Table 3.

The association analysis for AUSPC, LTAF, and LCAF in GWBP.

Trait	FBCMa	Marker locus	Alleleb	Positionc	p	PVE %d	Allele Frequencye	Allele Effectsf
H_AUSPC	CM01	Vf_Mt5g046030_001	T:C	293.36	0.00045	7.93	0.53	−6.82
	CM01	Vf_Mt5g015280_001	T:C	62.66	0.00164	4.53	0.37	−5.09
	CM01	Vf_Mt2g027240_001	C:T	401.92	0.00230	4.05	0.54	−5.13
	CM02	Vf_Mt3g086600_001	G:T	103.65	0.00032	7.19	0.89	−10.96
	CM02	Vf_Mt4g007030_001	C:A	234.93	0.00164	4.54	0.34	−5.43
	CM02	Vf_Mt5g075540_001	G:C	31.06	0.00296	3.55	0.49	−4.53
	CM03	Vf_Mt1g105040_001	G:T	97.13	0.00256	5.22	0.85	−7.68
	CM03	Vf_Mt1g056180_001	A:G	227.32	0.00953	4.23	0.29	−5.44
	CM04	Vf_Mt4g101130_001	T:C	24.50	0.00296	3.42	0.26	−6.92
	CM04	Vf_Mt8g040550_001	A:G	192.4	0.00329	3.03	0.41	−4.26
	LG03	GLIP081SNP	G:C	21.99	0.00632	2.66	0.41	−3.99
LTAF	CM01	Vf_Mt5g046030_001	T:C	293.36	0.00001	11.89	0.53	−0.63
	CM01	Vf_Mt2g027240_001	C:T	401.92	0.00193	5.15	0.54	−0.41
	CM01	Vf_Mt5g015280_001	T:C	62.66	0.00499	4.18	0.37	−0.39
	CM02	Vf_Mt3g086600_001g	G:T	103.65	0.00001	8.84	0.89	−0.87
	CM02	Vf_Mt4g007030_001	C:A	234.93	0.30018	5.14	0.34	−0.43
	CM03	Vf_Mt1g105040_001	G:T	97.13	0.00733	4.23	0.85	−0.52
	CM03	Vf_Mt1g056180_001	A:G	227.32	0.00885	3.74	0.29	−0.38
	CM04	Vf_Mt2g086880_001	T:A	62.66	0.00289	4.98	0.40	−0.41
LCAF	CM01	Vf_Mt5g046030_001g	C:T	293.36	0.00043	8.20	0.53	−0.54
	CM01	Vf_Mt2g027240_001	C:T	401.92	0.00143	5.44	0.54	−0.44
	CM02	Vf_Mt3g086600_001	G:T	103.65	0.00009	7.93	0.89	−0.85
	CM02	Vf_Mt5g075540_001	G:C	31.06	0.00304	5.20	0.49	−0.43
	CM03	Vf_Mt1g105040_001	G:T	97.13	0.00733	4.95	0.85	−0.54
	CM04	Vf_Mt2g086880_001	T:A	62.66	0.00364	4.93	0.40	−0.42

Traits, AUSPC; area under symptoms progress curve after hardening conditions; LTAF, loss of leaf turgidty after frost; LCAF, loss of leaf color after frost.

^aLinkage group, CM refers to the consensus map, LG refers to genetic linkage in BPP.

^b“Left” allele decreases the trait.

^cPosition of the marker on the respective linkage group in CM or genetic linkage in BPP.

^dPhenotypic variation explained by marker (%).

^eThe allele frequency was calculated for the allele which decreases the trait.

^fThe effect of the left allele.

^gMarker showed significant association using MLM+kinsip at 20% FDR.

Bold markers showed significant association at 5% FDR.