Table 3. SNPs associated with AUDPC in 2009, 2010, and 2011.
| Year | Scaffold | SNP | Gene Model | SNP location | Arabidopsis Best hit | Annotated Gene | P value | Permutated P value | Marker R2 |
| 2009 | 10 | 19215715 | POPTR_0010s22230 | exon | At5g02810.1 | PRR7 (PSEUDO-RESPONSE REGULATOR 7) | 7.33414E-07 | 0.003 | 0.0289 |
| 14 | 3245282 | POPTR_0014s04070 | intron | At1g19330.1 | unknown protein | 1.45407E-06 | 0.003 | 0.0271 | |
| 14 | 3245414 | POPTR_0014s04070 | intron | At1g19330.1 | unknown protein | 1.45407E-06 | 0.003 | 0.0271 | |
| 12 | 1814218 | POPTR_0012s02170 | intron | At3g49220.1 | pectinesterase family protein | 4.44885E-06 | 0.012 | 0.0250 | |
| 12 | 1814164 | POPTR_0012s02170 | intron | At3g49220.1 | pectinesterase family protein | 5.76602E-06 | 0.018 | 0.0244 | |
| 5 | 23949327 | POPTR_0005s25750 | intergenic | At1g19870.1 | IQD32 (IQ-domain 32) | 7.86988E-06 | 0.025 | 0.0238 | |
| 2 | 13904004 | POPTR_0002s18010 | intergenic | no arabidopsis blast hit | unknown protein | 9.02706E-06 | 0.030 | 0.0236 | |
| 10 | 1844266 | POPTR_0010s01650 | intergenic | At4g15900.1 | PRL1 (PLEIOTROPIC REGULATORY LOCUS 1) | 1.06875E-05 | 0.033 | 0.0253 | |
| 1 | 31118784 | POPTR_0001s32810 | intron | At4g13980.1 | AtHSFA5; DNA binding/transcription factor | 1.40977E-05 | 0.037 | 0.0226 | |
| 2010 | 10 | 19215715 | POPTR_0010s22230 | exon | At5g02810.1 | PRR7 (PSEUDO-RESPONSE REGULATOR 7) | 4.49274E-11 | 0.001 | 0.0476 |
| 5 | 23949327 | POPTR_0005s25750 | intergenic | At1g19870.1 | IQD32 (IQ-domain 32) | 2.71307E-07 | 0.003 | 0.0302 | |
| 5 | 10782555 | POPTR_0005s13780 | intergenic | At2g23760.1 | BLH4 (BEL1-LIKE HOMEODOMAIN 4) | 4.67804E-07 | 0.004 | 0.0292 | |
| 5 | 23952538 | POPTR_0005s25750 | exon | At1g19870.1 | IQD32 (IQ-domain 32) | 7.99477E-07 | 0.004 | 0.0281 | |
| 6 | 1402770 | POPTR_0006s02140 | intergenic | At4g15090.1 | FAR1 (FAR-RED IMPAIRED RESPONSE 1) | 3.6489E-06 | 0.016 | 0.0253 | |
| 6 | 1397889 | POPTR_0006s02140 | 3′-UTR | At4g15090.1 | FAR1 (FAR-RED IMPAIRED RESPONSE 1) | 4.07883E-06 | 0.017 | 0.0250 | |
| 1 | 34721616 | POPTR_0001s36210 | exon | At3g27330.1 | zinc finger (C3HC4-type RING finger) family protein | 6.1898E-06 | 0.024 | 0.0244 | |
| 6 | 1399289 | POPTR_0006s02140 | exon | At4g15090.1 | FAR1 (FAR-RED IMPAIRED RESPONSE 1) | 7.28474E-06 | 0.029 | 0.0238 | |
| 9 | 10970414 | POPTR_0009s13880 | intergenic | At4g02390.1 | APP (ARABIDOPSIS POLY(ADP-RIBOSE) POLYMERASE) | 7.59421E-06 | 0.029 | 0.0239 | |
| 6 | 1402469 | POPTR_0006s02140 | intergenic | At4g15090.1 | FAR1 (FAR-RED IMPAIRED RESPONSE 1) | 8.05648E-06 | 0.031 | 0.0242 | |
| 14 | 10716774 | POPTR_0014s14650 | intron | At5g48560.1 | basic helix-loop-helix (bHLH) family protein | 1.1107E-05 | 0.041 | 0.0230 | |
| 2011 | 9 | 1676227 | POPTR_0009s01420 | intergenic | At1g08090.1 | PtNRT2.1 (NITRATE TRANSPORTER 2.1) | 3.52242E-07 | 0.003 | 0.0342 |
| 5 | 23949327 | POPTR_0005s25750 | intergenic | At1g19870.1 | IQD32 (IQ-domain 32) | 7.88901E-07 | 0.003 | 0.0308 | |
| 10 | 19215715 | POPTR_0010s22230 | exon | At5g02810.1 | PRR7 (PSEUDO-RESPONSE REGULATOR 7) | 8.34729E-07 | 0.003 | 0.0313 | |
| 9 | 1678826 | POPTR_0009s01420 | intergenic | At1g08090.1 | PtNRT2.1 (NITRATE TRANSPORTER 2.1) | 1.9236E-06 | 0.007 | 0.0308 | |
| 9 | 1606213 | POPTR_0009s01330 | exon | At3g45040.1 | phosphatidate cytidylyltransferase family protein | 2.96357E-06 | 0.008 | 0.0279 | |
| 9 | 1857142 | POPTR_0009s01490 | intergenic | At5g60720.1 | unknown protein | 4.83027E-06 | 0.014 | 0.0270 | |
| 8 | 4165833 | POPTR_0008s06920 | intergenic | At5g05610.1 | AL1 (ALFIN-LIKE 1) | 5.71705E-06 | 0.017 | 0.0266 | |
| 9 | 1676590 | POPTR_0009s01420 | 3′-UTR | At1g08090.1 | PtNRT2.1 (NITRATE TRANSPORTER 2.1) | 5.74407E-06 | 0.017 | 0.0266 | |
| 143 | 2955 | POPTR_0143s00200 | exon | At5g60770.1 | PtNRT2.4 (NITRATE TRANSPORTER 2.1) | 5.74407E-06 | 0.017 | 0.0266 | |
| 2 | 13131622 | POPTR_0002s17360 | intergenic | no arabidopsis blast hit | unknown protein | 7.73544E-06 | 0.022 | 0.0259 | |
| 2 | 4627286 | POPTR_0002s06880 | intron | At1g76900.1 | AtTLP1 (TUBBY LIKE PROTEIN 1) | 8.13072E-06 | 0.025 | 0.0259 | |
| 10 | 21451968 | POPTR_0010s26100 | 5′-UTR | At3g54540.1 | AtGCN4; transporter | 8.23563E-06 | 0.025 | 0.0261 | |
| 17 | 12392905 | POPTR_0017s12210 | 3′-UTR | At5g61430.1 | ANAC100 (ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 100) | 1.02655E-05 | 0.035 | 0.0254 | |
| 9 | 1679212 | POPTR_0009s01420 | intergenic | At1g08090.1 | PtNRT2.1 (NITRATE TRANSPORTER 2.1) | 1.09575E-05 | 0.039 | 0.0252 | |
| 12 | 1811250 | POPTR_0012s02170 | intergenic | At3g49220.1 | pectinesterase family protein | 1.10236E-05 | 0.039 | 0.0253 | |
| 9 | 1679805 | POPTR_0009s01420 | intergenic | At1g08090.1 | PtNRT2.1 (NITRATE TRANSPORTER 2.1) | 1.16257E-05 | 0.040 | 0.0250 | |
| 8 | 8157244 | POPTR_0008s12610 | exon | At5g17350.1 | unknown protein | 1.1642E-05 | 0.040 | 0.0251 | |
| 6 | 1405713 | POPTR_0006s02150 | exon | At3g22170.1 | FHY3 (FAR-RED ELONGATED HYPOCOTYLS 3) | 1.22801E-05 | 0.041 | 0.0250 | |
| 9 | 2563210 | POPTR_0009s01990 | intron | At5g60690.1 | REV (REVOLUTA) | 1.28046E-05 | 0.043 | 0.0249 | |
| 8 | 8261867 | POPTR_0008s12780 | exon | At1g71010.1 | phosphatidylinositol-4-phosphate 5-kinase family protein | 1.31391E-05 | 0.046 | 0.0248 |
Permutated P value of α = 0.05 was used as the threshold for multiple testing corrections after SNP pre-selection.
Bonferroni correction threshold was applied at P = 1.70×10−6 without SNP pre-selection.
Arabidopsis best hit and annotated function is derived from BLAST results of poplar gene models in POPGENIE. R2 value explains the effect of each SNP on the phenotype.