Genetic diversity in Mexican creole donkeys

Genetic diversity in Mexican creole donkeys

The aim of this study was to evaluate the genetic diversity of the Mexican criollo donkey with SNP-type genetic markers. Sixteen individuals (eight males and eight females) were randomly sampled and genotyped using the GGP Equine 70K chip (71 947 loci). Within chromosome the polymorphic SNPs were identified, determining the expected (He) and observed (Ho) heterozygosity, polymorphic information content (PIC), the fixation index (FIS) and the Hardy-Weinberg equilibrium (HW). Linkage disequilibrium was assessed based on the correlation (r2) between frequencies across loci. An analysis of molecular variance (AMOVA) and a cluster study were performed to infer the number of clusters (k). It was found that 3579 loci (4.9%) presented genetic variability, but 24.9% presented HW disequilibrium (p<0.05). Across chromosomes, the number of polymorphic loci ranged from 50 to 269 with a mean of 115. The (within chromosome) means for PIC and FIS ranged from 0.222 to 0.267 and -0.392 to -0.208, respectively. In all chromosomes Ho was superior to He. For r2, the mean values within chromosome were greater than 0.10; the optimal k corresponded to 2. In the AMOVA, the genetic variability within individuals explained 67%. The SNPs identified as polymorphic make up a first panel of genetic markers for the Mexican creole burro, and the estimated genetic variability can be used in development and conservation schemes.

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Main Authors: Domínguez-Viveros, Joel, Rodríguez-Almeida, Felipe Alonso, Alonso-Alcalá, David, Barreda-Elizondo, Carlos, Ramírez-Reyes, Juan Manuel, García-Robles, Efreen, Aguilar-Palma, Guadalupe Nelson
Format: Digital revista
Language:spa
Published: Universidad Nacional Mayor de San Marcos, Facultad de Medicina Veterinaria 2022
Online Access:https://revistasinvestigacion.unmsm.edu.pe/index.php/veterinaria/article/view/21943
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record_format ojs
institution UNMSM
collection OJS
country Perú
countrycode PE
component Revista
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databasecode rev-rivep
tag revista
region America del Sur
libraryname Biblioteca de la Facultad de Medicina Veterinaria
language spa
format Digital
author Domínguez-Viveros, Joel
Rodríguez-Almeida, Felipe Alonso
Alonso-Alcalá, David
Barreda-Elizondo, Carlos
Ramírez-Reyes, Juan Manuel
García-Robles, Efreen
Aguilar-Palma, Guadalupe Nelson
spellingShingle Domínguez-Viveros, Joel
Rodríguez-Almeida, Felipe Alonso
Alonso-Alcalá, David
Barreda-Elizondo, Carlos
Ramírez-Reyes, Juan Manuel
García-Robles, Efreen
Aguilar-Palma, Guadalupe Nelson
Genetic diversity in Mexican creole donkeys
author_facet Domínguez-Viveros, Joel
Rodríguez-Almeida, Felipe Alonso
Alonso-Alcalá, David
Barreda-Elizondo, Carlos
Ramírez-Reyes, Juan Manuel
García-Robles, Efreen
Aguilar-Palma, Guadalupe Nelson
author_sort Domínguez-Viveros, Joel
title Genetic diversity in Mexican creole donkeys
title_short Genetic diversity in Mexican creole donkeys
title_full Genetic diversity in Mexican creole donkeys
title_fullStr Genetic diversity in Mexican creole donkeys
title_full_unstemmed Genetic diversity in Mexican creole donkeys
title_sort genetic diversity in mexican creole donkeys
description The aim of this study was to evaluate the genetic diversity of the Mexican criollo donkey with SNP-type genetic markers. Sixteen individuals (eight males and eight females) were randomly sampled and genotyped using the GGP Equine 70K chip (71 947 loci). Within chromosome the polymorphic SNPs were identified, determining the expected (He) and observed (Ho) heterozygosity, polymorphic information content (PIC), the fixation index (FIS) and the Hardy-Weinberg equilibrium (HW). Linkage disequilibrium was assessed based on the correlation (r2) between frequencies across loci. An analysis of molecular variance (AMOVA) and a cluster study were performed to infer the number of clusters (k). It was found that 3579 loci (4.9%) presented genetic variability, but 24.9% presented HW disequilibrium (p<0.05). Across chromosomes, the number of polymorphic loci ranged from 50 to 269 with a mean of 115. The (within chromosome) means for PIC and FIS ranged from 0.222 to 0.267 and -0.392 to -0.208, respectively. In all chromosomes Ho was superior to He. For r2, the mean values within chromosome were greater than 0.10; the optimal k corresponded to 2. In the AMOVA, the genetic variability within individuals explained 67%. The SNPs identified as polymorphic make up a first panel of genetic markers for the Mexican creole burro, and the estimated genetic variability can be used in development and conservation schemes.
publisher Universidad Nacional Mayor de San Marcos, Facultad de Medicina Veterinaria
publishDate 2022
url https://revistasinvestigacion.unmsm.edu.pe/index.php/veterinaria/article/view/21943
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spelling oai:ojs.csi.unmsm:article-219432022-09-01T07:16:53Z Genetic diversity in Mexican creole donkeys Diversidad genética en burros criollos de México Domínguez-Viveros, Joel Rodríguez-Almeida, Felipe Alonso Alonso-Alcalá, David Barreda-Elizondo, Carlos Ramírez-Reyes, Juan Manuel García-Robles, Efreen Aguilar-Palma, Guadalupe Nelson genetic marker AMOVA Hardy-Weinberg equilibrium linkage disequilibrium heterozygosity marcador genético AMOVA equilibrio Hardy-Weinberg desequilibrio ligamiento heterocigosis The aim of this study was to evaluate the genetic diversity of the Mexican criollo donkey with SNP-type genetic markers. Sixteen individuals (eight males and eight females) were randomly sampled and genotyped using the GGP Equine 70K chip (71 947 loci). Within chromosome the polymorphic SNPs were identified, determining the expected (He) and observed (Ho) heterozygosity, polymorphic information content (PIC), the fixation index (FIS) and the Hardy-Weinberg equilibrium (HW). Linkage disequilibrium was assessed based on the correlation (r2) between frequencies across loci. An analysis of molecular variance (AMOVA) and a cluster study were performed to infer the number of clusters (k). It was found that 3579 loci (4.9%) presented genetic variability, but 24.9% presented HW disequilibrium (p<0.05). Across chromosomes, the number of polymorphic loci ranged from 50 to 269 with a mean of 115. The (within chromosome) means for PIC and FIS ranged from 0.222 to 0.267 and -0.392 to -0.208, respectively. In all chromosomes Ho was superior to He. For r2, the mean values within chromosome were greater than 0.10; the optimal k corresponded to 2. In the AMOVA, the genetic variability within individuals explained 67%. The SNPs identified as polymorphic make up a first panel of genetic markers for the Mexican creole burro, and the estimated genetic variability can be used in development and conservation schemes. El estudio tuvo como objetivo evaluar la diversidad genética del burro criollo mexicano con marcadores genéticos de tipo SNP. Se muestreó aleatoriamente a 16 individuos (ocho machos y ocho hembras) y el genotipado se hizo con el chip GGP Equine 70K (71 947 loci). Dentro de cromosoma se identificaron los SNP polimórficos, determinándose la heterocigosis esperada (He) y observada (Ho), contenido de información polimórfica (CIP), el índice de fijación (FIS) y el equilibrio (HW) Hardy-Weinberg. El desequilibrio de ligamiento se evaluó con base en la correlación (r2) entre frecuencias a través de locus. Se realizó un análisis de varianza molecular (AMOVA) y un estudio de agrupamiento para inferir el número de cluster (k). Se encontró que 3579 loci (4.9%) presentaron variabilidad genética, pero el 24.9% presentó desequilibrio HW (p<0.05). A través de cromosomas, el número de loci polimórficos osciló de 50 a 269 con un promedio de 115. Los promedios (dentro de cromosoma) para PIC y FIS fluctuaron de 0.222 a 0.267 y de -0.392 a -0.208, respectivamente. En todos los cromosomas Ho fue superior a He. Para r2, los valores promedio dentro de cromosoma fueron superior a 0.10; el k óptimo correspondió a 2. En el AMOVA, la variabilidad genética dentro de individuos explicó el 67%. Los SNP identificados como polimórficos, conforman un primer panel de marcadores genéticos para el burro criollo mexicano, y la variabilidad genética estimada puede ser utilizada en esquemas de desarrollo y conservación. Universidad Nacional Mayor de San Marcos, Facultad de Medicina Veterinaria 2022-08-31 info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/article application/pdf https://revistasinvestigacion.unmsm.edu.pe/index.php/veterinaria/article/view/21943 10.15381/rivep.v33i4.21943 Revista de Investigaciones Veterinarias del Perú; Vol. 33 No. 4 (2022); e21943 Revista de Investigaciones Veterinarias del Perú; Vol. 33 Núm. 4 (2022); e21943 1682-3419 1609-9117 spa https://revistasinvestigacion.unmsm.edu.pe/index.php/veterinaria/article/view/21943/18635 Derechos de autor 2022 Joel Domínguez-Viveros, Felipe Alonso Rodríguez-Almeida, David Alonso-Alcalá, Carlos Barreda-Elizondo, Juan Manuel Ramírez-Reyes, Efreen García-Robles, Guadalupe Nelson Aguilar-Palma http://creativecommons.org/licenses/by/4.0

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