Supplementary Table 3. SNP effect (b) and percentage of genetic variance explained by SNP (%VA) for branch cluster frequency at sites Kinleith, Tarawera and Woodhill in POP3 (fA: frequency of allele A)

SNP code / fA / Tarawera / Kinleith / Woodhill / Across-sites
b / %VA / b / %VA / b / %VA / b / %VA
AGP_SNP1361 / 0.58 / -0.26 c / 8.15 / -0.33 c / 8.76 / -0.20 c / 5.26 / -0.24 c / 6.80
BTUB_SNP2263 / 0.12 / - / - / - / - / 0.18 b / 1.74 / - / -
BTUB_SNP532 / 0.14 / -0.13 a / 1.00 / -0.15 a / 0.97 / -0.15 b / 1.38 / -0.14 b / 1.30
COBRA_SNP130 / 0.40 / 0.18 b / 3.93 / 0.19 b / 3.00 / 0.20 c / 5.13 / 0.18 b / 4.00
GRP_SNP286 / 0.15 / 0.12 a / 0.93 / - / - / 0.14 b / 1.31 / 0.12 a / 0.92
HCT_SNP1075 / 0.07 / -0.09 a / 0.27 / -0.10 a / 0.23 / - / - / -0.09 a / 0.25
LTP_SNP486 / 0.50 / - / - / 0.13 a / 1.44 / - / - / - / -
SCPL_SNP590 / 0.44 / - / - / 0.15 a / 1.80 / - / - / - / -
SWAP_SNP169 / 0.59 / -0.17 c / 3.53 / -0.21 c / 3.66 / -0.15 c / 2.86 / -0.18 c / 3.76
UCL3_SNP110 / 0.38 / -0.11 a / 1.45 / -0.16 b / 1.88 / - / - / -0.10 a / 1.10
UNKP6_SNP409 / 0.42 / - / - / -0.14 a / 1.58 / - / - / - / -
UNKP6_SNP627 / 0.44 / - / - / 0.23 b / 4.39 / - / - / - / -
UNKS2_SNP302 / 0.31 / -0.11 a / 1.41 / -0.15 a / 1.58 / - / - / -0.12 a / 1.53

Note:Only SNPs which had significant associations with performance are presented: - SNP effect is not significant, a P<0.05, b P<0.01 and c P < 0.001.

Page 1 of 2