Haplotype Affinities Resolve a Major Component of Goat (Capra hircus) MtDNA D-Loop Diversity and Reveal Specific Features of the Sardinian Stock

Daniela Piras,Rossana Cammelli,Graziano Lai,Salvatore Naitana,Piergiorgio Demuro,Sandro Cui,Mario Pirastu,Giuseppina Casu,Francesca Marchiori,Ombretta Querci,Simona Vaccargiu,Maria Grazia Doro,Roberto Piras,Salvatore Sale,Franco Atzori,Giuseppe Argiolas,Paolo Mereu,Andrea Novelletto,Roberto Boi,Walter Cattari,Pier Paolo Loddo,Debora Parracciani,Roberta Stradoni,Bruno Frongia,Ignazio S Piras ,A Spiga ,Gian Franco Pili ,Giovanni Leoni ,M Mancosu ,Paola Melis

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.

Highlights

The genetics of domestic goat, Capra hircus, has recently received considerable interest to understand various breeding aspects
Patterns of DNA diversity We sampled the Sardinian goat population from 5 Sardinian subregions comprising 1,591 specimens analyzed in the current study (Table 1, Fig. 1 and Table S1)
We explored the mtDNA D-loop variation in a large sample of animals grown by breeders in the entire Southern part of the island of Sardinia by examining a DNA region exactly overlapping previous studies

Summary

Introduction

The genetics of domestic goat, Capra hircus, has recently received considerable interest to understand various breeding aspects. Polymorphism of the mitochondrial (mtDNA) control region has been the tool of choice to initially describe the diversity of extant breeds and to reconstruct the places and timing of domestication [1,2,3,4,5,6,7,8]. A first exploration of goat mtDNA diversity [2] revealed three divergent lineages which increased to six in a large series of samples collected worldwide [5].

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Conclusion