TABLE 4.

SNPs significant for association with pitch canker resistance and best hits based on BLASTx search using the contig sequence as query

SNP_ID	Best hit (expect < 1e-10)	Best hit (no cutoff)	Predicted SNP location	Effect on aa sequence	No. SNPs in LDa
0_15227_01_159	ATP binding protein, lectin-like protein kinase	ATP binding protein, lectin-like protein kinase (expect = 7e-27)	Coding region	Synonymous	0
0_15382_01_99	Geranylgeranyl transferase type I beta subunit	Geranylgeranyl transferase type I beta subunit (expect = 2e-30)	Coding region	V to A	0
0_2234_01_128	Putative long-chain acyl-CoA synthetase	Putative long-chain acyl-CoA synthetase (expect = 5e-63)	Coding region	D to Y	0
0_6323_01_240	DELLA protein	DELLA protein (expect = 3e-59)	Coding region	Synonymous	0
0_9288_01_370	No hits found	Predicted protein Populus trichocarpa (expect = 4e-06)	Coding region	Synonymous	0
1_3327_01_113b	No hits found	Unnamed protein product (Vitis vinifera) (expect = 0.23)	Coding region	C to Y	8
2_4484_02_622	Plastid hexose transporter	Plastid hexose transporter (expect = 8e-64)	Coding region	C to Y	0
2_6181_02_400	Hexokinase	Hexokinase (expect = 2e-31)	Noncoding, putative 3′-UTR	NA	0
2_8946_02_435	Cucumber peeling cupredoxin	Cucumber peeling cupredoxin (expect = 3e-10)	Non-coding, Putative 3′UTR	NA	1
CL4336Contig1_01_180	Unknown (Picea sitchensis)	Unknown (Picea sitchensis) (expect = 2e-72)	Coding region	Synonymous	1

Predicted SNP location and effect on amino acid sequence are also shown on the basis of sequence alignments with genomic DNA sequences. NA, not applicable.

^aTests for departure from Hardy–Weinberg equilibrium and linkage disequilibrium were performed for all pairwise combinations of the 3938 SNPs available for this study. None of the significant SNPs detected were in LD with each other.

^bDeparture from Hardy–Weinberg equilibrium was significant at 5% FDR. Linkage disequilibrium was also considered significant at 5% FDR.