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Genome-wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds

Ciani, Elena and Crepaldi, Paola and Nicoloso, Letizia and Lasagna, Emiliano and Sarti, Francesca Maria and Moioli, Bianca and Napolitano, Francesco and Carta, Antonello and Usai, Mario Graziano and D'Andrea, Maria Silvia and Marletta, Donata and Ciampolini, Roberta and Riggio, Valentina and Occidente, Maria Consiglia and Matassino, Donato and Kompan, Daniel and Modesto, Paola and Macciotta, Nicolò Pietro Paolo and Ajmonemarsan, Paolo and Pilla, Fabio (2014) Genome-wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds. Animal Genetics, Vol. 45 (2), p. 256-266. ISSN 0268-9146. eISSN 1365-2052. Article.

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DOI: 10.1111/age.12106

Abstract

Italy counts several sheep breeds, arisen over centuries as a consequence of ancient and recent genetic and demographic events. To finely reconstruct genetic structure and relationships between Italian sheep, 496 subjects from 19 breeds were typed at 50K single nucleotide polymorphism loci. A subset of foreign breeds from the Sheep HapMap dataset was also included in the analyses. Genetic distances (as visualized either in a network or in a multidimensional scaling analysis of identical by state distances) closely reflected geographic proximity between breeds, with a clear north-south gradient, likely because of high levels of past gene flow and admixture all along the peninsula. Sardinian breeds diverged more from other breeds, a probable consequence of the combined effect of ancient sporadic introgression of feral mouflon and long-lasting genetic isolation from continental sheep populations. The study allowed the detection of previously undocumented episodes of recent introgression (Delle Langhe into the endangered Altamurana breed) as well as signatures of known, or claimed, historical introgression (Merino into Sopravissana and Gentile di Puglia; Bergamasca into Fabrianese, Appenninica and, to a lesser extent, Leccese). Arguments that would question, from a genomic point of view, the current breed classification of Bergamasca and Biellese into two separate breeds are presented. Finally, a role for traditional transhumance practices in shaping the genetic makeup of Alpine sheep breeds is proposed. The study represents the first exhaustive analysis of Italian sheep diversity in an European context, and it bridges the gap in the previous HapMap panel between Western Mediterranean and Swiss breeds. , , , Carta A, Usai G, D'Andrea M, Marletta D, Ciampolini R, Riggio V, Occidente M, Matassino D, Kompan D, Modesto P, Macciotta N, Ajmone-Marsan P, Pilla F.

Item Type:Article
ID Code:10122
Status:Published
Refereed:Yes
Uncontrolled Keywords:Ovis aries, genetic diversity, genetic structure, genome-wide single nucleotide polymorphisms, multidimensional scaling, neighbor network
Subjects:Area 07 - Scienze agrarie e veterinarie > AGR/17 Zootecnica generale e miglioramento genetico
Divisions:001 Università di Sassari > 01-a Nuovi Dipartimenti dal 2012 > Agraria
002 Altri enti e centri di ricerca del Nord Sardegna > AGRIS Sardegna, Olmedo > Dipartimento per la ricerca nelle produzioni animali > Settore genetica e biotecnologie
Publisher:Blackwell / Wiley
ISSN:0268-9146
eISSN:1365-2052
Copyright Holders:© 2013 Stichting International Foundation for Animal Genetics
Deposited On:22 Sep 2014 17:33

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