The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce

Prunier, Julien; Pelgas, Betty; Gagnon, France; Desponts, Mireille; Isabel, Nathalie; Beaulieu, Jean; Bousquet, Jean

doi:10.1186/1471-2164-14-368

Table 2 List and description of gene SNPs significantly associated with adaptive trait variation in P. mariana

From: The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce

SNP	Gene ID^a	Gene family	LG^b	Site ^c	Trait	Age	p-value	PVE^d	q-value	Correlated climatic factors^e
c06511e	GQ02808_G21	AUX/IAA	1	4	budset	7	0.01	1.40	0.06	TWM
c11176n	GQ03816_N20	Unknown	1	3	budset	7	0.08	0.33	0.08	-
c16364e	GQ04002_G01	C2H2 zinc finger	1	3	height	12	0.02	2.23	0.10	PWM*
c02239c	GQ03118_J01	BAM1	3	3	budset	7	0.04	0.11	0.08	PWM**, AAP
c03870a	GQ0168_K17	C3HC4 Ring finger	3	4	budset	8	0.02	1.95	0.08	MAT, TWM**
c09889a	GQ02801_L07	NAC	3	4	height	7	0.07	0.74	0.10	MAT, TWM, TCM*
c04073m	GQ03313_I07	Zinc ion binding	4	4	budset	7	0.00	2.26	0.03	-
c05720c	GQ03009_F08	C3HC4 Ring finger	4	4	height	6	0.06	1.29	0.06	-
				3	budset	7	0.06	0.41	0.10
				3	height	12	0.01	2.36	0.1
c10254m	GQ0197_M23	Beta-glucosidase	4	3	budset	7	0.01	0.48	0.05	-
c02343e	GQ03102_D15	AP2	5	3	budset	7	0.06	0.33	0.08	TWM, DGD
c04662f	GQ0011_L04	AP2	5	4	height	7	0.08	0.73	0.10	-
c09406f	GQ03511_H09	LEA	5	3	budset	7	0.06	0.41	0.10	TCM, TWM*
c09898f	GQ02813_D01	RAP2	5	4	height	6	0.01	2.01	0.03	MAT*, TWM, TCM
				4	height	7	0.00	2.53	0.03
c10140e	GQ04111_I24	AP2	5	4	budset	7	0.00	2.85	0.01	-
				4	budset	8	0.03	1.70	0.08
				3	budset	7	0.02	0.24	0.05
c12722e	GQ03309_B18	U-box superfamily	5	3	budset	7	0.07	0.11	0.08	-
				3	height	12	0.03	2.16	0.10
c14320f	GQ0178_D07	transcription factor	5	4	height	6	0.02	1.70	0.03	TWM
				4	height	7	0.03	1.67	0.04
				3	height	12	0.01	2.40	0.10
c04312b	GQ02754_G07	C2H2 zinc finger	6	4	height	6	0.02	1.85	0.03	-
				4	height	7	0.02	1.72	0.04
c04554n	GQ0201_E19	MYB (10)	7	4	height	6	0.03	1.69	0.03	MAT, TCM
				4	height	7	0.05	1.41	0.05
c04671m	GQ03310_H09	PLATZ	7	3	budset	7	0.06	0.65	0.08	TCM*
c07142s	GQ0171_A23	GASA	7	4	budset	8	0.05	1.42	0.08	-
c08080a	GQ0082_F08	MYB (5)	7	4	budset	8	0.09	1.16	0.10	TWM, DGD
				3	budset	7	0.05	0.12	0.08
c08085m	GQ03515_N01	Scarecrow-like	7	4	height	7	0.06	0.83	0.07	-
				3	budset	7	0.09	0.17	0.08
				4	height	6	0.10	1.07	0.09
c13572n	GQ0178_D07	Homeobox	7	4	height	6	0.02	1.86	0.03	MAT, TWM, TCM*
				4	height	7	0.03	1.67	0.04
				3	budset	7	0.08	0.34	0.10
c15051g	GQ0195_G17	NAM	8	3	budset	7	0.06	0.19	0.10	-
c03650g	GQ03503_G05	B-box zinc family	9	4	budset	8	0.04	1.50	0.08	TCM, MAT*
				4	height	6	0.04	1.47	0.05
				3	budset	7	0.04	0.36	0.08
c05937s	GQ0207_N03	Chaperone DnaJ Heat	9	3	height	6	0.01	1.29	0.06	DGD, TWM, PWM*
		Shock Prot.		3	height	7	0.02	1.12	0.03
				3	height	12	0.04	0.99	0.01
c09063f	GQ02825_P07	PATATIN	9	4	budset	8	0.08	1.21	0.10	TCM*
				4	height	7	0.10	0.63	0.10
c13855n	GQ0255_K05	MYB (11)	9	4	budset	8	0.03	1.65	0.08	MAT**, TCM, TWM***
c02623e	GQ03208_E14	HLH	10	4	budset	8	0.06	1.38	0.08	-
c09573a	GQ02904_H04	HTH	11	4	height	7	0.06	0.84	0.10	-
c05535s	GQ0206_M13	WRKY	12	4	height	7	0.05	0.90	0.07	-
c07602a	GQ0013_G12	MYB domain	12	3	height	6	0.01	0.85	0.06	-
c15328f	GQ0071_N15	MYB	12	4	budset	7	0.03	1.71	0.08	-
				4	budset	8	0.00	2.77	0.03

^a Gene ID follows the nomenclature of the white spruce gene catalogue GCAT [39].
^b LG: Linkage group following the nomenclature of [31].
^c Site numbers as indicated on Figure 1.
^d PVE: Proportion of variance explained.
^e Climatic factors significantly correlated with the allele frequency variation of significant gene SNPs: PWM: precipitation of the wettest month; AAP: annual amount of precipitation; TWM: temperature of the warmest month; DGD: annual number of degree-days above 5°C; TCM: temperature of the coldest month; MAT: mean annual temperature. *: P ≤ 0.05; **: P ≤ 0.01; ***:P ≤ 0.005.

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ISSN: 1471-2164

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