No. of markers used in IBD method | ||||||
---|---|---|---|---|---|---|

Alternate scenario | 1 | 2 | 4 | 6 | 10 | |

Noncentral QTL position | LSMD | 1.53^{a} | 1.33^{b,c} | 1.19^{d} | 1.23^{c,d} | 1.38^{b} |

Bias | 0.62 | 0.60 | 0.53 | 0.52 | 0.51 | |

69.5% | 71.5% | 71.1% | 66.8% | |||

Random founder allele frequencies | LSMD | 1.57^{a} | 1.36^{b} | 1.32^{b} | 1.33^{b} | 1.36^{b} |

Bias | 0.016 | 0.003 | −0.034 | 0.038 | −0.025 | |

63.9% | 64.2% | 64% | 63.9% | |||

“Worst-case” scenario | LSMD | 2.67^{a} | 2.61^{a,b} | 2.38^{c} | 2.38^{c} | 2.45^{b,c} |

Bias | 1.75 | 1.91 | 1.60 | 1.55 | 1.56 | |

35.0% | 37.9% | 37.2% | 36.8% | |||

Effective population size = 50 | LSMD | 1.91^{a} | 1.66^{b} | 1.53^{c} | 1.64^{b,c} | 1.68^{b} |

Bias | −0.182 | −0.034 | −0.013 | 0.172 | 0.004 | |

56.6% | 60.0% | 54.9% | 56.7% | |||

Effective population size = 200 | LSMD | 1.44^{a} | 1.18^{b} | 1.15^{b} | 1.09^{b} | 1.17^{b} |

Bias | 0.017 | −0.009 | −0.107 | −0.029 | −0.075 | |

70.0% | 71.8% | 72.3% | 70.9% | |||

Smaller QTL effect | LSMD | 1.83^{a} | 1.76^{a} | 1.55^{b} | 1.60^{b} | 1.80^{a} |

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).