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.

Piras, D., Doro, M., Casu, G., Melis, P., Vaccargiu, S., Piras, I., et al. (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, 7(2), e30785 [10.1371/journal.pone.0030785].

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

NOVELLETTO, ANDREA
2012

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.
Pubblicato
Rilevanza internazionale
Articolo
Esperti anonimi
Settore BIO/18 - Genetica
English
Phylogeny; Genetic Variation; Animals; Goats; DNA, Mitochondrial; Nucleic Acid Conformation; Italy; Cities; Base Sequence; Breeding; Conserved Sequence; Haplotypes; Molecular Sequence Data; DNA; Geography
Piras, D., Doro, M., Casu, G., Melis, P., Vaccargiu, S., Piras, I., et al. (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, 7(2), e30785 [10.1371/journal.pone.0030785].
Piras, D; Doro, M; Casu, G; Melis, P; Vaccargiu, S; Piras, I; Parracciani, D; Stradoni, R; Frongia, B; Lai, G; Sale, S; Cattari, W; Piras, R; Querci, O; Demuro, P; Cui, S; Atzori, F; Mancosu, M; Marchiori, F; Cammelli, R; Spiga, A; Loddo, P; Pili, G; Boi, R; Argiolas, G; Mereu, P; Leoni, G; Naitana, S; Pirastu, M; Novelletto, A
Articolo su rivista
File in questo prodotto:
File Dimensione Formato  
Capra.pone.0030785.pdf

accesso aperto

Licenza: Non specificato
Dimensione 374.07 kB
Formato Adobe PDF
374.07 kB Adobe PDF Visualizza/Apri

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2108/99888
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 15
  • ???jsp.display-item.citation.isi??? 9
social impact