TABLE 4

Least-squares mean absolute difference (centimorgans), bias (centimorgans), and percentage of QTL position estimates at or flanking the QTL obtained from the IBD method using different haplotype sizes in six alternate scenarios with 1-cM marker spacing

No. of markers used in IBD method
Alternate scenario124610
Noncentral QTL positionLSMD1.53a1.33b,c1.19d1.23c,d1.38b
Bias0.620.600.530.520.51
69.5%71.5%71.1%66.8%
Random founder allele frequenciesLSMD1.57a1.36b1.32b1.33b1.36b
Bias0.0160.003−0.0340.038−0.025
63.9%64.2%64%63.9%
“Worst-case” scenarioLSMD2.67a2.61a,b2.38c2.38c2.45b,c
Bias1.751.911.601.551.56
35.0%37.9%37.2%36.8%
Effective population size = 50LSMD1.91a1.66b1.53c1.64b,c1.68b
Bias−0.182−0.034−0.0130.1720.004
56.6%60.0%54.9%56.7%
Effective population size = 200LSMD1.44a1.18b1.15b1.09b1.17b
Bias0.017−0.009−0.107−0.029−0.075
70.0%71.8%72.3%70.9%
Smaller QTL effectLSMD1.83a1.76a1.55b1.60b1.80a
Bias−0.016−0.083−0.056−0.086−0.024
51.6%56.6%54.8%49.2%
  • The mean absolute difference of the QTL position estimate from its true position and bias for the IBD mapping method used in populations created under six alternate scenarios with 1-cM marker spacing are shown. The percentage of position estimates at or flanking the true QTL position is given for each haplotype size except for one marker. For a given alternate scenario, least-squares means with different superscripts (a, b, c, d) are significantly different (P < 0.05).