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Table 3 Variance component estimates (standard deviation) under different subsets of FSTbased and randomly selected SNPs for populations1P1and P2(average over 5 replicates)

From: Increasing accuracy of genomic selection in presence of high density marker panels through the prioritization of relevant polymorphisms

 

P1(LD =0.3)

P2(LD = 0.7)

GV2

RV3

GV

RV

FST based

 2.5 K

0.126 (0.017)

0.728 (0.027)

0.198 (0.029)

0.736 (0.006)

 5 K

0.149 (0.016)

0.706 (0.030)

0.204 (0.005)

0.711 (0.001)

 10 K

0.175 (0.023)

0.684 (0.037)

0.195 (0.009)

0.697 (0.004)

 20 K

0.203 (0.031)

0.663 (0.044)

0.195 (0.007)

0.686 (0.007)

 40 K

0.226 (0.041)

0.649 (0.052)

0.203 (0.009)

0.677 (0.007)

 80 K

0.247 (0.048)

0.641 (0.055)

0.217 (0.008)

0.671 (0.008)

 160 K

0.264 (0.045)

0.642 (0.047)

0.235 (0.008)

0.670 (0.008)

Random

 2.5 K

0.104 (0.013)

0.834 (0.012)

0.155 (0.012)

0.788 (0.006)

 5 K

0.139 (0.016)

0.796 (0.013)

0.185 (0.013)

0.757 (0.005)

 10 K

0.173 (0.019)

0.762 (0.006)

0.215 (0.011)

0.730 (0.012)

 20 K

0.203 (0.023)

0.733 (0.013)

0.234 (0.010)

0.712 (0.008)

 40 K

0.227 (0.026)

0.710 (0.015)

0.242 (0.007)

0.703 (0.005)

 80 K

0.238 (0.027)

0.770 (0.015)

0.246 (0.008)

0.699 (0.007)

 160 K

0.242 (0.027)

0.696 (0.016)

0.250 (0.008)

0.696 (0.006)

Full panel

 400 K

0.247 (0.027)

0.692 (0.016)

0.251 (0.007)

0.695 (0.006)

  1. 1P1: 200 QTLs and linkage disequilibrium (LD) between adjacent markers equal to 0.3 and P2: 200 QTLs and LD between adjacent markers equal to 0.7; 2genetic variance, 3residual variance