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Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock

Piras, Daniela and Doro, Maria Grazia and Casu, Giuseppina and Melis, Paola Maria and Vaccargiu, Simona and Piras, Ignazio and Parracciani, Debora and Stradoni, Roberta and Frongia, Bruno and Lai, Graziano and Sale, Salvatore and Cattari, Walter and Piras, Roberto and Querci, Ombretta and Demuro, Piergiorgio and Cui, Sandro and Atzori, Franco and Mancosu, Marco and Marchiori, Francesca and Cammelli, Rossana and Spiga, Alessandra and Loddo, Pier Paolo and Pili, Gian Franco and Boi, Roberto and Argiolas, Giuseppe and Mereu, Paolo and Leoni, Giovanni Giuseppe and Naitana, Salvatore and Pirastu, Mario and Novelletto, Andrea (2012) Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock. PLoS One, Vol. 7 (2), e30785. eISSN 1932-6203. Article.

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DOI: 10.1371/journal.pone.0030785

Abstract

Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1) to provide an operational definition of meaningful mtDNA units within haplogroup A, 2) to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection operated by breeders and 3) to identify the peculiarities of Sardinian mtDNA types. We sequenced the mtDNA D-loop in a large sample of animals (1,591) which represents a non-trivial quota of the entire goat population of Sardinia. We found that Sardinia mirrors a large quota of mtDNA diversity of Western Eurasia in the number of variable sites, their mutational pattern and allele frequency. By using Bayesian analysis, a distance-based tree and a network analysis, we recognized demographically coherent groups of sequences identified by particular subsets of the variable positions. The results showed that this assignment system could be reproduced in other studies, capturing the greatest part of haplotype diversity.
We identified haplotype groups overrepresented in Sardinian goats as a result of founder effects. We found that breeders maintain diversity of matrilines most likely through equalization of the reproductive potential. Moreover, the relevant amount of inter-farm mtDNA diversity found does not increase proportionally with distance. Our results illustrate the effects of breeding practices on the composition of maternal gene pool and identify mtDNA types that may be considered in projects aimed at retrieving the maternal component of the oldest breeds of Sardinia.

Item Type:Article
ID Code:7148
Status:Published
Refereed:Yes
Uncontrolled Keywords:Goat, Capra hircus, mtDNA D-loop, Sardinia
Subjects:Area 07 - Scienze agrarie e veterinarie > VET/02 Fisiologia veterinaria
Area 05 - Scienze biologiche > BIO/10 Biochimica
Divisions:002 Altri enti e centri di ricerca del Nord Sardegna > CNR-Consiglio Nazionale delle Ricerche
001 Università di Sassari > 01-a Nuovi Dipartimenti dal 2012 > Scienze Biomediche
001 Università di Sassari > 01-a Nuovi Dipartimenti dal 2012 > Medicina Veterinaria
Publisher:Public Library of Science
eISSN:1932-6203
Copyright Holders: © 2012 Piras et al.
Deposited On:23 Feb 2012 13:46

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