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Table 3 Significant SNP marker-trait associations tested in the population (n = 300) after a correction for multiple testing [false discovery rate FDR ≤ 0.10]

From: Identification and characterization of nuclear genes involved in photosynthesis in Populus

Trait Gene symbol Locus Missense mutation P-value Phenotypic variation (%) FDR Frequency (%)
Pn XET 5′UTR XET-SNP2   < 0.001 5.4 0.0003 0.48 (G)
XET 5′UTR XET-SNP3   < 0.001 7.2 0.0006 0.41 (T)
XET Exon1 XET-SNP5 Leu to Pro < 0.001 5.2 0.0012 0.41 (C)
XET Exon1 XET-SNP6 Ala to Pro < 0.001 5.4 0.0009 0.38 (C)
Dabb Exon2 Dabb-SNP2 Ala to Val 0.001 4.8 0.0019 0.45 (T)
GASA 3′UTR GASA-SNP3   < 0.001 8.0 < 0.0001 0.46 (C)
SAUR Exon SAUR-SNP1 Glu to Gln 0.008 2.3 0.0158 0.26 (G)
CGSS Exon1 CGSS-SNP1 Met* to Val < 0.001 7.0 < 0.0001 0.15 (G)
Cond XET 5′UTR XET-SNP3   < 0.001 7.9 < 0.0001 0.41 (T)
XET Exon1 XET-SNP6 Ala to Pro < 0.001 5.9 0.0005 0.38 (C)
Dabb Exon2 Dabb-SNP2 Ala to Val < 0.001 7.0 < 0.0001 0.45 (T)
GASA 3′UTR GASA-SNP3   < 0.001 12.6 < 0.0001 0.46 (C)
SAUR Exon SAUR-SNP1 Glu to Gln < 0.001 5.8 < 0.0001 0.26 (G)
CGSS Exon1 CGSS-SNP1 Met* to Val < 0.001 6.8 < 0.0001 0.15 (G)
Ci XET 5′UTR XET-SNP3   0.003 3.8 0.0073 0.41 (T)
SAUR Exon SAUR-SNP1 Glu to Gln 0.007 2.4 0.0149 0.26 (G)
Trmmol XET 5′UTR XET-SNP3   0.002 4.3 0.0040 0.41 (T)
Dabb Exon2 Dabb-SNP2 Ala to Val 0.004 3.6 0.0100 0.45 (T)
CGSS Exon1 CGSS-SNP1 Met* to Val 0.008 2.3 0.0158 0.15 (G)
H PI 3′UTR PI-SNP1   0.005 2.6 0.0651 0.38 (T)
  1. Pn, photosynthetic rate; Cond, conductance to H2O; Ci, intercellular CO2 concentration; Trmmol, transpiration rate; H, tree height; Frequency, Allele frequency of either the derived or minor allele. Single nucleotide polymorphism (SNP) alleles corresponding to the frequency listed are given in parentheses.