Table 3. Outlier loci detected by Fdist2 (P<0.99), Arlequin (P<0.99) and BayeScan (Bayes factor >2) analyses, and their linkage group and putative function by BLASTx search (E-value cutoff ⩽1 × 10⁻³).

Locus	Fdist2					Arlequin FST	BayeScan			Linkage group	Putative function
	All populations			Omote	Ura	P value	All populations	Omote	Ura
	He	FST	P				P
SNPg03850	0.4314	0.2237	0.0000	*	*	0.0010	0.0000		*	—	No hit
SNPg04215	0.0965	0.5006	0.0000	*		0.0000	0.0062			7	Endo-1,4-beta-glucanase
SNPg01385	0.5036	0.2231	0.0000			0.0004	0.0000			—	No hit
SNPg04024	0.4856	0.2173	0.0000	*		0.0004	0.0000			11	MYBPA1 protein
SNPg01330	0.2321	0.2050	0.0000	*		0.0002	0.0000			11	Adenosine 3′-phospho 5′-phosphosulfate transporter
SNPg04607	0.2399	0.1927	0.0000		*	0.0017	0.0016			—	No hit
SNPg04808	0.3198	0.1837	0.0001	*		0.0026				3	Leucine-rich repeat receptor protein kinase EXS precursor
SNPg02882	0.4127	0.1772	0.0001				0.0032			2	Putrescine aminopropyltransferase-related protein
SNPg05302	0.4025	0.1679	0.0001		*					—	Dead box ATP-dependent RNA helicase
SNPg02447	0.2492	0.1766	0.0002		*		0.0060			—	Amidophosphoribosyltransferase
SNPg00860	0.2554	0.1675	0.0004			0.0030	0.0022			6	No hit
SNPg00921	0.2987	0.1582	0.0005	*				*		—	GDSL-motif lipase hydrolase family protein
SNPg04111	0.4737	0.1490	0.0005	*						2	No hit
SNPg03578	0.4289	0.1486	0.0005	*						—	2-Hydroxyacid dehydrongenase
SNPg04480	0.1938	0.1560	0.0010	*		0.0008	0.0022			11	Glucan endo-1,3-beta-glucosidase precursor
SNPg01805	0.4264	0.1386	0.0012			0.0022				11	Glucan endo-1,3-beta-glucosidase precursor
SNPg03910	0.1887	0.1887	0.0012	*		0.0012				3	Endo-1,4-beta-glucanase
SNPg02822	0.1943	0.1525	0.0013			0.0011	0.0002			11	Methyltransferase-like protein 13-like
SNPg03082	0.4573	0.1376	0.0013			0.0008	0.0100			2	No hit
SNPg03744	0.5032	0.1437	0.0014			0.0074	0.0034			—	No hit
SNPg03195	0.5025	0.1429	0.0015			0.0019	0.0016			—	Protein-binding protein
SNPg01042	0.3742	0.1366	0.0019			0.0038	0.0028			10	Harpin-induced protein-like
SNPg03273	0.3429	0.1397	0.0019		*					11	Putative TIR/NBS/LRR disease resistance protein
SNPg01079	0.5026	0.1117	0.0022		*		0.0098		*	—	No hit
SNPg04166	0.3650	0.1342	0.0023	*			0.0082			—	No hit
SNPg00581	0.4857	0.1353	0.0025							9	No hit
SNPg04244	0.4947	0.1104	0.0025							2	Major facilitator protein
SNPg02884	0.3551	0.1324	0.0026							—	LPXTG-motif cell wall anchor domain protein
SNPg04589	0.4082	0.1313	0.0028							2	Extracellular ligand-gated ion channel
SNPg00517	0.3589	0.1310	0.0029		*					—	lon protease homolog peroxisomal-like
SNPg04896	0.4868	0.1085	0.0029							2	TIR-NBS class disease resistance protein
SNPg02875	0.3063	0.1311	0.0036							8	No hit
SNPg00066	0.0580	0.2161	0.0036	*		0.0021				2	VTC2-like protein
SNPg03555	0.5042	0.1058	0.0037							10	Strictosidine synthase family protein
SNPg05041	0.4941	0.1051	0.0039							—	No hit
SNPg01589	0.4926	0.1047	0.0040							—	S-receptor kinase
SNPg05257	0.2724	0.1186	0.0040		*					4	20-s Proteasome subunit paf1
SNPg01300	0.4314	0.1225	0.0041	*						—	Light-regulated zinc finger protein 1
SNPg01839	0.1095	0.2095	0.0043	*	*	0.0009				—	No hit
SNPg02637	0.4356	0.1210	0.0046			0.0014	0.0062			—	p-Aminobenzoate synthase
SNPg02373	0.4827	0.1109	0.0047							5	Unknown
SNPg05351	0.4849	0.1108	0.0047							5	No hit
SNPg00531	0.1106	0.1537	0.0048				0.0026			3	Chaperone protein DnaJ chloroplast
SNPg02059	0.2579	0.1161	0.0048		*					—	Aldo keto reductase
SNPg04667	0.4172	0.1104	0.0049							1	No hit
SNPg05574	0.4359	0.1101	0.0050			0.0077				10	No hit
SNPg04724	0.4084	0.1100	0.0050		*					8	Hexokinase 1
SNPg02675	0.4385	0.1100	0.0050							3	Glycoside hydrolase, family 17
SNPg01003	0.1929	0.1151	0.0052							7	Late embryogenesis-abundant hydroxyproline-rich glycoprotein
SNPg03769	0.4170	0.1220	0.0055			0.0019				7	Brassinosteroid insensitive 1-associated receptor kinase 1precursor
SNPg02786	0.3866	0.1085	0.0056							5	2-Hydroxyacid dehydrongenase
SNPg01044	0.4640	0.1174	0.0060							7	Lactoylglutathione lyase
SNPg03110	0.4545	0.1067	0.0064							10	No hit
SNPg00114	0.5056	0.1203	0.0066							2	No hit
SNPg02495	0.0659	0.1912	0.0070	*		0.0051				2	Early-responsive to dehydration 7
SNPg00236	0.2515	0.1106	0.0070							—	F-box and wd40 domain protein
SNPg02706	0.3823	0.1176	0.0076			0.0078				8	ATP-dependent RNA helicase DHX8
SNPg03565	0.4769	0.1133	0.0081			0.0080				—	Histone h4
SNPg01835	0.5041	0.1153	0.0091							10	No hit
SNPg00660	0.4872	0.1147	0.0094							8	Nitrite reductase
SNPg01833	0.3560	0.1142	0.0096		*					1	No hit
SNPg05180	0.3810	0.1141	0.0097							1	F-box-like protein
SNPg03808	0.4746	0.1106	0.0098							6	ARC6h-like protein
SNPg00006						0.0004				—	Pinus taeda anonymous locus umn_2311_01 genomic sequence
SNPg04004					*	0.0009				—	No hit
SNPg01566					*	0.0010				3	No hit
SNPg04934						0.0012				5	Ankyrin partial
SNPg01953						0.0014				6	PREDICTED: uncharacterized protein LOC100253581
SNPg05269						0.0019				7	No hit
SNPg04802						0.0020				9	Galactose oxidase-like
SNPg01166						0.0022				4	P. taeda anonymous locus 0_6264_01 genomic sequence
SNPg03800						0.0027				—	LRR-kinase protein
SNPg03964						0.0030				11	GCK domain-containing protein
SNPg02633						0.0031				9	Leucine-rich repeat transmembrane protein kinase
SNPg04798					*	0.0032				—	No hit
SNPg03049						0.0038				—	Pentatricopeptide repeat-containing
SNPg04439						0.0039				4	No hit
SNPg01041					*	0.0041				7	Cell number regulator 1
SNPg00017					*	0.0044				—	No hit
SNPg02303						0.0045				—	No hit
SNPg00923					*	0.0050				—	Acidic endochitinase-like
SNPg01152						0.0055				8	Transmembrane receptors ATP-binding protein
SNPg01574						0.0055				9	UDP-glycosyltransferase
SNPg03804						0.0057				7	No hit
SNPg00315						0.0060				—	Predicted protein (Micromonas sp. RCC299)
SNPg00024						0.0064				—	Pyruvate kinase
SNPg05588						0.0065				4	Vesicle-associated protein 4-2-like
SNPg05020						0.0067				—	No hit
SNPg02220					*	0.0072				6	DNA-binding protein
SNPg00438						0.0073				—	No hit
SNPg02428						0.0080				3	Maternal effect embryo arrest 12 protein
SNPg00094						0.0082				—	No hit
SNPg01108						0.0082				3	Unknown
SNPg00054						0.0091				—	PI-PLC × domain-containing protein at5g67130-like
SNPg00531						0.0093				—	Chaperone protein DnaJ
SNPg02256						0.0096				11	Microtubule-associated protein map65-1a
SNPg03226						0.0096				11	Vps51 Vps67 family (components of vesicular transport) protein
SNPg00161					*					—	Pseudo-response receiver
SNPg01491				*		0.0084				1	Glycoside hydrolase family 47 protein
SNPg02982					*					—	Glycosylphosphatidylinositol anchor biosynthesis protein 11
SNPg04411					*					2	Resistance gene region between conserved kinase-2 and p-loop domains
SNPg05191							0.0052			2	E3 ubiquitin-protein ligase ring1-like
SNPg00033				*						3	Yippee-like protein
SNPg00140				*	*					3	Nramp transporter
SNPg02378					*					3	No hit
SNPg00718					*					5	No hit
SNPg01667					*					—	FAD/NAD(P)-binding oxidoreductase family protein
SNPg02442					*					5	Condensation domain-containing protein
SNPg05366				*						5	Phenylalanine ammonia lyase
SNPg00892				*						—	Nucleotide-sugar transporter family protein
SNPg01169				*						7	EREBP transcription factor
SNPg02235				*						1	No hit
SNPg02348					*					7	No hit
SNPg02489				*						10	Unknown
SNPg04760				*						10	No hit
SNPg02148					*				*	11	Transmembrane protein 45B-like
SNPg02671					*					11	No hit
SNPg03025				*						11	Lysyl-tRNA synthetase
SNPg01727					*					—	FAD NAD-binding oxidoreductase family protein
SNPg01899					*					—	Unknown
SNPg03715				*						—	No hit
SNPg04159					*					—	opc-8:0 ligase1
SNPg04392				*						—	Leucine-rich repeat-containing protein
SNPg04510				*						—	No hit
SNPg04924				*						—	No hit
SNPg05020				*						—	No hit
SNPg05148				*						—	Ilectin receptor-like kinase

Abbreviation: SNP, single-nucleotide polymorphism.

Statistically siginificant level. *<0.01.