title: Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock.
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.
authors.affiliation: Institute of Population Genetics, National Research Council, Sassari, Italy.
authors.forename: Daniela
authors.initials: D
authors.lastname: Piras
authors.forename: Maria Grazia
authors.initials: MG
authors.lastname: Doro
authors.forename: Giuseppina
authors.initials: G
authors.lastname: Casu
authors.forename: Paola Maria
authors.initials: PM
authors.lastname: Melis
authors.forename: Simona
authors.initials: S
authors.lastname: Vaccargiu
authors.forename: Ignazio
authors.initials: I
authors.lastname: Piras
authors.forename: Debora
authors.initials: D
authors.lastname: Parracciani
authors.forename: Roberta
authors.initials: R
authors.lastname: Stradoni
authors.forename: Bruno
authors.initials: B
authors.lastname: Frongia
authors.forename: Graziano
authors.initials: G
authors.lastname: Lai
authors.forename: Salvatore
authors.initials: S
authors.lastname: Sale
authors.forename: Walter
authors.initials: W
authors.lastname: Cattari
authors.forename: Roberto
authors.initials: R
authors.lastname: Piras
authors.forename: Ombretta
authors.initials: O
authors.lastname: Querci
authors.forename: Piergiorgio
authors.initials: P
authors.lastname: Demuro
authors.forename: Sandro
authors.initials: S
authors.lastname: Cui
authors.forename: Franco
authors.initials: F
authors.lastname: Atzori
authors.forename: Marco
authors.initials: M
authors.lastname: Mancosu
authors.forename: Francesca
authors.initials: F
authors.lastname: Marchiori
authors.forename: Rossana
authors.initials: R
authors.lastname: Cammelli
authors.forename: Alessandra
authors.initials: A
authors.lastname: Spiga
authors.forename: Pier Paolo
authors.initials: PP
authors.lastname: Loddo
authors.forename: Gianfranco
authors.initials: G
authors.lastname: Pili
authors.forename: Roberto
authors.initials: R
authors.lastname: Boi
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Argiolas
authors.forename: Paolo
authors.initials: P
authors.lastname: Mereu
authors.forename: Giovanni Giuseppe
authors.initials: GG
authors.lastname: Leoni
authors.forename: Salvatore
authors.initials: S
authors.lastname: Naitana
authors.forename: Mario
authors.initials: M
authors.lastname: Pirastu
authors.forename: Andrea
authors.initials: A
authors.lastname: Novelletto
mesh_terms: D000818:Animals; D001483:Base Sequence; D001947:Breeding; D002947:Cities; D017124:Conserved Sequence / Q000235:genetics; D004247:DNA / Q000235:genetics; D004272:DNA, Mitochondrial / Q000737:chemistry* / Q000235:genetics*; D014644:Genetic Variation; D005843:Geography; D006041:Goats / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics*; D007558:Italy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny
chemical_list: D004272:DNA, Mitochondrial; D004247:DNA