Skip to main content

Advertisement

Table 2 List and description of gene SNPs significantly associated with adaptive trait variation in P. mariana

From: The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce

SNP Gene IDa Gene family LGb Site c Trait Age p-value PVEd q-value Correlated climatic factorse
c06511e GQ02808_G21 AUX/IAA 1 4 budset 7 0.01 1.40 0.06 TWM
c11176n GQ03816_N20 Unknown 1 3 budset 7 0.08 0.33 0.08 -
c16364e GQ04002_G01 C2H2 zinc finger 1 3 height 12 0.02 2.23 0.10 PWM*
c02239c GQ03118_J01 BAM1 3 3 budset 7 0.04 0.11 0.08 PWM***, AAP*
c03870a GQ0168_K17 C3HC4 Ring finger 3 4 budset 8 0.02 1.95 0.08 MAT*, TWM***
c09889a GQ02801_L07 NAC 3 4 height 7 0.07 0.74 0.10 MAT*, TWM*, TCM*
c04073m GQ03313_I07 Zinc ion binding 4 4 budset 7 0.00 2.26 0.03 -
c05720c GQ03009_F08 C3HC4 Ring finger 4 4 height 6 0.06 1.29 0.06 -
     3 budset 7 0.06 0.41 0.10  
     3 height 12 0.01 2.36 0.1  
c10254m GQ0197_M23 Beta-glucosidase 4 3 budset 7 0.01 0.48 0.05 -
c02343e GQ03102_D15 AP2 5 3 budset 7 0.06 0.33 0.08 TWM*, DGD*
c04662f GQ0011_L04 AP2 5 4 height 7 0.08 0.73 0.10 -
c09406f GQ03511_H09 LEA 5 3 budset 7 0.06 0.41 0.10 TCM*, TWM**
c09898f GQ02813_D01 RAP2 5 4 height 6 0.01 2.01 0.03 MAT***, TWM***, TCM*
     4 height 7 0.00 2.53 0.03  
c10140e GQ04111_I24 AP2 5 4 budset 7 0.00 2.85 0.01 -
     4 budset 8 0.03 1.70 0.08  
     3 budset 7 0.02 0.24 0.05  
c12722e GQ03309_B18 U-box superfamily 5 3 budset 7 0.07 0.11 0.08 -
     3 height 12 0.03 2.16 0.10  
c14320f GQ0178_D07 transcription factor 5 4 height 6 0.02 1.70 0.03 TWM
     4 height 7 0.03 1.67 0.04  
     3 height 12 0.01 2.40 0.10  
c04312b GQ02754_G07 C2H2 zinc finger 6 4 height 6 0.02 1.85 0.03 -
     4 height 7 0.02 1.72 0.04  
c04554n GQ0201_E19 MYB (10) 7 4 height 6 0.03 1.69 0.03 MAT*, TCM*
     4 height 7 0.05 1.41 0.05  
c04671m GQ03310_H09 PLATZ 7 3 budset 7 0.06 0.65 0.08 TCM*
c07142s GQ0171_A23 GASA 7 4 budset 8 0.05 1.42 0.08 -
c08080a GQ0082_F08 MYB (5) 7 4 budset 8 0.09 1.16 0.10 TWM*, DGD*
     3 budset 7 0.05 0.12 0.08  
c08085m GQ03515_N01 Scarecrow-like 7 4 height 7 0.06 0.83 0.07 -
     3 budset 7 0.09 0.17 0.08  
     4 height 6 0.10 1.07 0.09  
c13572n GQ0178_D07 Homeobox 7 4 height 6 0.02 1.86 0.03 MAT*, TWM*, TCM*
     4 height 7 0.03 1.67 0.04  
     3 budset 7 0.08 0.34 0.10  
c15051g GQ0195_G17 NAM 8 3 budset 7 0.06 0.19 0.10 -
c03650g GQ03503_G05 B-box zinc family 9 4 budset 8 0.04 1.50 0.08 TCM*, MAT**
     4 height 6 0.04 1.47 0.05  
     3 budset 7 0.04 0.36 0.08  
c05937s GQ0207_N03 Chaperone DnaJ Heat 9 3 height 6 0.01 1.29 0.06 DGD*, TWM*, PWM*
   Shock Prot.   3 height 7 0.02 1.12 0.03  
     3 height 12 0.04 0.99 0.01  
c09063f GQ02825_P07 PATATIN 9 4 budset 8 0.08 1.21 0.10 TCM*
     4 height 7 0.10 0.63 0.10  
c13855n GQ0255_K05 MYB (11) 9 4 budset 8 0.03 1.65 0.08 MAT***, TCM*, TWM***
c02623e GQ03208_E14 HLH 10 4 budset 8 0.06 1.38 0.08 -
c09573a GQ02904_H04 HTH 11 4 height 7 0.06 0.84 0.10 -
c05535s GQ0206_M13 WRKY 12 4 height 7 0.05 0.90 0.07 -
c07602a GQ0013_G12 MYB domain 12 3 height 6 0.01 0.85 0.06 -
c15328f GQ0071_N15 MYB 12 4 budset 7 0.03 1.71 0.08 -
     4 budset 8 0.00 2.77 0.03  
  1. a Gene ID follows the nomenclature of the white spruce gene catalogue GCAT [39].
  2. b LG: Linkage group following the nomenclature of [31].
  3. c Site numbers as indicated on Figure 1.
  4. d PVE: Proportion of variance explained.
  5. e Climatic factors significantly correlated with the allele frequency variation of significant gene SNPs: PWM: precipitation of the wettest month; AAP: annual amount of precipitation; TWM: temperature of the warmest month; DGD: annual number of degree-days above 5°C; TCM: temperature of the coldest month; MAT: mean annual temperature. *: P ≤ 0.05; **: P ≤ 0.01; ***:P ≤ 0.005.