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Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes

SIMPLE SUMMARY: Domestic livestock diversity is an important component of global biodiversity and molecular data have become essential for the characterization of genetic diversity in cattle. The aim of this study was to assess the effectiveness of a 30-short tandem repeat (STR) panel and reveal the...

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Autores principales: Gamarra, David, Taniguchi, Masaaki, Aldai, Noelia, Arakawa, Aisaku, Lopez-Oceja, Andres, de Pancorbo, Marian M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7552125/
https://www.ncbi.nlm.nih.gov/pubmed/32899488
http://dx.doi.org/10.3390/ani10091584
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author Gamarra, David
Taniguchi, Masaaki
Aldai, Noelia
Arakawa, Aisaku
Lopez-Oceja, Andres
de Pancorbo, Marian M.
author_facet Gamarra, David
Taniguchi, Masaaki
Aldai, Noelia
Arakawa, Aisaku
Lopez-Oceja, Andres
de Pancorbo, Marian M.
author_sort Gamarra, David
collection PubMed
description SIMPLE SUMMARY: Domestic livestock diversity is an important component of global biodiversity and molecular data have become essential for the characterization of genetic diversity in cattle. The aim of this study was to assess the effectiveness of a 30-short tandem repeat (STR) panel and reveal the genetic structure of a local Pirenaica breed compared with other breeds (Terreña, Blonde d’Aquitaine, Limousin, Salers and Holstein-Friesian) typically raised in the same geographic Basque region. The proposed STR panel could be used as an appropriate genetic tool to trace Pirenaica animals and their Protected Geographic Indication (PGI) products. ABSTRACT: Pirenaica is the most important autochthonous cattle breed within the Protected Geographic Indication (PGI) beef quality label in the Basque region, in northern Spain. The short tandem repeats (STRs) are powerful markers to elucidate forensic cases and traceability across the agri-food sector. The main objective of the present work was to study the phylogenetic relationships of Pirenaica cattle and other breeds typically raised in the region and provide the minimum number of STR markers for parentage and traceability purposes. The 30-STR panel recommended by the International Society of Animal Genetics-Food and Agriculture Organization of the United Nations (ISAG-FAO) was compared against other commercial STR panels. The 30-STR panel showed a combined matching probability of 1.89 × 10(−25) and a power of exclusion for duos of 0.99998. However, commercial STR panels showed a limited efficiency for a reliable parentage analysis in Pirenaica, and at least a 21-STR panel is needed to reach a power of exclusion of 0.9999. Machine-learning analysis also demonstrated a 95% accuracy in assignments selecting the markers with the highest F(ST) in Pirenaica individuals. Overall, the present study shows the genetic characterization of Pirenaica and its phylogeny compared with other breeds typically raised in the Basque region. Finally, a 21-STR panel with the highest F(ST) markers is proposed for a confident parentage analysis and high traceability.
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spelling pubmed-75521252020-10-16 Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes Gamarra, David Taniguchi, Masaaki Aldai, Noelia Arakawa, Aisaku Lopez-Oceja, Andres de Pancorbo, Marian M. Animals (Basel) Article SIMPLE SUMMARY: Domestic livestock diversity is an important component of global biodiversity and molecular data have become essential for the characterization of genetic diversity in cattle. The aim of this study was to assess the effectiveness of a 30-short tandem repeat (STR) panel and reveal the genetic structure of a local Pirenaica breed compared with other breeds (Terreña, Blonde d’Aquitaine, Limousin, Salers and Holstein-Friesian) typically raised in the same geographic Basque region. The proposed STR panel could be used as an appropriate genetic tool to trace Pirenaica animals and their Protected Geographic Indication (PGI) products. ABSTRACT: Pirenaica is the most important autochthonous cattle breed within the Protected Geographic Indication (PGI) beef quality label in the Basque region, in northern Spain. The short tandem repeats (STRs) are powerful markers to elucidate forensic cases and traceability across the agri-food sector. The main objective of the present work was to study the phylogenetic relationships of Pirenaica cattle and other breeds typically raised in the region and provide the minimum number of STR markers for parentage and traceability purposes. The 30-STR panel recommended by the International Society of Animal Genetics-Food and Agriculture Organization of the United Nations (ISAG-FAO) was compared against other commercial STR panels. The 30-STR panel showed a combined matching probability of 1.89 × 10(−25) and a power of exclusion for duos of 0.99998. However, commercial STR panels showed a limited efficiency for a reliable parentage analysis in Pirenaica, and at least a 21-STR panel is needed to reach a power of exclusion of 0.9999. Machine-learning analysis also demonstrated a 95% accuracy in assignments selecting the markers with the highest F(ST) in Pirenaica individuals. Overall, the present study shows the genetic characterization of Pirenaica and its phylogeny compared with other breeds typically raised in the Basque region. Finally, a 21-STR panel with the highest F(ST) markers is proposed for a confident parentage analysis and high traceability. MDPI 2020-09-05 /pmc/articles/PMC7552125/ /pubmed/32899488 http://dx.doi.org/10.3390/ani10091584 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Gamarra, David
Taniguchi, Masaaki
Aldai, Noelia
Arakawa, Aisaku
Lopez-Oceja, Andres
de Pancorbo, Marian M.
Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes
title Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes
title_full Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes
title_fullStr Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes
title_full_unstemmed Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes
title_short Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes
title_sort genetic characterization of the local pirenaica cattle for parentage and traceability purposes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7552125/
https://www.ncbi.nlm.nih.gov/pubmed/32899488
http://dx.doi.org/10.3390/ani10091584
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