"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