TABLE 3

Accuracy of GEBVs with high-density (HD) genotyping and loss of accuracy using approaches based on genotyping evenly spaced low-density (ELD) SNPs, as a percentage of the accuracy of HD-BayesB (HD-BB) in generations after training and for a trait with 100, 500, and 1000 simulated QTL

No. of simulated QTLGeneration
Method234
HD-BB70.9 (±1.64)69.0 (±1.55)65.1 (±1.96)
100ELD-104.4 (±3.16)9.5 (±3.50)15.8 (±4.60)
ELD-10+4.4 (±3.16)5.0 (±3.08)4.5 (±3.63)
HD-BB64.4 (±1.03)58.2 (±1.41)55.3 (±1.37)
500ELD-104.4 (±3.29)8.6 (±4.82)13.9 (±5.43)
ELD-10+4.4 (±3.29)5.7 (±3.89)5.2 (±3.71)
HD-BB63.2 (±1.20)57.1 (±1.69)56.1 (±1.79)
1000ELD-104.6 (±2.98)8.6 (±3.81)14.2 (±4.90)
ELD-10+4.6 (±2.98)4.5 (±3.12)6.0 (±3.86)
  • One thousand individuals each having 1000 HD-SNPs were used to estimate HD-SNP effects with BayesB and LD-SNPs at intervals of 10 cM were used to trace HD-SNP alleles (±SE, based on 25 replicates). ELD-10+ indicates that individuals used for breeding in each generation were also genotyped for HD-SNPs.