Table 2.

Notable regions under selection during chestnut domestication with statistical support and functional annotations.

LGa	Startb	Genec	Gene function potentially under selectiond	Doe	Dwf	pg	het_cmh	pi-cmi	pi-cdj	cd/cmk	FSTl
LGA	17560000	lga_g2116	1-aminocyclopropane-1-carboxylate oxidase	−1.57	0.31	0.006	0.19	0.0014	0.0015	1.11	0.76
LGA	28940000	lga_g3565	Putative phytosulfokines PSK6	−1.65	1.23	<0.001*	0.14	0.0009	0.0037	4.26	0.44
LGA	46000000	lga_g5798	Flowering time control protein FCA	−2.03	−0.47	0.020	0.00	0.0000	0.0005	483.33	0.81
LGA	46360000	lga_g5850	Alkane hydroxylase MAH1	−1.98	−0.05	0.005	0.05	0.0013	0.0032	2.54	0.92
LGA	53300000	lga_g6764	Transcription factor bHLH78	−1.25	0.44	0.013	0.11	0.0009	0.0016	1.73	0.82
LGA	53710000	lga_g6816	Late embryogenesis abundant protein LEA5	−1.70	−0.07	0.016	0.10	0.0001	0.0007	4.56	0.85
LGA	58690000	lga_g7476	Probable polygalacturonase ADPG2	−2.12	−0.47	0.015	0.10	0.0008	0.0014	1.66	0.64
LGA	72490000	lga_g9205	Anthocyanidin 3-O-glucosyltransferase 2	−1.59	0.07	0.019	0.10	0.0008	0.0017	2.08	0.89
LGA	104070000	lga_g13074	Transcription factor GATA-type	−1.86	0.13	0.003	0.07	0.0012	0.0022	1.83	0.86
LGB	3070000	lgb_g404	Homeobox-leucine zipper protein ATHB-14	−1.92	−0.08	0.011	0.12	0.0009	0.0012	1.30	0.74
LGB	7750000	lgb_g1007	Transcription factor bHLH147	−1.64	0.43	0.004	0.14	0.0031	0.0043	1.37	0.38
LGB	8100000	lgb_g1054	Desiccation-related protein PCC13-62	−2.51	0.17	<0.001*	0.12	0.0030	0.0061	2.05	0.70
LGB	8690000	lgb_g1139	ZF-BED domain protein RICESLEEPER 1	−1.71	0.17	0.009	0.20	0.0012	0.0018	1.50	0.81
LGB	19610000	lgb_g2523	Sucrose synthase 2	−1.96	0.44	<0.001	0.16	0.0022	0.0045	2.04	0.46
LGC	6500000	lgc_g807	Cytochrome P450 CYP71D312	−1.65	0.07	0.013	0.07	0.0019	0.0125	6.61	0.82
LGC	21310000	lgc_g2594	Reticuline oxidase	−1.68	0.56	< 0.001	0.07	0.0008	0.0024	2.84	0.86
LGC	30360000	lgc_g3816	Histone-lysine N-methyltransferase SUVH4	−1.61	0.27	0.007	0.23	0.0012	0.0008	0.72	0.68
LGC	49350000	lgc_g6157	1-aminocyclopropane-1-carboxylate oxidase 4	−1.52	0.15	0.015	0.04	0.0001	0.0017	17.21	0.91
LGC	50850000	lgc_g6330	Transcription factor RAX2	−1.53	0.49	0.003	0.02	0.0005	0.0029	5.90	0.97
LGD	7620000	lgd_g1017	SHOOT GRAVITROPISM 5, IDD15	−1.44	0.33	0.009	0.10	0.0002	0.0008	3.34	0.58
LGD	18020000	lgd_g2376	Major allergens Pru1	−2.51	0.17	< 0.001	0.12	0.0006	0.0033	5.34	0.88
LGE	50780000	lge_g6427	POLLENLESS 3, MS5	−1.71	0.39	0.001	0.04	0.0014	0.0116	8.25	0.63
LGG	13830000	lgg_g2955	Peroxisome biogenesis protein 1	−1.87	0.09	0.003	0.00	0.0001	0.0027	23.02	0.94
LGG	24830000	lgg_g3130	LEA protein D-29	−1.29	0.52	0.007	0.15	0.0011	0.0012	1.07	0.79
LGG	49050000	lgg_g6369	Syntaxin-132, isocitrate lyase	−2.08	−0.29	0.008	0.13	0.0008	0.0015	1.84	0.73
LGH	780000	lgh_g105	Ras-related protein RAA4b	−2.23	0.35	< 0.001	0.17	0.0025	0.0046	1.88	0.67
LGI	10470000	lgi_g1363	Syntaxin-132	−1.59	0.34	0.008	0.19	0.0010	0.0006	0.58	0.68
LGI	33370000	lgi_g4214	FT (Flowering Time) -interacting protein 1	−2.08	0.33	< 0.001	0.10	0.0017	0.0023	1.36	0.77
LGI	40500000	lgi_g5153	Peroxidase 24	−1.94	0.33	0.001	0.10	0.0017	0.0073	4.39	0.66
LGJ	16440000	lgj_g2112	Transcription factor VRN1	−2.09	0.03	0.002	0.23	0.0024	0.0043	1.76	0.52
LGJ	16890000	lgj_g2169	Universal stress protein PHOS34	−1.78	0.28	0.003	0.17	0.0019	0.0030	1.63	0.39
LGK	25200000	lgk_g3168	Floral homeotic protein AGAMOUS	−2.02	0.10	0.001	0.19	0.0010	0.0026	2.55	0.72
LGL	38090000	lgl_g4810	1-aminocyclopropane-1-carboxylate synthase 7	−2.08	0.25	< 0.001	0.24	0.0059	0.0038	0.65	0.50

Bolded entries indicate intervals with local false discovery rates < 0.25, calculated by qvalue (Storey, 2002).

^aLinkage group and

^bstarting position of 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;

^eTajima's D for orchard and

^fwild Chinese chestnut pools across the sweep interval;

^gPermutation-derived p value for sweep;

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

ⁱNucleotide diversity among Castanea mollissima (Cm) and

^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.

^*Local false discovery rate < 0.05.