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Table 3 Results of the association study: significant SNP-phenotype associations along with the co-located QTL

From: Dissecting genetic architecture of grape proanthocyanidin composition through quantitative trait locus mapping

Chr Gene Marker Position Syn/Ns Tissue Trait n.obs p.MLM p.adj.GLM QTL
1 VvLAR1 int2687 intron 4   skin catT 112 2.92E-04 9.99E-04 Yes
   e5-2734 exon 5 Syn skin catT 112 1.22E-05 9.99E-04 Yes
   e1-82 exon 1 Ns (Ala ↔ Thr) skin mDP 115 7.08E-04 0.025 Yes
   e1-132 exon 1 Syn skin mDP 113 5.44E-04 9.99E-04 Yes
   e1-138 exon 1 Syn skin mDP 105 0.0013 0.0021 Yes
   e1-156 exon 1 Ns (Asn ↔ Lys) skin mDP 111 5.19E-04 9.99E-04 Yes
   e3-665 exon 3 Syn skin mDP 117 3.41E-04 9.99E-04 Yes
   e3-734 exon 3 Syn skin mDP 110 5.66E-04 9.99E-04 Yes
   int2405 intron 3   skin mDP 94 1.85E-04 9.99E-04 Yes
   e4-2524 exon 4 Syn skin mDP 103 5.58E-04 9.99E-04 Yes
   int2636 intron 4   skin mDP 104 6.49E-04 9.99E-04 Yes
   e5-2722 exon 5 Syn skin mDP 107 4.82E-04 9.99E-04 Yes
   e5-2776 exon 5 Syn skin mDP 107 4.82E-04 9.99E-04 Yes
   e5-2779 exon 5 Syn skin mDP 107 5.61E-04 9.99E-04 Yes
   e5-2785 exon 5 Syn skin mDP 107 5.61E-04 9.99E-04 Yes
   e5-2872 exon 5 Ns (Ile ↔ Met) skin mDP 104 6.37E-04 9.99E-04 Yes
   e5-2896 exon 5 Syn skin mDP 104 6.37E-04 9.99E-04 Yes
   e5-2902 exon 5 Syn skin mDP 104 6.37E-04 9.99E-04 Yes
   e1-156 exon 1 Ns (Asn ↔ Lys) skin Ftranscis_all 109 0.0032 0.0509 No
   int2687 intron 4   skin Ftranscis_all 114 0.0025 0.042 No
   e5-2734 exon 5 Syn skin Ftranscis_all 114 1.84E-04 9.99E-04 No
11 VvMYBPA2 intron06Y intron   skin concP 117 9.77E-04 9.99E-04 No
   p19_GA promoter   skin concK 55 4.37E-04 9.99E-04 No
   p18 promoter   skin mDP 54 1.76E-04 9.99E-04 No
   p19_GA promoter   skin mDP 55 3.36E-06 9.99E-04 No
   intron05M intron   seed galT 82 0.0015 0.3377 No
   1293 W exon 3 Syn seed galT 93 0.0014 0.3067 No
   1322 W exon 3 Ns (Leu ↔ His) seed galT 92 0.0013 0.3387 No
   1398Y exon 3 Syn seed galT 92 0.0029 0.6773 No
   1473Y exon 3 Syn seed galT 93 0.0026 0.5135 No
13 VvCHI1 Y183 exon 4 Syn skin concP 108 0.0025 0.049 No
15 VvMYBPA1 p277R promoter   skin epiT 125 0.0018 0.03 No
   702W exon 2 Ns (Ser ↔ Thr) seed Ftranscis_T 68 0.0036 0.6783 No
  1. p.MLM, p-value from mixed model, p.adj.GLM, adjusted p-value from GLM. Bold cases indicate significant associations in both MLM and GLM results. QTL, the candidate genes were under QTLs of the same PA variables as those associated with SNP.