Table 4.

List and properties of single-nucleotide polymorphisms (SNPs) potentially affected by artificial selection identified with Fisher’s exact test at a minimum confidence level of P ≤ 0.01^*

SNP	Populations compared	Locus†	e-value‡	Gene family	Putative biological function§	Position	P-value (Fisher’s exact test)	Q-value (false discovery rate)	FST¶	P-value (FST)	P-value/PVE** (association with breeding value)
08Pg03931f	Large case vs Large control	AT5G54160	1.00E-63	O-Methyltransferase 1	Lignin composition	Exon (synonymous)	0.001	1.000	−0.004	1.0	0.0399/4.5
pa08Pg12255f††	Large case vs Large control	AT3G13750	4.00E-102	Beta galactosidase 1 (BGAL1)	Cell elongation, fruit ripening and storage mobilization, functional stability of the wall during cell death as cotyledons undergo senescence	Intron (N/A)	0.005	1.000	−0.004	1.0	0.0174/4.6
i08pg01084a††	Large case vs Large control	AT3G22960	0	Pyruvate kinase	Glycolysis regulation	Exon (N/A)	0.006	1.000	0.667	1.0	0.0804/3.6
10614t2††	Large case vs Large control	N/A	N/A	N/A	N/A	Exon (non-synonymous)	0.006	1.000	0.038	0.015	0.3944/1.3
08pg02707e	Large case vs Large control	AT5G48900	2.00E-106	Pectate lyase family protein	Fruit ripening, cell wall degradation	3′ UTR	0.007	1.000	0.000	1.000	0.0012/9.2
08pg10691j	Large case vs Large control	AT3G07720	3.00E-113	Kelch repeat-containing protein	Role in oogenesis, organization of cytoskeletal, plasma membrane or organelle structures, coordination of morphology and growth in yeast cells	Exon (synonymous)	0.008	1.000	0.003	0.349	0.1324/2.9
08pg02707f	Large case vs Large control	AT5G48900	2.00E-106	Pectate lyase family protein	Fruit ripening, cell wall degradation	3′ UTR	0.008	1.000	0.000	1.0	0.0263/5.1
Py08pg10659-2††	Large case vs Large control	AT3G12780	0	Phosphoglycerate kinase (PGK1)	Glycolysis	Exon (non-synonymous)	0.008	1.000	0.002	0.384	0.0979/3.3
08pg04210d	Large case vs Large control	AT1G48110	1.00E-92	Evolutionarily conserved C-terminal region 7(ECT7)	Plant development	Exon (non-synonymous)	0.009	1.000	−0.001	0.489	0.0493/2.7
08Pg00936e	Large case vs Large control	AT5G65700	7.00E-77	Barely any meristem 1 (BAM1)	Leaf development, male gametophyte development, ovule specification, and function	Exon (non-synonymous)	0.009	1.000	−0.007	1.0	0.3981/1.5
08pg02761g	Small case vs Small control	AT4G24780	7.00E-123	Pectate lyase family protein	Fruit ripening, cell wall degradation	Exon (synonymous)	0.001	0.648	0.034	0.124	0.0009/26.7
09121m††	Small case vs Small control	AT5G20510	7.00E-99	ALFIN-like 5 (AL5)	Abiotic stress and development	3′ UTR	0.001	0.648	0.043	0.097	0.0032/19.5
08pgsb29b††	Small case vs Small control	AT1G77450	3.00E-18	Arabidopsis NAC domain containing protein 32	Embryonic, floral, and vegetative development, lateral root formation and auxin signalling, defense and abiotic stress.	Exon (synonymous)	0.005	0.971	0.132	0.005	0.1149/7.8
08Pg05193f	Small case vs Small control	AT2G38120	2.00E-165	Auxin-resistant 1 (AUX1)	Root development, response to nematode	Intron (N/A)	0.006	0.971	0.129	0.005	0.0008/23.6
08Pg05193h	Small case vs Small control	AT2G38120	2.00E-165	Auxin-resistant 1 (AUX1)	Root development, response to nematode	Intron (N/A)	0.006	0.971	0.129	0.004	0.0008/23.6
Py08pg10192	Small case vs Small control	AT2G32910	2.00E-41	N/A	N/A	3′ UTR	0.007	0.971	0.123	0.011	0.0680/9.7
08pgsb08a	Small case vs Small control	AT5G38650	6.00E-49	Proteasome maturation factor UMP1 family protein	Maturation of the 20S proteasome	Intron (N/A)	0.007	0.971	0.123	0.004	0.0338/12.0
08pgsb08b††	Small case vs Small control	AT5G38650	6.00E-49	Proteasome maturation factor UMP1 family protein	Maturation of the 20S proteasome	Exon (synonymous)	0.007	0.971	0.123	0.002	0.0338/12.0
Py08pg9772-1	Small case vs Small control	AT1G08510	3.00E-112	Fatty acyl-ACP thioesterases B (FATB)	Plant growth and seed development	3′ UTR	0.008	0.971	0.120	0.010	0.1624/6.6

^*SNPs with P > 0.01 were not included because they are more likely to be false positives, as explained in the Discussion.

^†SNP annotations and nomenclature are as in the study of Pavy et al. (2008).

^‡Related transcript sequences can be found upon request in the Arborea database at http://www.arborea.ulaval.ca.

^§Biological functions were based on literature research for the GO annotations obtained for each locus through BLASTx searches against Arabidopsis blast sets database at http://www.arabidopsis.org/tools/bulk/go/index.jsp.

^¶F_ST between case and control populations was calculated as an estimate of θ_RH proposed by Robertson and Hill (1984) and corrected by Raufaste and Bonhomme (2000).

^**P-value of association tests between the SNP and the breeding value for height at 15 years of age, and percentage of variation explained (PVE). The tests were carried out using the GLM procedure available in the TASSEL software (http://www.maizegenetics.net/tassel) and in combining both the control and the case populations for each set.

^††SNP associated with a quantitative trait loci (QTL) for height growth and/or bud phenology in white spruce (see Pelgas et al. 2011).