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Whole-genome resequencing reveals signatures of selection in European pig breeds and wild boars

Authors :
Bovo, S.
Schiavo, G.
Ribani, A.
Federica di Palma, F.
Utzeri, Valerio Joe
Moscatelli, G.
Geraci, Claudia
Gallo, M.
Munoz, M.
Fernández, A.I.
Usai, G.
Riquet, Juliette
Charneca, Rui
Djurkin-Kušec, I.
Savic, R.
Araujo, J.P.
Quintanilla, Raquel
Razmaite, Violeta
Mercat, Marie J.
Zimmer, C.
Karolyi, Danijel
Garcia, F.
Núñez, Y.
FONTANESI, Luca
Department of Agricultural and Food Sciences
University of Bologna
Earlham Institute
Associazione Nazionale Allevatori Suini
Departamento de Mejora Genética Animal
Instituto Nacional de Investigaciones Agronomicas
AGRIS sardegna
Génétique Physiologie et Systèmes d'Elevage (GenPhySE )
École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT)
Institut National Polytechnique (Toulouse) (Toulouse INP)
Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP)
Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Universidade de Évora
University of Osijek
Faculty of Agriculture
Université nationale du Rwanda
Instituto Politécnico de Viana do Castelo
Institute of Agrifood Research and Technology (IRTA)
Lithuanian University of Health Science (LUSH)
Institut du Porc (IFIP)
Bäuerliche Erzeugergemeinschaft Schwäbisch Hall (BESH)
Department of Animal Science, Faculty of Agriculture
University of Ghana
ProdInra, Migration
Source :
37. International Society for Animal Genetics Conference (ISAG), 37. International Society for Animal Genetics Conference (ISAG), Jul 2019, LLeida, Spain. 2019
Publication Year :
2019
Publisher :
HAL CCSD, 2019.

Abstract

International audience; Natural and artificial directional selection in cosmopolitan and autochthonous livestock and wild relative populations have shaped their genomes defining the level of variability and determining selective sweeps as final adaptation to different environmental conditions and production systems. In this study we analyzed the genetic variability and selection signatures in 19 European local pig breeds sampled from 7 countries (Croatia, France, Germany, Italy, Lithuania, Portugal, Serbia, Slovenia and Spain) (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian, Casertana, Cinta Senese, Gascon, Krskopolje, Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein, Swallow-Bellied Mangalitsa and Turopolje), 3 cosmopolitan Italian breeds (Large White, Landrace and Duroc) and Italian wild boars. For each population, we prepared DNA pools using equimolar DNA from 30 to 35 animals. Whole-genome 150-bp paired-end sequencing was carried out on an Illumina HiSeq machine. More than 18.4 billion of reads were obtained and mapped on the Sscrofa11.1 genome version with BWA, obtaining a mean depth of sequencing of 42X, respectively. CRISP, coupled to an ad hoc bioinformatic pipeline, was used to detect more than 30 million of high-quality variants (18% not included in dbSNP yet). Variant annotation, carried out with VEP, highlighted that the 0.34% of the autosomal SNPs impacted genes at the protein level. Selection signature analyses (Fst and the Pooled Heterozygosity) highlighted more than 400 sweep regions distributed along the 18 porcine autosomes and scaffolds. Some of these genome regions harboured major genes affecting body shape/size (e.g., NR6A1, PLAG1, LCORL and CASP10), coat color (e.g., KIT, MC1R) and growth/fatness (e.g., MC4R), providing a first global variability analysis of European Sus scrofa populations. This study has been funded by European Union’s H2020 RIA program (grant agreement No 634476).

Details

Language :
English
Database :
OpenAIRE
Journal :
37. International Society for Animal Genetics Conference (ISAG), 37. International Society for Animal Genetics Conference (ISAG), Jul 2019, LLeida, Spain. 2019
Accession number :
edsair.dedup.wf.001..ce7e427fbbc145f5952b7fad6566b0ed