1

SUPPLEMENTARY INFORMATION

Figure S1. Heatmap produced using the molecular relationship matrix (G), computed using all available autosomal SNPs. Sample codes are in Table S1. Sample codes: WA, Asian wild boar; WE, European wild boar; MS, Meishan; HT, Hetao; TT, Tibetan pig (Tibet); BX, Bamaxiang; IB, Iberian; MG, Mangalica; DU, Duroc; LW, Large White.

2

Figure S2. Relationship between number of SNPs and heritability estimates for the 605 pathways considered.

3

Figure S3. Scheme of ovarian steroidogenesis pathway (SSC04913 from KEGG).

Genes are colored according to associated estimate of heritability, ranging from

yellow for the smallest heritability in the pathway (0.23) to bright red for the

maximum value (0.71). Arrow heads denote positive signals, filled in circles denote

repressive signals. Cell membranes are in blue.

4

Figure S4. Fst distributions of random SNPs (black line), SNPs within the potentially selective regions identified in Rubin et al. (blue line), and of the most differentiated SNPs described by Rubin et al. (red line).

Figure S5. Distribution of Fst between wild and domestic pigs of the 782 SNPs located in KIT gene (SSC8: 43,550,236-43,602,062).

5

Table S1: Sample listStatus Continent Breed* Country** Sample ID Sex Depth AccessionWild Asia WA JP WB20U02_Japan WA1 F 10.9 ERX149175

WA CN WB29U04_SChina WA2 M 5.3 ERX149182WA CN WB29U12_SChina WA3 F 10.1 ERX149183WA CN WB30U01_NChina WA4 M 5.2 ERX149184WA CN WB30U08_NChina WA5 M 9.7 ERX149185WA RU WBRU1064 WA6 M 6.9 SAMN05362551WA CN CWB_SYWB103 WA7 M 13.7 SRS465717WA CN CWB_ZJWB02 WA8 M 9.6 SRS465721

Wild Europe WE NL WB21F05_Netherlands WE1 M 9.2 ERX149176WE NL WB21M03_Netherlands WE2 M 11.4 ERX149177WE NL WB22F02_NL WE3 F 8.0 ERX149179WE FR WB25U11 WE4 M 9.4 ERX149180WE CH WB26M09_Malcantone WE5 M 14.4 ERX149181WE ES WBES0494 WE6 M 12.6 SAMN05362552WE ES WBES0717 WE7 M 13.0 SRR1513306WE TN WBTN0965 WE8 F 12.4 SAMN05362553

Domestic Asia BX CN BMX_BMX0005 BX1 F 14.2 SRR949743BX CN BMX_BMX0013 BX2 F 13.6 SRS465765BX CN BMX_BMX0014 BX3 F 13.1 SRS465766BX CN BMX_BMX0015 BX4 F 13.5 SRS465767HT CN HTDE_HTDE12 HT1 F 13.1 SRS465750HT CN HTDE_HTDE70 HT2 F 12.0 SRS465751HT CN HTDE_HTDE201 HT3 M 11.9 SRS465753HT CN HTDE_HTDE314 HT4 F 12.6 SRS465754MS CN MS20U10_Meishan MS1 F 9.1 ERX149162MS CN MS20U11_Meishan MS2 F 9.1 ERX149163

6

MS CN MS21M07_Meishan MS3 M 8.8 ERX149164MS CN MS21M14_Meishan MS4 M 10.1 ERX149165TT CN TT_B12 TT1 F 13.3 SRS465728TT CN TT_B40 TT2 M 12.4 SRS465729TT CN TT_MLZ30 TT3 F 11.3 SRS465732TT CN TT_B26 TT4 M 13.6 SRS465733

Domestic Europe DU na DU23M01_Duroc DU1 M 10.7 ERX149133DU na DU23M02_Duroc DU2 M 11.6 ERX149134DU na DU23M03_Duroc DU3 M 6.1 ERX149135DU na DU23M04_Duroc DU4 M 7.6 ERX149136IB ES IBGM0327 IB1 M 13.0 SRR1513307IB ES IBGU1802 IB2 M 13.0 SRX245748IB ES IBGU1803 IB3 M 12.4 SAMN05362554IB ES IBGU1804 IB4 M 14.5 SRR1917381LW na LW22F02 LW1 F 10.0 ERX149149LW na LW22F03 LW2 F 10.1 ERX149150LW na LW22F04 LW3 F 10.1 ERX149151LW na LW22F07 LW4 F 11.6 ERX149153MG HU MGSB_SRR1178916 MG1 M 8.7 SRX476910MG HU MGBlond_SRR1178923 MG2 M 14.5 SRX476911MG HU MGRed_SRR1178925 MG3 M 14.1 SRX476909

* WA, Asian wild boar; WE, European wild boar; MS, Meishan; HT, Hetao; TT, Tibetan pig (Tibet); BX, Bamaxiang; IB, Iberian; MG, Mangalica; DU, Duroc; LW, Large White.** ISO two-letter country code (https://www.iso.org/obp/ui/#search); na, not available.

7

Table S2. Number of SNPs classified by annotation using variant effect predictor*.

Annotation Feature Nintergenic_variant 17437294intron_variant 6295000upstream_gene_variant 871894downstream_gene_variant 7805833_prime_UTR_variant 89016synonymous_variant 73342missense_variant 42195intron_variant,non_coding_transcript_variant 33747splice_region_variant 119585_prime_UTR_variant 8287non_coding_transcript_exon_variant 5993missense_variant,splice_region_variant 1108splice_donor_variant 521stop_gained 517intron_variant,NMD_transcript_variant 444splice_acceptor_variant 260initiator_codon_variant 106stop_lost 48mature_miRNA_variant 42stop_retained_variant 38

* Only annotations with N>30 are shown.

8

Table S3: Top 5% pathways in terms of genomic heritability.

Path id Name Database** hG2 # Fst

*82997 Glycosphingolipid biosynthesis - ganglio series

KEGG 0.84 0.08

790011 Ovarian steroidogenesis KEGG 0.81 0.03905995 Formation of Senescence-Associated

Heterochromatin Foci (SAHF)REACTOME 0.81 0.03

373900 Synaptic vesicle cycle KEGG 0.80 0.0182973 Glutathione metabolism KEGG 0.80 0.03672464 SRF and miRs in Smooth Muscle

Differentiation and ProliferationWP 0.80 0.01

106223 eNOS activation and regulation REACTOME 0.79 0.03138012 Signaling mediated by p38-alpha and

p38-betaPID 0.79 0.03

645290 MHC class II antigen presentation REACTOME 0.79 0.03576276 YAP1- and WWTR1 (TAZ)-stimulated

gene expressionREACTOME 0.79 0.02

138031 Syndecan-2-mediated signaling events PID 0.79 0.03160141 Interleukin-1 signaling REACTOME 0.79 0.04905994 DNA Damage/Telomere Stress Induced

SenescenceREACTOME 0.79 0.03

83094 Type II diabetes mellitus KEGG 0.78 0.03695200 HIF-1 signaling pathway KEGG 0.78 0.03*138076 Cellular roles of Anthrax toxin PID 0.78 0.0582957 Arginine and proline metabolism KEGG 0.78 0.03673221 Chemical carcinogenesis KEGG 0.77 0.03*1127556 Attenuation phase REACTOME 0.77 0.05530744 Nuclear signaling by ERBB4 REACTOME 0.77 0.0383122 Systemic lupus erythematosus KEGG 0.77 0.03*137935 FOXM1 transcription factor network PID 0.77 0.04138005 E-cadherin signaling in the nascent

adherens junctionPID 0.77 0.03

*905997 Signaling by Leptin REACTOME 0.77 0.06119549 G alpha (s) signalling events REACTOME 0.77 0.03198766 Inflammatory Response Pathway WP 0.76 0.0283092 Melanogenesis KEGG 0.76 0.03530763 Prolactin receptor signaling REACTOME 0.76 0.03137993 Calcineurin-regulated NFAT-dependent

transcription in lymphocytesPID 0.76 0.02

* Also in top 5% in terms of Fst.** PID: Pathway interaction database; WP: WikiPathways# Mean posterior standard deviations were 0.19 on average

9

Table S4: Multivariate linear regression of heritability on population genetic statistics across 100 kb windows.

Item Mean z-score2 P-valueFst 0.02 63.2 <10-5

Diversity wild1 4.2x10-3 6.6 <10-5

Diversity domestic1

3.9x10-3 -4.0 0.01

Tajima's D wild -0.38 -8.6 <10-5

Tajima's D domestic

-0.08 0.9 0.40

1 Achaz's nucelotide diversity estimate by bp.2 Estimate divided by standard error.

10

Table S5: Top 5% pathways in terms of Fst.

Path Name Database** hG2 # Fst

*82997 Glycosphingolipid biosynthesis - ganglio series

KEGG 0.84 0.08

198794 Cytokines and Inflammatory Response WP 0.70 0.07106373 Nucleotide-like (purinergic) receptors REACTOME 0.74 0.07198783 Alanine and aspartate metabolism WP 0.71 0.07413412 Immunoproteasome KEGG 0.49 0.06187188 Passive transport by Aquaporins REACTOME 0.58 0.06*905997 Signaling by Leptin REACTOME 0.77 0.06755436 AhR pathway WP 0.62 0.05105814 Golgi Cisternae Pericentriolar Stack

ReorganizationREACTOME 0.48 0.05

*1127556 Attenuation phase REACTOME 0.77 0.05530770 ATF6-alpha activates chaperone genes REACTOME 0.66 0.05105819 Mitotic Telophase/Cytokinesis REACTOME 0.67 0.05469200 Legionellosis KEGG 0.73 0.05*138076 Cellular roles of Anthrax toxin PID 0.78 0.05198876 Nucleotide Metabolism WP 0.59 0.05730316 Condensation of Prometaphase

ChromosomesREACTOME 0.72 0.04

137957 LKB1 signaling events PID 0.72 0.04106273 Purine salvage REACTOME 0.73 0.04137927 Arf1 pathway PID 0.62 0.04198894 FAS pathway and Stress induction of

HSP regulationWP 0.73 0.04

198780 Senescence and Autophagy WP 0.68 0.04198852 Statin Pathway WP 0.61 0.04138023 Ceramide signaling pathway PID 0.66 0.0482940 Steroid hormone biosynthesis KEGG 0.71 0.04105656 Intrinsic Pathway for Apoptosis REACTOME 0.73 0.04187217 N-glycan trimming in the ER and

Calnexin/Calreticulin cycleREACTOME 0.57 0.04

198899 Sulfation Biotransformation Reaction WP 0.71 0.04*137935 FOXM1 transcription factor network PID 0.77 0.04576261 Mitochondrial protein import REACTOME 0.63 0.04

* Also in top 5% in terms of genomic heritability** PID: Pathway interaction database; WP: WikiPathways # Mean posterior standard deviations were 0.19 on average

11

Table S6: Features of genes within selected pathways

Gene No. SNPs Pi D Pi W Tajima D Tajima W hG2

FstGlycosphingolipidbiosynthesisST6GALNAC6 103 6.8E-03 2.9E-03 0.44 -1.06 0.39 0.10HEXB 232 1.3E-03 1.3E-03 -1.12 -1.06 0.57 0.03ST3GAL1 1501 9.9E-03 9.0E-03 0.49 0.16 0.54 0.03ST6GALNAC4 108 6.9E-03 5.5E-03 -0.16 -0.25 0.36 0.02ST3GAL5 56 3.8E-03 2.7E-03 -0.48 -0.80 0.29 0.01SLC33A1 196 1.7E-03 1.9E-03 -1.07 -0.78 0.33 -0.01HEXA 143 1.2E-03 1.2E-03 -0.20 -0.21 0.38 -0.02Signaling by LeptinHEXA 143 1.2E-03 1.2E-03 -0.20 -0.21 0.38 -0.02IL6R 445 3.8E-03 4.4E-03 -0.11 -0.13 0.69 0.18YWHAB 250 3.6E-03 3.3E-03 -0.11 -0.41 0.56 0.16CDK1 125 3.6E-03 2.8E-03 0.77 -0.44 0.33 0.11MAPK1 85 4.4E-04 1.1E-03 -2.08 -0.46 0.53 0.11MAP2K1 23 3.5E-03 2.0E-03 0.11 -0.39 0.44 0.06IL6ST 243 9.3E-04 9.0E-04 -1.32 -1.59 0.40 0.04TYK2 95 1.3E-03 1.1E-03 -1.09 -0.78 0.29 0.04IRS1 5 5.0E-03 5.0E-03 0.03 0.64 0.27 0.04SH2B1 52 2.8E-03 3.7E-03 -0.66 0.21 0.38 0.02STAT3 695 3.9E-03 3.7E-03 -0.30 -0.15 0.44 0.02STAT5B 231 2.5E-03 2.3E-03 -1.04 -0.80 0.54 0.01RAF1 126 1.0E-03 7.6E-04 -0.84 -1.11 0.32 0.00JAK2 1065 4.2E-03 4.7E-03 1.06 0.45 0.36 0.01JAK1 244 3.9E-03 3.9E-03 -0.09 0.44 0.33 0.00PTPN11 489 2.0E-03 1.9E-03 -0.19 -0.56 0.31 -0.01LEP 31 8.5E-03 9.2E-03 1.22 1.76 0.30 -0.01Ovarian steroidogenesisFSHB 113 6.4E-03 6.7E-03 1.00 0.37 0.61 0.13IGF1 617 2.3E-03 2.0E-03 0.31 -0.83 0.63 0.10IGF1R 1562 1.4E-03 1.3E-03 -0.58 -1.17 0.62 0.08FSHR 776 2.3E-03 1.8E-03 0.08 -0.89 0.58 0.08STAR 55 1.8E-03 1.3E-03 -0.57 -0.32 0.62 0.06HSD17B1 22 4.3E-03 4.3E-03 -0.31 0.79 0.38 0.06ADCY6 40 3.8E-03 2.6E-03 -0.13 -0.80 0.71 0.04CGA 165 2.7E-03 2.5E-03 -0.27 -0.94 0.49 0.04PLA2G4A 2389 4.5E-03 4.1E-03 -0.20 -0.39 0.49 0.04CYP17A1 19 7.3E-04 1.2E-03 -1.85 -1.26 0.32 0.04PLA2G4D 343 5.3E-03 5.1E-03 0.11 -0.31 0.39 0.03CYP19A1 354 8.1E-03 6.5E-03 -0.56 -0.89 0.31 0.03PLA2G4E 213 4.7E-03 5.9E-03 0.46 1.23 0.32 0.03ALOX5 370 4.3E-03 3.7E-03 0.19 -0.18 0.69 0.03GDF9 32 1.5E-03 7.0E-04 -1.41 -1.84 0.32 0.03ADCY5 1074 5.2E-03 3.9E-03 -0.11 -0.65 0.51 0.03INSR 376 1.4E-03 1.3E-03 -0.87 -0.93 0.42 0.02AKR1C3 187 5.2E-03 3.8E-03 0.20 -0.56 0.35 0.02ADCY4 73 1.9E-03 1.1E-03 -0.49 -1.25 0.59 0.02CYP2J2 2716 1.1E-02 7.9E-03 0.08 -0.50 0.52 0.02HSD17B7 140 2.5E-03 2.2E-03 -0.06 -0.29 0.56 0.02PLA2G4F 114 4.3E-03 4.2E-03 0.07 0.14 0.35 0.02HSD3B2 57 2.4E-03 1.7E-03 -0.73 -1.04 0.25 0.01HSD3B1 57 2.4E-03 1.7E-03 -0.73 -1.04 0.27 0.01PRKACG 176 1.7E-03 1.0E-03 0.01 -0.45 0.42 0.01BMP6 3817 9.6E-03 9.1E-03 0.35 0.07 0.41 0.01LHCGR 281 3.1E-03 2.9E-03 -0.28 -0.25 0.23 0.01

12

Number of SNPs excluding singletons; Pi D: Estimate of diversity for domestic pigs, excluding singletons; Pi W: estimate of diversity for wild pigs, excluding singletons; Tajima D: Tajima's D in domestic samples; Tajima W: Tajima's D for wild pigs; h2: heritability; Fst: Fst excluding singletons.

13

Table S7. List of 30 GO terms found to be in either the top 10 enriched from each approach or in the intersection of the two approaches at P < 0.001.

GO Description

GO:0000975 regulatory_region_DNA_bindingGO:0000976 transcription_regulatory_region_sequence-specific_DNA_bindingGO:0000977 RNA_polymerase_II_regulatory_region_sequence-specific_DNA_bindingGO:0000981 sequence-specific_DNA_binding_RNA_polymerase_II_transcription_factor_activityGO:0001012 RNA_polymerase_II_regulatory_region_DNA_bindingGO:0001067 regulatory_region_nucleic_acid_bindingGO:0001071 nucleic_acid_binding_transcription_factor_activityGO:0001077 RNA_polymerase_II_core_promoter_proximal_region_sequence-

specific_DNA_binding_transcription_factor_activity_involved_in_positive_regulation_of_transcription

GO:0001228 RNA_polymerase_II_transcription_regulatory_region_sequence-specific_DNA_binding_transcription_factor_activity_involved_in_positive_regulation_of_transcription

GO:0001664 G-protein_coupled_receptor_bindingGO:0003700 sequence-specific_DNA_binding_transcription_factor_activityGO:0003707 steroid_hormone_receptor_activityGO:0004012 phospholipid-translocating_ATPase_activityGO:0004364 glutathione_transferase_activityGO:0004871 signal_transducer_activityGO:0004896 cytokine_receptor_activityGO:0005102 receptor_bindingGO:0005179 hormone_activityGO:0005515 protein_bindingGO:0005548 phospholipid_transporter_activityGO:0016765 transferase_activity,_transferring_alkyl_or_aryl_(other_than_methyl)_groupsGO:0019899 enzyme_bindingGO:0019900 kinase_bindingGO:0032403 protein_complex_bindingGO:0043492 ATPase_activity,_coupled_to_movement_of_substancesGO:0043565 sequence-specific_DNA_bindingGO:0044212 transcription_regulatory_region_DNA_bindingGO:0046982 protein_heterodimerization_activityGO:0046983 protein_dimerization_activityGO:0060089 molecular_transducer_activity