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Genome‐wide analysis of I talian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds
Author(s) -
Ciani E.,
Crepaldi P.,
Nicoloso L.,
Lasagna E.,
Sarti F. M.,
Moioli B.,
Napolitano F.,
Carta A.,
Usai G.,
D'Andrea M.,
Marletta D.,
Ciampolini R.,
Riggio V.,
Occidente M.,
Matassino D.,
Kompan D.,
Modesto P.,
Macciotta N.,
AjmoneMarsan P.,
Pilla F.
Publication year - 2014
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12106
Subject(s) - introgression , international hapmap project , biology , breed , genetic diversity , evolutionary biology , context (archaeology) , endangered species , gene flow , zoology , genetic variation , single nucleotide polymorphism , genetics , ecology , population , genotype , gene , demography , habitat , paleontology , sociology
Summary I taly 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 I talian 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 I talian sheep diversity in an E uropean context, and it bridges the gap in the previous HapMap panel between W estern M editerranean and S wiss breeds.