Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data

Christos Dadousis; Maria Muñoz; Cristina Óvilo; Maria Chiara Fabbri; José Pedro Araújo; Samuele Bovo; Marjeta Čandek Potokar; Rui Charneca; Alessandro Crovetti; Maurizio Gallo; Juan María García-Casco; Danijel Karolyi; Goran Kušec; José Manuel Martins; Marie-José Mercat; Carolina Pugliese; Raquel Quintanilla; Anisa Ribani; Juliet Riquet; Čedomir Radović; Violeta Razmaite; Radomir Savić; Giuseppina Schiavo; Martin Škrlep; Silvia Tinarelli; Graziano Usai; Christoph Zimmer; Luca Fontanesi; Riccardo Bozzi

doi:10.1038/s41598-022-10698-8

Back

Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data

Journal article

Open access

Peer reviewed

Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data

Christos Dadousis, Maria Muñoz, Cristina Óvilo, Maria Chiara Fabbri, José Pedro Araújo, Samuele Bovo, Marjeta Čandek Potokar, Rui Charneca, Alessandro Crovetti, Maurizio Gallo, …

Scientific reports, Vol.12(1), 7346

05/05/2022

DOI: https://doi.org/10.1038/s41598-022-10698-8

PMID: 35513520

Abstract

Animals

Biological Specimen Banks

Genome

Polymorphism, Single Nucleotide

Sus scrofa - genetics

Swine - genetics

Plant Breeding

Preserving diversity of indigenous pig (Sus scrofa) breeds is a key factor to (i) sustain the pork chain (both at local and global scales) including the production of high-quality branded products, (ii) enrich the animal biobanking and (iii) progress conservation policies. Single nucleotide polymorphism (SNP) chips offer the opportunity for whole-genome comparisons among individuals and breeds. Animals from twenty European local pigs breeds, reared in nine countries (Croatia: Black Slavonian, Turopolje; France: Basque, Gascon; Germany: Schwabisch-Hällisches Schwein; Italy: Apulo Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda; Lithuania: Indigenous Wattle, White Old Type; Portugal: Alentejana, Bísara; Serbia: Moravka, Swallow-Bellied Mangalitsa; Slovenia: Krškopolje pig; Spain: Iberian, Majorcan Black), and three commercial breeds (Duroc, Landrace and Large White) were sampled and genotyped with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. A dataset of 51 Wild Boars from nine countries was also added, summing up to 1186 pigs (~ 49 pigs/breed). The aim was to: (i) investigate individual admixture ancestries and (ii) assess breed traceability via discriminant analysis on principal components (DAPC). Albeit the mosaic of shared ancestries found for Nero Siciliano, Sarda and Moravka, admixture analysis indicated independent evolvement for the rest of the breeds. High prediction accuracy of DAPC mark SNP data as a reliable solution for the traceability of breed-specific pig products.

Files and links (2)

pdf

2022_Dadousis_Admixture and breed traceability in European indigenous pig breeds and wild boar using genome‑wide SNP data_Scientific_Reports5.22 MBDownload View

Published (Version of record)CC BY V4.0, Open Access

url

https://doi.org/10.1038/s41598-022-10698-8View

Published (Version of record)

Metrics

1 File views/ downloads

15 Record Views

10 Times Cited - Web of Science

See more details

Details

Title: Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data
Creators: Christos Dadousis - University of Florence
Maria Muñoz - Departamento Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Crta. de la Coruña, km. 7, 5, 28040, Madrid, Spain
Cristina Óvilo - Departamento Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Crta. de la Coruña, km. 7, 5, 28040, Madrid, Spain
Maria Chiara Fabbri - Dipartimento Di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università Di Firenze, 50144, Firenze, Italy
José Pedro Araújo - Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Viana Do Castelo, Escola Superior Agrária, Refóios do Lima, 4990‑706, Ponte de Lima, Portugal
Samuele Bovo - Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
Marjeta Čandek Potokar - Kmetijski inštitut Slovenije, Hacquetova 17, 1000, Ljubljana, Slovenia
Rui Charneca - MED-Mediterranean Institute for Agriculture, Environment and Development & Escola de Ciências E Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554, Évora, Portugal
Alessandro Crovetti - Dipartimento Di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università Di Firenze, 50144, Firenze, Italy
Maurizio Gallo - Associazione Nazionale Allevatori Suini (ANAS), Via Nizza 53, 00198, Rome, Italy
Juan María García-Casco - Departamento Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Crta. de la Coruña, km. 7, 5, 28040, Madrid, Spain
Danijel Karolyi - Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000, Zagreb, Croatia
Goran Kušec - Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000, Osijek, Croatia
José Manuel Martins - MED-Mediterranean Institute for Agriculture, Environment and Development & Escola de Ciências E Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554, Évora, Portugal
Marie-José Mercat - IFIP Institut du Porc, La Motte au Vicomte, BP 35104, 35651, Le Rheu Cedex, France
Carolina Pugliese - Dipartimento Di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università Di Firenze, 50144, Firenze, Italy
Raquel Quintanilla - Programa de Genética y Mejora Animal, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Barcelona, Spain
Anisa Ribani - Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
Juliet Riquet - Génétique Physiologie Et Systèmes d'Elevage (GenPhySE), Université de Toulouse, INRA, Chemin de Borde‑Rouge 24, Auzeville Tolosane, 31326, Castanet Tolosan, France
Čedomir Radović - Department of Pig Breeding and Genetics, Institute for Animal Husbandry, 11080, Belgrade‑Zemun, Serbia
Violeta Razmaite - Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, Lithuania
Radomir Savić - Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080, Belgrade-Zemun, Serbia
Giuseppina Schiavo - Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
Martin Škrlep - Kmetijski inštitut Slovenije, Hacquetova 17, 1000, Ljubljana, Slovenia
Silvia Tinarelli - Associazione Nazionale Allevatori Suini (ANAS), Via Nizza 53, 00198, Rome, Italy
Graziano Usai - AGRIS SARDEGNA, Loc. Bonassai, 07100, Sassari, Italy
Christoph Zimmer - Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Schwäbisch Hall, Germany
Luca Fontanesi - Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
Riccardo Bozzi - Dipartimento Di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università Di Firenze, 50144, Firenze, Italy
Publication Details: Scientific reports, Vol.12(1), 7346
Date published: 05/05/2022
Date accepted: 11/04/2022
Grants: 634476 , Horizon 2020
Identifiers: 99841465802346
Academic Unit: School of Health Sciences
Language: English
Resource Type: Journal article

Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data

Abstract

Files and links (2)

Metrics

Details

Usage Policy