Table 1.

Seasonal immune SNPs identified using whole-genome resequencing of the Pennsylvania spring and autumn populations across three consecutive years. SNPs with a seasonal q-value (SQ)<0.3 are classified as seasonal and the SNPs investigated here are in bold. Most of seasonal SNPs do not have significant clinal q-values (CQ) and were not significant in a genome wide association study (GWAS) for response to P. rettgeri pathogenic infection [52].

gene	position	effect	molecular function	SQ	CQ	GWAS
Tep2	2 L:2834400	upstream modifier	effector	0.242	0.956	0.253
Tep3	2 L:7703202	NS coding	effector	0.243	0.159	0.420
Tep3	2 L:7703509	upstream modifier	effector	0.151	0.529	0.084
Tep3	2 L:7703518	upstream modifier	effector	0.220	0.643	0.084
Tep3	2 L:7703748	upstream modifier	effector	0.271	0.819	0.114
Tep3	2 L:7703757	upstream modifier	effector	0.291	0.956	0.632
Tep3	2 L:7705370	upstream modifier	effector	0.219	0.163	0.385
bsk	2 L:10247834	intron	signalling	0.300	0.822	0.255
bsk	2 L:10252450	intron	signalling	0.257	0.749	0.962
Tep1	2 L:15887030	downstream modifier	effector	0.227	0.188	0.089
Tep1	2 L:15888031	downstream modifier	effector	0.221	0.520	NA
cact	2 L:16309682	downstream modifier	signalling	0.135	0.782	0.829
cact	2 L:16310896	downstream modifier	signalling	0.235	0.635	0.375
cact	2 L:16318067	intron	signalling	0.281	0.719	0.335
sick	2 L:19923496	intron	signalling	0.232	0.032	0.505
IM1	2 R:14270817	upstream modifier	effector	0.256	0.695	0.423
Dro6	3 L:3334769	upstream modifier	effector	0.201	0.427	0.000
Drs-l	3 L:3336529	upstream modifier	effector	0.251	0.975	0.028
GNBP1	3 L:18671289	downstream modifier	recognition	0.187	0.150	0.729
GNBP2	3 L:18671295	downstream modifier	recognition	0.218	0.167	0.666
Fadd	3 R:17861054	UTR 3'modifier	signalling	0.200	0.006	0.822
Fadd	3 R:17861073	UTR 3'modifier	signalling	0.287	0.425	0.712
kay	3 R:25600668	intron	signalling	0.200	0.588	0.743
Tak1	X:20388404	intron	signalling	0.227	0.326	0.964