TABLE 3

SNP markers associated with rAUDPC, PM, or MCR (P < 0.001)

LocusChr. no.Allele 1/2TraitaP-value aρ1h1/h2/h3P-value hρ2
BA106c14t7_SNP300IVT/GrAUDPC2.3e−3/07.6e−10.0NS6.9e−2/−3.2e−2/6.2e−33.0e−49.3
StAOS2_SNP678XIA/GrAUDPC−3.2e−2/06.4e−58.65.3e−2/7.8e−2/3.5e−24.6e−22.8NS
StAOS2_SNP681XIT/ArAUDPC−3.1e−2/06.8e−58.65.3e−2/7.4e−2/3.5e−25.4e−22.6NS
StAOS2_SNP691XIA/GrAUDPC−5.3e−2/05.1e−2039.32.7e−2/5.3e−2/2.3e−22.2e−22.8NS
StAOS2_SNP692XIC/GrAUDPC−5.3e−2/01.4e−2243.53.4e−3/−1.8e−2/−5.1e−22.0e−12.4NS
StAOS2_SNP727XIC/TrAUDPC−3.3e−2/02.8e−59.52.6e−2/8.5e−2/3.4e−25.1e−13.6NS
StAOS2_SNP744XIA/GrAUDPC−4.0e−2/02.2e−1021.0NA
StAOS2_SNP774XIC/TrAUDPC−3.3e−2/02.4e−59.63.1e−2/9.2e−2/3.0e−21.5e−24.0NS
StAOS2_SNP879XIA/GrAUDPC−3.1e−2/07.4e−610.94.7e−2/5.5e−2/3.0e−21.4e−11.4NS
StAOS2_SNP900XIA/TrAUDPC−2.8e−2/04.3e−59.01.4e−2/4.4e−2/2.3e−22.5e−10.6NS
StAOS2_SNP954XIC/TrAUDPC−3.1e−2/05.2e−58.85.2e−2/7.2e−2/3.3e−26.1e−22.4NS
Simultaneous fit47.70.1
StSGT1-1_SNP169IIIT/CPM−2.7e−1/05.9e−712.5NA
S1b3_SNP175IIIA/GPM−2.5e−1/01.1e−610.8NA
P4H6_SNP248VG/CPM4e−3/01.9e−10.9NS6.7e−1/8.0e−1/1.02.9e−45.8
BA213c14t7_SNP457VT/GPM−2.3e−1/07.5e−611.2NA
239E4left_INDEL211VT/N aPM−2.3e−1/06.8e−47.5NA
239E4left_SNP133VG/APM−2.5e−1/08.8e−47.21.6e−1/−2.7e−1/−3.1e−14.3e−10NS
StAOS2_SNP691XIA/GPM−3.7e−1/02.3e−513.2−3.0e−3/2.6e−1/9.6e−27.1e−10.0NS
StAOS2_SNP692XIC/GPM−3.6e−1/01.5e−513.7−3.8e−1/−3.7e−1/−3.1e−15.4e−10.0NS
Osm8e_SNP873XIC/TPM−2.4e−1/01.8e−11.1NS−9.3e−1/−3.1e−1/6.9e−22.2e−46.2
GP122_SNP231XIIT/APM−6.7e−1/01.8e−45.4NA
GP122_SNP440XIIG/TPM−7.2e−1/01.9e−45.2NA
Simultaneous fit23.44.8
BA106c14t7_SNP300IVT/GMCR−3.0e−3/06.7e−10.0NS3.6e−2/−3.7e−2/−8.0e−33.2e−310.6
StAOS1_SNP803IVA/GMCR−2.6e−2/06.4e−47.0NA
StAOS2_SNP691XIA/GMCR−3.3e−2/01.9e−1330.92.6e−2/4.0e−2/2.1e−22.8e−22.8NS
StAOS2_SNP692XIC/GMCR−3.4e−2/07.2e−1636.11.9e−2/1.0e−3/−1.9e−21.7e−10.9NS
StAOS2_SNP744XIA/GMCR−2.3e−2/06.5e−714.8NA
StAOS2_SNP774XIC/TMCR−1.9e−2/08.5e−46.84.3e−2/7.0e−2/2.9e−29.7e−35.4
StAOS2_SNP879XIA/GMCR−2.1e−2/06.7e−59.85.4e−2/5.5e−2/2.7e−22.4e−24.1NS
StAOS2_SNP900XIA/TMCR−2.1e−2/02.5e−511.02.7e−2/5.2e−2/1.8e−22.2e−24.1NS
StAOS2_SNP954XIC/TMCR−1.9e−2/09.8e−46.74.0e−2/6.4e−2/2.9e−21.4e−24.9NS
Simultaneous fit47.22.7
  • a, allele substitution effect, i.e., the effect of replacing one copy of allele 2 by allele 1. ρ1, proportion of the genotypic variance explained by the allele substitution effects a. h1, h2, and h3 are the bi-, tri-, and tetragenic interaction effects (the interaction effects of the heterozygous genotypes 1222, 1122, and 1112), respectively, at the corresponding marker locus. ρ2 is the proportion of the genotypic variance explained by h1, h2, and h3. NA, not applicable: interaction effects could not be estimated, because both homozygous genotype classes did not occur in the data set; NS, not significant.

  • a The indel consisted of a single nucleotide insertion/deletion.