Table 3.

Additional regions under selection due to domestication and regional climatic variation identified by allelic fixation at SNPs.

LGa	Startb	Genec	Annotationd	Oe	Wf	Sdg	Het-Cmh	π-Cmi	π-Cdj	Cd/Cmk	FSTl
LGA	50030000	lga_g6327	THOC6_ARATH THO complex subunit, ABA signaling	0.93	0.63	>3	0.05	0.0004	0.0019	4.47	0.82
LGA	65859000	lga_g8373	RPE_SOLTU Ribulose-phosphate epimerase	0.86	0.56	>3	0.04	0.0006	0.0021	3.53	0.93
LGC	31478000	lgc_g3960	PP14_ARATH Serine/threonine protein phosphatase	0.86	0.64	>3	0.04	0.0006	0.0019	3.27	0.72
LGE	25481000	lge_g3428	MYBF_ARATH, transcription factor	0.87	0.71	>3	0.08	0.0007	0.0020	2.87	0.67
LGE	29262000	lge_g3727	CE101_ARATH lectin receptor kinase	0.93	0.66	>3	0.07	0.0003	0.0057	18.48	0.82
LGE	44249000	lge_g5605	DRE2D_ARATH Dehydration-responsive element	0.92	0.61	>5	0.03	0.0002	0.0015	6.67	0.85
LGF	16717000	lgf_g2053	ALsF1_ARATH Aldehyde dehydrogenase	0.84	0.60	>3	0.09	0.0002	0.0009	5.13	0.86
LGF	27956000	lgf_g3433	SAUR32_ARATH Auxin responsive element	0.84	0.63	>3	0.09	0.0004	0.0007	1.81	0.90
LGG	8420000	lgg_g5871	CDPK_SOYBN calcium-dependent protein kinase SK5	0.96	0.64	>3	0.11	0.0015	0.0025	1.64	0.49
LGG	2054000	lgg_g2558	GONS1_ARATH GDP-mannose transporter	0.90	0.68	>3	0.08	0.0006	0.0016	2.63	0.86
LGG	23410000	lgg_g1699	LEA34_GOSHI late-embryogenesis-abundant protein	0.85	0.59	>3	0.20	0.0004	0.0015	3.82	0.68
LGG	33377000	lgg_g4266	MEE14_ARATH CCG-binding AGAMOUS interactor	0.92	0.64	>3	0.11	0.0009	0.0029	3.16	0.78

^aLinkage group and

^bstarting position of 10 kb sweep region in pseudochromosome draft assembly (Staton et al., 2014);

^cPredicted gene selected from sweep based on annotation and statistical significance;

^dAnnotation of selected gene;

^eAverage major allele frequency for SNPs in orchard and

^fwild Chinese chestnut pools across the sweep interval (10 kb);

^gPermutation-derived p value for sweep;

^hAverage heterozygosity for the selected gene in an independent sample of 12 individual Chinese chestnut genomes;

ⁱNucleotide diversity among orchard-derived Chinese chestnut, Castanea mollissima (Cm) and American chestnut

^jCastanea dentata (Cd) for the selected gene;

^kFactor by which π was greater in wild Cd than in domesticated Cm;

^lF_ST calculated between Cm and Cd using SNPs in the selected gene interval.