Chromosome | Marker position (cM) | No. of eQTL^{a} | Negative^{b} | Positive^{c} | % Bay-0^{d} | % Sha^{e} | P-value^{f} |
---|---|---|---|---|---|---|---|

I | 0.01 | 164 | 142 | 22 | 86.6 | 13.4 | 2.37 × 10^{−26} |

I | 61.51 | 353 | 16 | 337 | 4.5 | 95.5 | 2.00 × 10^{−53} |

I | 99.88 | 193 | 51 | 142 | 26.4 | 73.6 | 1.38 × 10^{−7} |

I | 101.88 | 186 | 175 | 11 | 94.1 | 5.9 | 9.52 × 10^{−41} |

II | 0.01 | 1202 | 1028 | 174 | 85.5 | 14.5 | 1.06 × 10^{−172} |

II | 13.59 | 1439 | 1341 | 98 | 93.2 | 6.8 | 1.35 × 10^{−291} |

II | 22.97 | 182 | 164 | 18 | 90.1 | 9.9 | 6.16 × 10^{−34} |

II | 42.44 | 2528 | 5 | 2523 | 0.2 | 99.8 | 0 |

II | 55.87 | 710 | 10 | 700 | 1.4 | 98.6 | 4.64 × 10^{−122} |

III | 9.14 | 381 | 367 | 14 | 96.3 | 3.7 | 4.68 × 10^{−89} |

III | 72.38 | 162 | 26 | 136 | 16.0 | 84.0 | 7.48 × 10^{−14} |

III | 77.48 | 163 | 30 | 133 | 18.4 | 81.6 | 5.27 × 10^{−12} |

IV | 55.40 | 256 | 255 | 1 | 99.6 | 0.4 | 3.08 × 10^{−68} |

V | 63.54 | 195 | 123 | 72 | 63.1 | 36.9 | 6.14 × 10^{−7} |

V | 66.48 | 261 | 245 | 16 | 93.9 | 6.1 | 5.58 × 10^{−56} |

V | 70.70 | 417 | 69 | 348 | 16.5 | 83.5 | 4.12 × 10^{−32} |

V | 75.51 | 202 | 37 | 165 | 18.3 | 81.7 | 1.32 × 10^{−14} |

All eQTL with their LRT statistic maxima mapping to a marker at a

*trans*-eQTL hotspot were analyzed for additive-effect estimates contributed by each parental allele. Permutation analysis established 133 eQTL as the significance threshold (α = 0.05) for declaring a significant*trans*-eQTL hotspot (see materials and methods). Within each hotspot, the number of eQTL with a negative additive-effect estimate (*i.e*., Bay-0 allele increased transcript level) was compared with the number of eQTL with a positive additive-effect estimate (*i.e*., Sha allele increased transcript level).↵

*a*Number of eQTL with LRT statistic maxima located at the marker.↵

*b*Number of eQTL with a negative additive-effect estimate.↵

*c*Number of eQTL with a positive additive-effect estimate.↵

*d*Percentage of transcripts positively influenced by the Bay-0 allele.↵

*e*Percentage of transcripts positively influenced by the Sha allele.↵

*f**P*-values for χ^{2}test for significant deviation from expected 50% contribution from each allele.