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Table 3 Percentage explained variance (%Var), phenotypic means of SNP alleles, and significant (P < 0.05) marker-trait associations

From: DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits

Candidate gene Site position1 %Var P-value Means of SNP alleles2
(accession classes)
BLZ1 Flowering time [days after sowing]
  1733 6.46 0.0033 A: 67.96 C: 69.87
  1825 7.38 0.0031 G: 67.96 A: 69.91
  1888 6.46 0.0033 C: 67.96 T: 69.87
  1890 7.10 0.0017 G: 67.50 A: 69.54
  2038 7.52 0.0011 Del: 67.62 AT: 69.68
  2520 7.10 0.0017 G: 67.50 A: 69.54
  2562 6.46 0.0033 C: 67.96 T: 69.87
  2774 7.10 0.0017 T: 67.50 C: 69.54
BPBF Crude protein content [%]
  -368 6.65 0.0003 G: 14.85 A: 15.63
  -315 5.40 0.0003 T: 14.85 C: 15.63
  -303 6.50 0.0003 T: 14.87 A: 15.63
  -215 6.86 0.0002 C: 14.86 G: 15.63
  -209 6.19 0.0004 A: 14.88 G: 15.63
  -166 6.07 0.0003 A: 14.87 G: 15.64
  -101 5.38 0.0004 T: 14.88 C: 15.64
  -27 4.94 0.0003 C: 14.88 T: 15.65
  -3 6.76 0.0002 T: 14.82 C: 15.64
  62 4.02 <.0001 T: 14.79 C: 15.66
  579 12.40 0.0003 T: 14.90 C: 15.66
  586 3.34 0.0025 G: 14.93 A: 15.58
  618 3.42 0.0019 A: 14.91 G: 15.58
  713 5.45 0.0008 A: 14.88 G: 15.60
  797 4.06 0.0029 G: 14.94 T: 15.58
  972 4.40 0.0016 G: 14.91 A: 15.59
  1026 7.91 0.0019 T: 14.98 G: 15.62
  1075 3.51 0.0007 A: 14.91 G: 15.63
  1129 5.57 0.0007 C: 14.92 A: 15.63
  Starch content [%]
  -368 4.44 0.0004 A: 55.58 G: 56.74
  -315 7.30 0.0007 C: 55.57 T: 56.66
  -303 5.39 0.0002 A: 55.56 T: 56.77
  -215 4.41 0.0004 G: 55.58 C: 56.73
  -209 4.84 0.0003 G: 55.57 A: 56.74
  -166 5.12 0.0001 G: 55.55 A: 56.78
  -101 4.79 0.0001 C: 55.53 T: 56.78
  -27 4.22 0.0001 T: 55.55 C: 56.79
  -3 3.27 0.0008 C: 55.61 T: 56.72
  62 0.16 0.0009 C: 55.56 T. 56.70
  1. 1: Positions refer to the sequence alignment given in additional file 3
  2. 2: All differences between classes for a given site position are significant at P = 0.05