2)6.5 (±4.8)4.02 (±5.0)
SLD-FSS-0.0110.7 (±2.7)10.6 (±4.0)12.1 (±4.1)
SLD-FSS-11012.5 (±2.8)14.2 (±2.8)18.8 (±4.3)
SLD-BB-1103.0 (±3.3)2.6 (±3.8)2.3 (±4.9)
1000SLD-BB-409.2 (±3.3)9.7 (±3.7)8.4 (±4.9)
SLD-FSS-0.0112.8 (±3.2)17.7 (±4.1)21.0 (±4.6)
SLD-FSS-11013.7 (±3.5)18.4 (±3.8)22.0 (±4.2)
  • One thousand individuals were used to estimate HD-SNP effects (±SE, based on 25 replicates). SLD-BB-110 and SLD-BB-40 refer to selection of 110 and 40 SNPs using BayesB; SLD-FSS-0.01 and SLD-FSS-110 refer to selection of SNPs by forward stepwise selection with a significance level of 0.01 or with a total of 110 SNPs selected.