Table S1 Primers and Amplicons for Determination of TYRP1 Coding Sequence from Genomic DNA

Table S1 Primers and amplicons for determination of TYRP1 coding sequence from genomic DNA.

TYRP1 exon Exon size Amplicon size Forward and reverse primers (5’-3’) Tm (oC) 2 435 795 F: TTAAAGGTGGGTGGGAAGG 64

R: TAAAGTGGCTGCTCCACAAG 3 323 736 F: GGGGTGAAGAAGGGATTTTG 55

R: CTCAGTTGGCTTCCTCATCAC 4 205 549 F: ACCACAGCTCACCAAAATGC 66

R: ATCACCTTAGGTTGCCCAGAC 5 168 974 F: CCCTGAGGCAACCAAGTATCC 65

R: GACAGGCTCAACATGGCATTC 6 180 774 F: CATGTAGACCAGTGTTAGCCTTG 63

R: CTTACAGGAACGTGGTAGTCATC 7 147 607 F: TCCCTGTTCTGCTGCTGTG 63

R: CATTTACTCCCTCTAAGCCTCATC 8 401 745 F: GAAAGACCTGGGCTCCAAAAC 65

R: GGTGCCACCCATCATTCTAAAG Table S2 Seven TYRP1 exonic mutations in 16 domestic pig breeds and wild pigs.

Breed Colour Exonic mutation site

2 2 2 2 3 3 3

-19 22 49 144 477 525 685

Chinese wild pig Wild type C T C G C C C

European wild pig Wild type C T C G C C C

Tibetan Reddish or silver brown C/T T/A C/A G/A C C/T C/T

Tibetan Black C T C G C C/T C

Kele Dark or pale brown C T C G C C C

Kele Black C T C G C C C

Dahe Yellow brown C T C G C C/T C

Dianan Small-Ear Black C T C G C/T C/T C

Duroc Red C T C G C C C

Erhualian Black C T C G C C C

Hampshire White belt and black body C T C G C C C

Hetao Large-Ear Black C T C G C C C

Jinhua Two-end-black C T C G C C C

Laiwu Black C/T T/A C/A G/A C C C/T

Landrace White C T C G C C C

Large White White C T C G C C C

Luchuan Black with white belly C T C G C C

Pietrain Spotted C T C G C C C

Rongchang White C T C G C/T C/T C

Yushan Black C T C G C C C

Wuzhishan Black with white belly C T C G C C C Table S3 Allele frequencies at the TYRP1 c.428G>A polymorphic site

(p.143His>Arg) in Chinese and European pig breeds.

Breed Coat colour No. Allele frequency

G A Chinese breed

Dahe Black, yellow or silver brown 43 0.244 0.756

Dianan Small-Ear Black 30 0.717 0.283

Erhualian Black 32 0.656 0.344

Hetao Large-Ear Black 32 0.828 0.172

Jinhua Two-end-black 33 0.985 0.015

Kele Black 60 0.600 0.400

Kele Dark or pale brown 29 0.172 0.828

Laiwu Black 32 0.641 0.359

Luchuan Black with white belly 33 1.000 0.000

New Dahe Black 43 0.244 0.756

Rongchang White 35 0.986 0.014

Tibetan Reddish or silver brown 54 0.463 0.537

Tibetan Black 105 0.910 0.090

Yushan Black 29 0.793 0.207

Wuzhishan Black with white belly 32 0.719 0.281

Wild boars Wild type 67 0.612 0.388

European breed

Duroc Red 61 0.189 0.811

Hampshire White belt and black body 41 0.317 0.683

Iberian Black 10 0.650 0.350

Landrace White 39 0.115 0.885

Large White White 62 0.403 0.597

Pietrain Spotted 23 0.261 0.739

Wild boars Wild type 11 0.364 0.636 Table S4 Epistasis relationships for TYRP1 and MC1R in Kele and Dahe pigs.

Breed Genotype No. Phenotype TYRP1 MC1R Kele +/+ ED1/ED1 17 Solid black +/+ ED1/ED2 4 Solid black +/+ ED1/e 1 Solid black +/del ED1/ED1 20 Dark brown +/del ED1/ED2 4 Dark brown del/del ED1/ED1 2 Pale brown Dahe +/+ ED1/ED1 1 Solid black +/del ED1/ED1 9 Black brown (n = 7); Yellow brown (n = 1); Silver brown (n = 1) +/del ED1/ED2 4 Black brown (n = 3); Silver brown (n = 1) +/del ED1/EP 2 Yellow brown del/del ED1/ED1 5 Yellow brown (n = 3); Silver brown (n = 2) The nomenclature for these MC1R alleles has been described in Reference Fang et al. (2009) Figure S1. Four families segregating for the brown coat colour in Tibetan pigs.

Circles represent females, squares represent males, black symbols indicate black pigs and red symbols indicate brown coated pigs. Figure S2. Genotype patterns at the TYRP1 c.1484_1489del and c.428G>A mutation sites. (A) The electrophoresis patterns of the TYRP1 c.1484_1489del mutation by a KpnI PCR-RFLP assay. Line 1: del/del. Lines 2, 8, 9: +/+. Lines 3-7,

10: +/del. (B) The electropherograms for the TYRP1 c.428G>A polymorphism by the

SNaPshot analysis. Figure S3. The TYRP1 c.1484_1489del mutation and multispecies alignment of the TYRP1 protein sequences. (A) Representative electropherograms for the TYRP1 c.1484_1489del mutation from a wild type (+/+), a heterozygote (+/del) and a homozygous mutant (del/del) pig. (B) Multispecies alignment of the TYRP1 protein sequence around the deletion. The sequences for the alignment were taken from the following accessions: NP_001020397 (pig), GU345799 (pig), NP_112479 (mouse),

NP_001100134 (rat), NP_776905 (cattle), NP_001075309 (horse), NP_001036025

(cat), XP_864543 (dog), NP_000541 (human), XP_520488 (chimpanzee),

XP_001111475 (rhesus monkey), NP_001123495 (sheep), NP_990376 (chicken),

NP_001080492 (frog). The horizontal line indicates the transmenbrane domain of the protein.