Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock.
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...
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2012
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oai:doaj.org-article:b4b21cdb95d0458f9f7fbff7c1cdd0eb2021-11-18T07:27:44ZHaplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock.1932-620310.1371/journal.pone.0030785https://doaj.org/article/b4b21cdb95d0458f9f7fbff7c1cdd0eb2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22363488/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Goat 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.Daniela PirasMaria Grazia DoroGiuseppina CasuPaola Maria MelisSimona VaccargiuIgnazio PirasDebora ParraccianiRoberta StradoniBruno FrongiaGraziano LaiSalvatore SaleWalter CattariRoberto PirasOmbretta QuerciPiergiorgio DemuroSandro CuiFranco AtzoriMarco MancosuFrancesca MarchioriRossana CammelliAlessandra SpigaPier Paolo LoddoGianfranco PiliRoberto BoiGiuseppe ArgiolasPaolo MereuGiovanni Giuseppe LeoniSalvatore NaitanaMario PirastuAndrea NovellettoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 2, p e30785 (2012) |
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Medicine R Science Q Daniela Piras Maria Grazia Doro Giuseppina Casu Paola Maria Melis Simona Vaccargiu Ignazio Piras Debora Parracciani Roberta Stradoni Bruno Frongia Graziano Lai Salvatore Sale Walter Cattari Roberto Piras Ombretta Querci Piergiorgio Demuro Sandro Cui Franco Atzori Marco Mancosu Francesca Marchiori Rossana Cammelli Alessandra Spiga Pier Paolo Loddo Gianfranco Pili Roberto Boi Giuseppe Argiolas Paolo Mereu Giovanni Giuseppe Leoni Salvatore Naitana Mario Pirastu Andrea Novelletto Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock. |
| description |
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. |
| format |
article |
| author |
Daniela Piras Maria Grazia Doro Giuseppina Casu Paola Maria Melis Simona Vaccargiu Ignazio Piras Debora Parracciani Roberta Stradoni Bruno Frongia Graziano Lai Salvatore Sale Walter Cattari Roberto Piras Ombretta Querci Piergiorgio Demuro Sandro Cui Franco Atzori Marco Mancosu Francesca Marchiori Rossana Cammelli Alessandra Spiga Pier Paolo Loddo Gianfranco Pili Roberto Boi Giuseppe Argiolas Paolo Mereu Giovanni Giuseppe Leoni Salvatore Naitana Mario Pirastu Andrea Novelletto |
| author_facet |
Daniela Piras Maria Grazia Doro Giuseppina Casu Paola Maria Melis Simona Vaccargiu Ignazio Piras Debora Parracciani Roberta Stradoni Bruno Frongia Graziano Lai Salvatore Sale Walter Cattari Roberto Piras Ombretta Querci Piergiorgio Demuro Sandro Cui Franco Atzori Marco Mancosu Francesca Marchiori Rossana Cammelli Alessandra Spiga Pier Paolo Loddo Gianfranco Pili Roberto Boi Giuseppe Argiolas Paolo Mereu Giovanni Giuseppe Leoni Salvatore Naitana Mario Pirastu Andrea Novelletto |
| author_sort |
Daniela Piras |
| title |
Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock. |
| title_short |
Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock. |
| title_full |
Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock. |
| title_fullStr |
Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock. |
| title_full_unstemmed |
Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock. |
| title_sort |
haplotype affinities resolve a major component of goat (capra hircus) mtdna d-loop diversity and reveal specific features of the sardinian stock. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2012 |
| url |
https://doaj.org/article/b4b21cdb95d0458f9f7fbff7c1cdd0eb |
| work_keys_str_mv |
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