This Is the Pre-Peer Reviewed Version of the Following

"This is the pre-peer reviewed version of the following article: Bovo S, Ribani A, Muñoz M, Alves E, Araujo JP, Bozzi R, Charneca R, Di Palma F, Etherington G, Fernandez AI, García F, García-Casco J, Karolyi D, Gallo M, Gvozdanović K, Martins JM, Mercat MJ, Núñez Y, Quintanilla R, Radović Č, Razmaite V, Riquet J, Savić R, Schiavo G, Škrlep M, Usai G, Utzeri VJ, Zimmer C, Ovilo C, Fontanesi L. Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states. Anim Genet. 2020 Aug;51(4):541-556. doi: 10.1111/age.12954 which has been published in final form at [https://doi.org/10.1111/age.12954]. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions."

Supplementary material

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole genome sequencing of DNA pools

Samuele Bovo, Anisa Ribani, Maria Muñoz, Estefania Alves, Jose P. Araujo, Riccardo Bozzi, Rui

Charneca, Federica Di Palma, Graham Etherington, Ana I. Fernandez, Fabián García, Juan García-

Casco, Danijel Karolyi, Maurizio Gallo, Kristina Gvozdanović, José Manuel Martins, Marie-José

Mercat, Yolanda Núñez, Raquel Quintanilla, Čedomir Radović, Violeta Razmaite, Juliette Riquet,

Radomir Savić, Giuseppina Schiavo, Martin Škrlep, Graziano Usai, Valerio J. Utzeri, Christoph

Zimmer, Cristina Ovilo, Luca Fontanesi

Table S1. Details on the analysed animals and investigated breeds, including geographical distribution and phenotypic description.

Acronym of the Country / Geographic Standard coat Breed name Native Name Alternative name Ear Size Size Population Additional Info breed region colour name https://www.intechopen.com/boo Black coat colour 6464 breeding sows and ks/european-local-pig-breeds- Alentejano, PT / Southwest of the and scarce black, 510 boars distributed by Alentejana AL Alentejano Small Medium diversity-and-performance-a- Alentejana Iberian Peninsula blonde or reddish 137 herds (End of study-of-project- thin hair 2017).

treasure/alentejano-pig Apulo Calabrese, Calabrese, Nero Abruzzese, Nero Calabrese, Nero dei Lepini, Nero dei Monti Dauni https://www.intechopen.com/boo Meridionali, 489 breeding sows and IT / Central-South of ks/european-local-pig-breeds- Apulo Nero dei Monti Medium 93 boars distributed in Apulo-Calabrese AC Italy (Lazio, Basilicata Solid black Large diversity-and-performance-a- Calabrese Lepini, to small 45 registered farms and Calabria regions) study-of-project-treasure/apulo- Nero di Calabria, (August 2015).

calabrese-pig Nero di Capitanata, Nero Lucano, Nero Maremmano, Nero Pugliese, Nero Reatino, Pugliese Basque Pie Noir du Pays https://www.intechopen.com/boo FR / Basque Country, a 580 breeding sows Basque Piebald, black and ks/european-local-pig-breeds- region located in the distributed in 28 Basque BA Basque Bigourdan white: black head Large Medium diversity-and-performance-a- South-West of France registered farms Béarnais and rump. study-of-project-treasure/basque- and across Spain border. (Jenuary 2017).

Basco-Béarnais pig Navarrin https://www.intechopen.com/boo 5460 breeding sows and ks/european-local-pig-breeds- Bísaro, Grey or black and 520 boars distributed Bísara BI Bísaro PT / North of Portugal Extra large Large diversity-and-performance-a- Bísara white or spotted in189 registered farms study-of-project-treasure/b-saro- (August 2017)

pig https://www.intechopen.com/boo 1930 breeding sows and ks/european-local-pig-breeds- Black 242 boarsdistributed in Black Slavonian BS Fajferica HR / East Croatia Solid black Large Medium diversity-and-performance-a- Slavonian 209 registered farms study-of-project-treasure/black- (December 2017).

slavonian-crna-slavonska-pig https://www.intechopen.com/boo Casertana, 545 breeding sows and IT / Central-South of ks/european-local-pig-breeds- Maiale di Teano, Solid black or dark 20 boars distributed in Casertana CA Casertana Italy (Campania and Medium Medium diversity-and-performance-a- Teanese, grey / Hairless 20 registered farms Molise regions) study-of-project-treasure/nero- Pelatella (August 2015).

casertano-pig Cinta Senese, https://www.intechopen.com/boo Cinta, ks/european-local-pig-breeds- Cinto, Cinto Toscano, IT / Central Italy Black with white 5000 animals distributed Cinta Senese CS Cinta Senese Medium Medium diversity-and-performance-a- Cinturello Umbro, (Tuscany region) belt in 140 farms study-of-project-treasure/cinta- Cinturino Umbro,

senese-pig Siena Belted 1423 breeding sows and https://www.intechopen.com/boo FR / Foot of the 177 breeding males ks/european-local-pig-breeds- Black skin and are Gascon GA Gascon Gascon Pyrénées mountains in Medium Medium distributed in 64 diversity-and-performance-a- black wire-haired the southwest of France. registered farms (year study-of-project-treasure/gascon-

2017). pig https://www.intechopen.com/boo 311 breeding sows and Black with white middle ks/european-local-pig-breeds- Krškopoljski 60 boars distributed in Krškopolje KR Krškopolje pig SI / Slovenia belt of varying size Medium/Large to large diversity-and-performance-a- prašič 130 registered farms and shape sized study-of-project-treasure/kr- (August 2015).

kopoljski-pra-i-kr-kopolje-pig-

Large black spots https://www.intechopen.com/boo on the body Colour 43 breeding sows and ks/european-local-pig-breeds- LT / Central part of Lithuanian Lietuvos Lithuanian indigenous variations include 11 boars distributed in 2 diversity-and-performance-a- LIW Lithuania, Baisogala, Medium/Large Medium Indigenous Wattle vietines wattle black and white, registered farms study-of-project- Radviliškis district ginger, black and (December 2017) treasure/lietuvos-vietin-

tricoloured lithuanian-indigenous-wattle-pig

https://www.intechopen.com/boo LT / Baisogala, 93 breeding sows and ks/european-local-pig-breeds- Senojo tipo Lithuanian White Old type Lithuanian Radviliškis district, in 19 boars distributed in 3 diversity-and-performance-a- LWOT Lietuvos White Medium Medium Old Type White the central part of registered farms study-of-project- baltosios Lithuania (December 2017). treasure/lietuvos-baltosios-

senojo-tipo-lithuanian-white-pig https://www.intechopen.com/boo Black Majorcan 969 breeding sows and ks/european-local-pig-breeds- Negre Porc Negre Mallorquí Black or grey skin 54 boars distributed in Majorcan Black MB ES / Balearic Islands Large Medium diversity-and-performance-a- Mallorquí Cerdo Negro colour 59 registered farms study-of-project-treasure/negre- Mallorquín (August, 2016).

mallorqu-majorcan-black-pig https://www.intechopen.com/boo 270 breeding sows and ks/european-local-pig-breeds- Mora IT / North of Italy Dark red/black with 67 boars distributed in Mora Romagnola MR Mora Romagnola Small Medium diversity-and-performance-a- Romagnola (Romagna region) paler abdomen the 31 registered farms study-of-project-treasure/mora- (August 2015).

romagnola-pig https://www.intechopen.com/boo 265 breeding sows and ks/european-local-pig-breeds- RS / Morava Valley of 15 boars distributed in Moravka MO Moravka Moravka Solid black Medium Medium diversity-and-performance-a- central Serbia 25 registered farms study-of-project- (February 2018).

treasure/moravka-pig https://www.intechopen.com/boo 1103 breeding sows and Nero dei Nebrodi, Solid black (a few ks/european-local-pig-breeds- 124 boars distributed in Nero Siciliano NS Nero Siciliano Nero delle Madonie, IT / Sicily island animals could have Small Medium diversity-and-performance-a- 87 registered farms Nero dell’Etna white spots) study-of-project-treasure/nero- (August 2015).

siciliano-pig https://www.intechopen.com/boo 61 breeding sows and ks/european-local-pig-breeds- No fixed coat Sarda SA Sarda Sarda IT / Sardinia island Small Small 20 boars distributed in diversity-and-performance-a- colour 13 registered farms. study-of-project-treasure/sarda-

pig

White in the centre, https://www.intechopen.com/boo Schwaebisch- with a black head 350 breeding sows and Schwäbisch- ks/european-local-pig-breeds- Schwäbisch- Haellisches Schwein DE / Area of and rear and narrow Medium 35 boars distributed in SHS Hällisches Large diversity-and-performance-a- Hällisches Schwein Swabian Hall pig, Schwäbisch Hall grey bands at the to large 15 registered farms Schwein study-of-project-treasure/schw- Swabian Hall swine transition from (August 2015).

bisch-h-llisches-pig white to black skin.

Grey/black (The https://www.intechopen.com/boo three Mangalica 925 sows, 605 gilts and ks/european-local-pig-breeds- Swallow-Bellied breed types are 42 boars distributed in diversity-and-performance-a- SBMA Mangulica Mangalitsa RS / Serbia Large Medium Mangalitsa blonde, swallow- 67 registered farm (End study-of-project- belly and red of 2017) treasure/mangalitsa-swallow-

Mangalitsa. ) belly-mangalitsa-pig https://www.intechopen.com/boo 116 breeding sows and ks/european-local-pig-breeds- Turopoljska White/grey/with 14 boars distributed in diversity-and-performance-a- Turopolje TU Turopolje pig HR / West Croatia Medium Medium svinja sporadic black spots 12 registered farms study-of-project- (August 2016). treasure/turopolje-pig-

turopoljska-svinja-

Italian Duroc IDU Duroc Italiana Duroc Italiana IT Dark red Small Large - www.anas.it

Large White Italian Large White ILW Large White Italiana IT Solid White Small Large - www.anas.it Italiana

Table S2. Summary statistics of whole-genome sequencing.

Acronym of the No. of read No. of Fraction of Breadth of Depth of coverage Breed Country breed name pairs animals duplicated reads coverage (%)* (X)* Autochthonous Alentejana AL PT 419,690,476 35 0.143 98.42 41.98 Apulo-Calabrese AC IT 418,529,727 35 0.137 98.49 42.12 Basque BA FR 407,698,128 30 0.130 98.35 39.55 Bísara BI PT 415,284,437 35 0.126 98.51 42.44 Black Slavonian BS HR 405,316,112 35 0.139 98.51 40.61 Casertana CA IT 435,598,516 35 0.142 98.50 43.61 Cinta Senese CS IT 422,120,850 35 0.139 98.47 42.42 Gascon GA FR 408,764,207 30 0.120 98.47 41.10 Krškopolje KR SI 404,204,144 35 0.134 98.52 40.80 Lithuanian Indigenous Wattle LIW LT 409,935,460 35 0.123 98.48 41.99 Lithuanian White Old Type LWOT LT 405,822,217 35 0.123 98.45 41.62 Majorcan Black MB ES 414,314,159 35 0.133 98.48 41.92 Mora Romagnola MR IT 411,095,541 35 0.138 98.45 41.21 Moravka MO RS 413,100,992 35 0.124 98.49 42.27 Nero Siciliano NS IT 405,812,223 35 0.137 98.44 38.92 Sarda SA IT 442,035,147 35 0.150 98.51 44.32 Schwäbisch-Hällisches Schwein SHS DE 428,982,876 35 0.135 98.48 42.69 Swallow-Bellied Mangalitsa SBMA RS 416,663,891 35 0.130 98.45 41.08 Turopolje TU HR 416,663,891 35 0.124 98.36 42.61 Commercial Italian Duroc IDU IT 420,384,723 35 0.154 98.51 41.91 Italian Large White ILW IT 450,673,024 35 0.148 98.38 45.24

*Statistics presented after the removal of duplicated reads.

Table S3. Summary statistics of detected CNVs, stratified by chromosome.

1 2 3 4 5 6 7 8 Chromosome CNV events CNV CNL CNG Mixed CN Ratio CNL/CNG LengthMin LengthMax LengthMedian SSC1 1124 741 348 342 51 1.02 2250 137250 3000 SSC2 1159 767 299 425 43 0.70 2250 39000 4500 SSC3 583 380 158 196 26 0.81 2250 99750 4125 SSC4 739 479 198 242 39 0.82 2250 81000 3750 SSC5 885 615 240 338 37 0.71 2250 46500 16500 SSC6 1056 704 275 370 59 0.74 2250 116250 2625 SSC7 575 411 169 224 18 0.75 2250 66000 3000 SSC8 924 530 229 259 42 0.88 2250 560250 3750 SSC9 1235 931 353 525 53 0.67 2250 126000 5250 SSC10 413 259 104 130 25 0.80 2250 85500 2250 SSC11 993 627 289 294 44 0.98 2250 147000 5250 SSC12 434 325 112 196 17 0.57 2250 108000 3000 SSC13 1356 885 376 442 67 0.85 2250 90750 3000 SSC14 1105 797 302 453 42 0.67 2250 105750 7500 SSC15 651 409 171 208 30 0.82 2250 58500 6000 SSC16 511 307 140 142 25 0.99 2250 32250 6750 SSC17 484 354 150 188 16 0.80 2250 78000 3375 SSC18 117 71 29 38 4 0.76 2250 15750 3000

1 Total no. of copy number variant events; 2 Total no. of copy number variants; 3 Total no. of copy number losses; 4 Total no. of copy number gains; 5 Total no. of copy number variants presenting both gains and losses; 6 Minimum length (bp) of CNVs; 7 Maximum length (bp) of CNVs; 8 Median length (bp) of CNVs Table S5. Summary statistics of detected CNVRs, stratified by pig breed.

Acronym of the No. of No. of breed No. of annotated Breed breed name CNVRs specific CNVRs protein coding genes Autochthonous Alentejana AL 529 43 217 Apulo-Calabrese AC 565 74 243 Basque BA 988 178 364 Bísara BI 347 15 141 Black Slavonian BS 425 40 177 Casertana CA 499 46 230 Cinta Senese CS 551 61 240 Gascon GA 668 83 278 Krškopolje KR 423 30 168 Lithuanian Indigenous Wattle LIW 607 77 244 Lithuanian White Old Type LWOT 614 78 256 Majorcan Black MB 459 45 193 Mora Romagnola MR 1114 207 430 Moravka MO 329 15 138 Nero Siciliano NS 244 16 106 Sarda SA 180 10 77 Schwäbisch-Hällisches SHS 512 63 187 Schwein Swallow-Bellied Mangalitsa SBMA 633 60 273 Turopolje TU 1257 278 490 Commercial Italian Duroc IDU 971 174 346 Italian Large White ILW 382 22 162

Table S6. Over-represented repeated element classes.

CNV CNV flanking regions (1-kb) CNVR CNVR flanking regions (1-kb) 1 2 3 1 2 3 1 2 3 1 2 3 FCNVR FGENOME p-value FCNVR FGENOME p-value FCNVR FGENOME p-value FCNVR FGENOME p-value srpRNA# 9.45E-04 3.39E-04 1.8E-101 2.15E-03 3.39E-04 5.1E-131 2.39E-03 3.39E-04 8.5E-289 0.00E+00 0.00E+00 - LTR^ 4.48E+00 4.23E+00 0 6.84E+00 4.23E+00 0 4.47E+00 4.23E+00 0 4.98E+00 4.23E+00 0 DNA§ 1.50E+00 2.26E+00 1 2.17E+00 2.26E+00 1 1.44E+00 2.26E+00 0.999998 1.91E+00 2.26E+00 0.999992 LINE+ 3.60E+01 1.89E+01 0 4.57E+01 1.89E+01 0 3.87E+01 1.89E+01 0 3.82E+01 1.89E+01 0 Low_complexity 2.07E-01 2.08E-01 0.875985 3.04E-01 2.08E-01 0 2.16E-01 2.08E-01 2.42E-19 2.62E-01 2.08E-01 1.1E-193 RC/Helitron 1.52E-02 9.99E-03 0 8.10E-03 9.99E-03 1 9.64E-03 9.99E-03 0.965814 8.52E-03 9.99E-03 0.999954 rRNA# 1.69E-02 3.48E-03 0 2.49E-02 3.48E-03 0 2.79E-02 3.48E-03 0 2.34E-02 3.48E-03 0 Satellite 2.08E+00 7.13E-02 0 3.72E+00 7.13E-02 0 2.13E+00 7.13E-02 0 2.12E+00 7.13E-02 0 Simple_repeat 1.05E+00 1.08E+00 1 1.48E+00 1.08E+00 0 1.10E+00 1.08E+00 1.29E-19 1.24E+00 1.08E+00 0 SINE$ 1.16E+01 1.33E+01 1 1.59E+01 1.33E+01 0 1.14E+01 1.33E+01 1 1.30E+01 1.33E+01 0.999991 snRNA# 8.77E-03 5.76E-03 1.4E-188 2.59E-02 5.76E-03 0 1.17E-02 5.76E-03 2.4E-260 2.26E-02 5.76E-03 0 tRNA# 1.00E-02 3.95E-03 0 1.65E-02 3.95E-03 0 8.06E-03 3.95E-03 6.6E-184 1.39E-02 3.95E-03 8E-228 Unknown 7.54E-03 2.58E-02 0.999996 1.94E-02 2.58E-02 0.999995 7.35E-03 2.58E-02 1 1.32E-02 2.58E-02 0.999993 RNA# 0.00E+00 0.00E+00 - 2.31E-04 2.17E-03 1 0.00E+00 0.00E+00 - 4.66E-04 2.17E-03 1

1 Fraction of the CNVRs bases covered by a repeated element class; 2 Fraction of the genome bases covered by a repeated element class; 3 p-value at the Fisher’s exact test. § hAT, hAT-Ac, hAT-Blackjack, hAT-Charlie, hAT-Tag1, hAT-Tip100, Kolobok, PiggyBac, TcMar, TcMar-Mariner, TcMar-Pogo, TcMar-Tc1, TcMar-Tc2, TcMar-Tigger; + CR1, Dong-R4, Jockey, L1, L1-Tx1, L2, Penelope, RTE-BovB, RTE-X; ^ ERV1, ERVK, ERVL, ERVL-MaLR, Gypsy; $ 5S-Deu-L2, MIR, tRNA, tRNA-Deu, tRNA-RTE; # Pseudogenes. Table S7. Over-represented QTLs.

Trait Coverage CNVR1 Coverage Genome2 P Intramuscular fat content 9.75E+00 3.90E+00 0.00E+00 Mean corpuscular volume 9.53E+00 2.79E+00 0.00E+00 Mean corpuscular hemoglobin content 5.73E+00 1.23E+00 0.00E+00 Loin muscle area 4.53E+00 1.37E+00 0.00E+00 Red blood cell count 4.35E+00 6.79E-01 0.00E+00 Obesity index 3.23E+00 6.46E-01 0.00E+00 Number of stillborn 3.16E+00 8.01E-01 0.00E+00 Hematocrit 2.88E+00 5.83E-01 0.00E+00 Total number born alive 2.76E+00 1.17E+00 0.00E+00 Lean meat percentage 2.60E+00 1.09E+00 0.00E+00 Lumbar vertebra number 2.49E+00 6.92E-01 0.00E+00 Thoracolumbar vertebra number 2.15E+00 8.58E-01 0.00E+00 Body weight (birth) 2.06E+00 6.87E-01 0.00E+00 Backfat at last rib 1.94E+00 8.26E-01 0.00E+00 Left teat number 1.79E+00 6.22E-01 0.00E+00 Right teat number 1.69E+00 4.73E-01 0.00E+00 Palmitic acid content 1.65E+00 7.48E-01 0.00E+00 Skatole, laboratory 1.50E+00 1.86E-01 0.00E+00 Fat to meat ratio 1.49E+00 4.96E-02 0.00E+00 Meat color a* 1.45E+00 6.50E-01 0.00E+00 Body weight (weaning) 1.45E+00 2.71E-01 0.00E+00 Meat color L* 1.41E+00 4.59E-01 0.00E+00 pH 24 hr post-mortem (loin) 1.37E+00 6.41E-01 0.00E+00 Loin muscle depth 1.23E+00 3.91E-01 0.00E+00 Plateletcrit 1.18E+00 2.06E-01 0.00E+00 Backfat between last rib and first lumbar 1.17E+00 2.22E-02 0.00E+00 Polyunsaturated fatty acid content 1.11E+00 1.94E-01 0.00E+00 Impedance 24 hours postmortem 1.06E+00 2.95E-01 0.00E+00 Myristic acid content 1.01E+00 2.99E-01 0.00E+00 Monounsaturated fatty acid content 9.94E-01 2.96E-01 0.00E+00 pH 24 hr post mortem (ham) 9.88E-01 4.58E-01 0.00E+00 Saturated fatty acid content 9.57E-01 3.39E-01 0.00E+00 Linoleic acid content 9.39E-01 3.01E-01 0.00E+00 Ear area 9.16E-01 2.07E-01 0.00E+00 Red cell distribution width 9.10E-01 2.92E-01 0.00E+00 Conductivity 24 hours post-mortem (ham) 8.90E-01 2.43E-01 0.00E+00 White blood cell number 8.31E-01 2.15E-01 0.00E+00 Marbling 8.13E-01 2.56E-01 0.00E+00 Meat color chroma 7.21E-01 2.53E-02 0.00E+00 Backfat thickness between 3rd and 4th rib 7.09E-01 6.84E-02 0.00E+00 Backfat at last lumbar 6.43E-01 1.71E-01 0.00E+00 Linolenic acid content 6.42E-01 1.12E-01 0.00E+00 Number of visits to feeder per day 6.38E-01 2.03E-01 0.00E+00 Shoulder subcutaneous fat thickness 6.35E-01 2.35E-01 0.00E+00 Monounsaturated fatty acid to saturated fatty acid ratio 6.06E-01 1.02E-01 0.00E+00 pH for Semimembranosus 6.03E-01 1.53E-01 0.00E+00 Androstenone, laboratory 5.85E-01 2.05E-01 0.00E+00 Hemoglobin 5.80E-01 2.00E-01 0.00E+00 Unsaturated fatty acid content 5.78E-01 9.08E-02 0.00E+00 Polyunsaturated fatty acid to saturated fatty acid ratio 5.74E-01 7.23E-02 0.00E+00 Umbilical hernia 5.64E-01 2.19E-01 0.00E+00 Body weight (slaughter) 5.34E-01 6.19E-02 0.00E+00 Omega-6 fatty acid content 5.26E-01 2.52E-02 0.00E+00 Cooking loss 5.23E-01 1.85E-01 0.00E+00 Backfat between the last 3rd and 4th lumbar 5.20E-01 6.30E-02 0.00E+00 Oleic acid to palmitoleic acid ratio 5.14E-01 1.83E-01 0.00E+00 Intermuscular fat content 4.94E-01 1.40E-01 0.00E+00 Arachidic acid content 4.70E-01 1.82E-01 0.00E+00 Palmitoleic acid to palmitic acid ratio 4.39E-01 1.26E-01 0.00E+00 Carcass temperature (45 minutes post-mortem) 4.32E-01 1.30E-02 0.00E+00 Conductivity 24 hours post-mortem 4.25E-01 1.42E-01 0.00E+00 Melanoma susceptibility 4.16E-01 1.79E-01 0.00E+00 Uterine horn weight 4.08E-01 1.33E-01 0.00E+00 Water holding capacity 3.88E-01 7.43E-02 0.00E+00 Basophil percentage 3.59E-01 1.48E-01 0.00E+00 Front feet conformation 3.56E-01 6.10E-02 0.00E+00 Semimembranosus angle 3.56E-01 2.61E-03 0.00E+00 Sperm motility 3.41E-01 5.49E-02 0.00E+00 Fat-cuts percentage 3.30E-01 1.08E-01 0.00E+00 Nonfunctional nipples 3.30E-01 3.20E-02 0.00E+00 Sperm progressive motility 3.16E-01 5.67E-02 0.00E+00 Cholesterol level in meat 2.93E-01 4.46E-02 0.00E+00 Fat androstenone level 2.90E-01 8.13E-02 0.00E+00 Platelet-large cell ratio 2.69E-01 7.64E-02 0.00E+00 Half carcass weight 2.67E-01 5.82E-02 0.00E+00 Average glycolytic potential 2.10E-01 7.67E-02 0.00E+00 Feed intake 2.07E-01 1.57E-02 0.00E+00 Mycoplasma hyopneumoniae antibody titer 1.98E-01 3.42E-02 0.00E+00 Ejaculation times 1.98E-01 2.67E-02 0.00E+00 Shoulder weight 1.95E-01 6.13E-02 0.00E+00 Salmonella shedding status 1.92E-01 2.38E-02 0.00E+00 Salmonella count in liver 1.92E-01 2.01E-02 0.00E+00 Salmonella count in spleen 1.92E-01 1.93E-02 0.00E+00 Saturated fatty acid to polyunsaturated fatty acid ratio 1.69E-01 4.68E-02 0.00E+00 Loin weight 1.61E-01 5.73E-02 0.00E+00 Muscle protein percentage 1.52E-01 5.23E-02 0.00E+00 PH for Biceps femoris 1.49E-01 2.81E-02 0.00E+00 Lean meat + bone in ham + back 1.41E-01 5.15E-02 0.00E+00 Lifetime number of offspring born alive 1.38E-01 4.24E-02 0.00E+00 Biceps brachii weight 1.38E-01 2.04E-02 0.00E+00 Immunoglobulin G level 1.32E-01 1.50E-02 0.00E+00 Body width 1.32E-01 1.48E-02 0.00E+00 45 min-3 hr pH decline 1.30E-01 2.21E-02 0.00E+00 Muscle fat content 1.21E-01 3.42E-02 0.00E+00 Percentage type I fibers 9.88E-02 3.21E-02 0.00E+00 Hematin pigmentation 9.76E-02 3.75E-02 0.00E+00 Insulin-like growth factor 1 level 7.75E-02 7.45E-03 0.00E+00 Monocyte number 6.65E-02 1.87E-02 0.00E+00 Average instron (star probe) force 5.46E-02 1.81E-02 0.00E+00 Body weight (8 weeks) 5.46E-02 1.51E-02 0.00E+00 Epididymis weight 4.31E-02 6.49E-03 0.00E+00 Lipid accretion rate 3.73E-02 9.88E-03 0.00E+00 Sarcocystis miescheriana IgG levels 1.72E-02 4.48E-03 0.00E+00 Non-return rate 1.44E-02 2.70E-03 0.00E+00 Relative area of type I fibers 1.44E-02 2.19E-03 0.00E+00 Cross-sectional area of muscle fibers 1.44E-02 2.19E-03 0.00E+00 Gadoleic acid content 1.52E-03 1.21E-05 0.00E+00 Femur dimensions 1.15E-02 2.74E-03 1.05E-281 Ham meat weight 1.49E-01 6.32E-02 1.46E-226 Body weight (10 weeks) 3.73E-02 1.33E-02 4.30E-219 Reflectance value 1.49E-01 6.53E-02 9.02E-151 Cryptorchidism 1.98E-01 8.91E-02 1.17E-129 Juiciness score 2.87E-01 1.33E-01 4.37E-110 Spinal curvature 1.45E+00 7.11E-01 2.80E-108 cis-9-Heptadecenoic acid content 3.79E-04 1.01E-05 6.43E-84 Capric acid content 3.79E-04 1.61E-05 1.61E-66 Ham meat percentage 1.69E-01 7.90E-02 1.20E-49 pH 45 minutes post mortem 1.08E+00 5.33E-01 4.17E-43 Backfat at rump 1.43E+00 7.14E-01 6.87E-29 Number of muscle fibers per unit area 1.44E-02 5.97E-03 6.52E-28 Time in feeder per visit 1.44E-02 6.05E-03 1.41E-24 Body weight (16 days) 7.47E-02 3.48E-02 7.54E-23 Number of non-viable fetuses 1.53E-04 1.45E-05 2.53E-16 3 hr-9 hr pH decline 2.01E-02 9.06E-03 1.08E-13 Blood alanine transaminase level 7.25E-02 3.49E-02 1.18E-07 Backfat at tenth rib 1.05E+00 5.29E-01 3.68E-05

1 Fraction of the CNVRs bases covered by the phenotypic trait; 2 Fraction of the genome covered by the phenotypic trait.

Table S8. Within CNVRs over-represented biological functions.

No. of No. of overlapping Biological function p-value FDR annotated genes input genes PANTHER GO-Slim Biological Process Detection of chemical stimulus involved in sensory perception (GO:0050907) 774 120 4.12E-31 7.38E-28 Sensory perception of chemical stimulus (GO:0007606) 804 121 2.65E-30 2.37E-27 Sensory perception (GO:0007600) 912 126 2.07E-28 1.23E-25 Nervous system process (GO:0050877) 1203 139 2.12E-24 9.50E-22 System process (GO:0003008) 1321 145 1.77E-23 6.35E-21 Multicellular organismal process (GO:0032501) 1996 176 6.29E-19 1.88E-16 Macromolecule metabolic process (GO:0043170) 2605 65 1.34E-06 3.44E-04 Gene expression (GO:0010467) 1985 46 3.50E-06 7.83E-04 Fatty acid metabolic process (GO:0006631) 159 22 5.39E-06 1.07E-03 Cellular lipid metabolic process (GO:0044255) 323 32 3.38E-05 4.65E-03 Biological adhesion (GO:0022610) 384 36 3.12E-05 4.65E-03 Cell adhesion (GO:0007155) 384 36 3.12E-05 5.08E-03 Transcription by RNA polymerase II (GO:0006366) 1041 22 2.59E-04 3.31E-02 Transcription, DNA-templated (GO:0006351) 1257 29 2.86E-04 3.42E-02 Metabolic process (GO:0008152) 4372 143 3.42E-04 3.82E-02 Cell-cell adhesion via plasma-membrane adhesion molecules (GO:0098742) 58 10 4.30E-04 4.53E-02 Reactome pathways Olfactory Signaling Pathway (R-SSC-381753) 329 51 9.26E-14 1.47E-10 G alpha (s) signalling events (R-SSC-418555) 436 59 2.05E-13 1.63E-10 Signaling by GPCR (R-SSC-372790) 835 74 1.89E-08 9.98E-06 GPCR downstream signalling (R-SSC-388396) 813 72 3.25E-08 1.29E-05 Signal Transduction (R-SSC-162582) 1890 117 9.95E-05 3.16E-02 SLIT2:ROBO1 increases RHOA activity (R-SSC-8985586) 4 4 1.72E-04 4.55E-02

Table S9. Allele frequency of the single nucleotide polymorphisms at the KIT and MSRB3 genes estimated from sequencing data.

Breed KIT MSRB3 rs345599765 rs340841870 rs326411202 Allele G Allele C Allele C Average CN1 Autochthonous Alentejana 1.00 1.00 0.88 0.97 Apulo-Calabrese 1.00 0.88 0.70 1.19 Basque 1.00 0.03 0.02 2.78 Bísara 1.00 0.03 0.03 2.79 Black Slavonian 1.00 0.18 0.06 2.57 Casertana 1.00 0.67 0.36 1.72 Cinta Senese 1.00 1.00 0.60 1.00 Gascon 1.00 0.52 0.41 1.89 Krškopolje 1.00 0.40 0.20 2.20 Lithuanian Indigenous Wattle 0.83 0.42 0.14 2.01 Lithuanian White Old Type 0.20 0.81 0.60 1.30 Majorcan Black 1.00 0.51 0.29 1.96 Mora Romagnola 1.00 1.00 1.00 1.01 Moravka 1.00 0.12 0.03 2.74 Nero Siciliano 1.00 0.52 0.32 1.32 Sarda 0.94 0.35 0.13 2.28 Schwäbisch-Hällisches Schwein 1.00 0.12 0.04 2.58 Swallow-Bellied Mangalitsa 1.00 0.07 0.00 2.84 Turopolje 1.00 0.60 0.28 1.76 Commercial Italian Duroc 1.00 0.79 0.32 1.02 Italian Large White 0.68 0.86 0.85 1.00 1Average value of the CN state of the windows encompassed by the CNV.

Table S10. Summary statistics of CNVRs previously identified.

No. of No. of interrogated HTS based study No. of animals2 No. of CNVRs3 No. of overlapped CNVRs5 % of overlapped CNVRs6 breeds1 CNVRs4 Paudel et al. (2013) 13 16 3118 2416* 401 10.8% Jiang et al. (2014) 10 13 3131 2791* 916 24.7% Paudel et al.(2015) 5+3 16 1408 917* 378 10.2% Revilla et al. (2017) 2 7 540 527* 527 14.2% Keel et al. (2019) 3 240 3538 3443 937 25.3%

1 No. of breeds analysed in the original study, Paudel et al. (2015) investigated five species of the Sus genus [S. cebifrons, S. celebensis, S. verrucosus, S. barbatus and S. scrofa (three breeds/populations)]; 2 No. of animals analysed in the original study; 3 No. of CNVRs detected in the original study; 4 No. of interrogated autosomal CNVRs; 5 No. of CNVRs here detected overlapping the known ones; 6 Percentage of CNVRs here detected supported by these studies; * CNVRs were converted to Sscrofa11.1 coordinates using the NCBI Genome Remapping tool.