REDUCED PANEL OF SINGLE-NUCLEOTIDE POLYMORPHISMS FOR BIODIVERSITY STUDIES IN BOVINES
The aim of this work was to evaluate a reduced panel of 200 single-nucleotide polymorphisms markers recommended by International Society of Animal Genetics and the International Committee for Animal Recording, using Next Gen Sequencing sequencing. Parameters such as number of usable loci, loci polymorphism, observed heterozygosis (Hob) and expected (He), average molecular diversity per loci (DML), distance between populations, fixation index that estimates the coefficient of inbreeding (Fis) and genetic differentiation value between populations (Fst). Of the total loci used, an average of 186 usable alleles were observed: maximum of 187 in the Guabala breed and a minimum of 183 in the Brahman. An average of 174 polymorphic loci with a maximum of 184 in crossed genotypes and a minimum of 149 in the Guabala breed. The values of Hob, He and DML were 0,378, 0,439 and 0,438, respectively. The molecular Analysis of Variance (AMOVA) showed a percentage of variation between populations of 19,25 and Fst index of 0,19. The percentage of variation and Fst between the Panamanian Creole and Zebu breeds were 5,22% and 0,22, respectively and the percentage of variation between Creole and Taurine breeds was 1,82% with genetic differentiation value (Fst) of 0,163, respectively. The Fis values ranged from 0,00302 (Guaymi) to 0,04333 (Holstein); negative values of Fis were observed for Senepol and Guabala breeds, so a Wahlund effect is presumed. The tree of circular distances showed a similar behavior to those reported in a previous work carried out with microsatellites, as was observed in the AMOVA and Fst in the populations. Preliminary results suggest that the single nucleotide polymorphism markers used have potential for genetic diversity studies and it is recommended to extend the study to more breeds and numbers of animals.
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Instituto de Innovación Agropecuaria de Panamá
2020
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Villalobos-Cortés, Axel González, Rita Murillo, Manuel Castillo, Hilda |
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Villalobos-Cortés, Axel González, Rita Murillo, Manuel Castillo, Hilda REDUCED PANEL OF SINGLE-NUCLEOTIDE POLYMORPHISMS FOR BIODIVERSITY STUDIES IN BOVINES |
| author_facet |
Villalobos-Cortés, Axel González, Rita Murillo, Manuel Castillo, Hilda |
| author_sort |
Villalobos-Cortés, Axel |
| title |
REDUCED PANEL OF SINGLE-NUCLEOTIDE POLYMORPHISMS FOR BIODIVERSITY STUDIES IN BOVINES |
| title_short |
REDUCED PANEL OF SINGLE-NUCLEOTIDE POLYMORPHISMS FOR BIODIVERSITY STUDIES IN BOVINES |
| title_full |
REDUCED PANEL OF SINGLE-NUCLEOTIDE POLYMORPHISMS FOR BIODIVERSITY STUDIES IN BOVINES |
| title_fullStr |
REDUCED PANEL OF SINGLE-NUCLEOTIDE POLYMORPHISMS FOR BIODIVERSITY STUDIES IN BOVINES |
| title_full_unstemmed |
REDUCED PANEL OF SINGLE-NUCLEOTIDE POLYMORPHISMS FOR BIODIVERSITY STUDIES IN BOVINES |
| title_sort |
reduced panel of single-nucleotide polymorphisms for biodiversity studies in bovines |
| description |
The aim of this work was to evaluate a reduced panel of 200 single-nucleotide polymorphisms markers recommended by International Society of Animal Genetics and the International Committee for Animal Recording, using Next Gen Sequencing sequencing. Parameters such as number of usable loci, loci polymorphism, observed heterozygosis (Hob) and expected (He), average molecular diversity per loci (DML), distance between populations, fixation index that estimates the coefficient of inbreeding (Fis) and genetic differentiation value between populations (Fst). Of the total loci used, an average of 186 usable alleles were observed: maximum of 187 in the Guabala breed and a minimum of 183 in the Brahman. An average of 174 polymorphic loci with a maximum of 184 in crossed genotypes and a minimum of 149 in the Guabala breed. The values of Hob, He and DML were 0,378, 0,439 and 0,438, respectively. The molecular Analysis of Variance (AMOVA) showed a percentage of variation between populations of 19,25 and Fst index of 0,19. The percentage of variation and Fst between the Panamanian Creole and Zebu breeds were 5,22% and 0,22, respectively and the percentage of variation between Creole and Taurine breeds was 1,82% with genetic differentiation value (Fst) of 0,163, respectively. The Fis values ranged from 0,00302 (Guaymi) to 0,04333 (Holstein); negative values of Fis were observed for Senepol and Guabala breeds, so a Wahlund effect is presumed. The tree of circular distances showed a similar behavior to those reported in a previous work carried out with microsatellites, as was observed in the AMOVA and Fst in the populations. Preliminary results suggest that the single nucleotide polymorphism markers used have potential for genetic diversity studies and it is recommended to extend the study to more breeds and numbers of animals. |
| publisher |
Instituto de Innovación Agropecuaria de Panamá |
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2020 |
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http://www.revistacienciaagropecuaria.ac.pa/index.php/ciencia-agropecuaria/article/view/298 |
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oai:ojs.revistacienciaagropecuaria.ac.pa:article-2982023-01-24T19:59:46Z REDUCED PANEL OF SINGLE-NUCLEOTIDE POLYMORPHISMS FOR BIODIVERSITY STUDIES IN BOVINES PANEL REDUCIDO DE POLIMORFISMOS DE NUCLEÓTIDO SIMPLE PARA ESTUDIOS DE BIODIVERSIDAD EN BOVINOS Villalobos-Cortés, Axel González, Rita Murillo, Manuel Castillo, Hilda The aim of this work was to evaluate a reduced panel of 200 single-nucleotide polymorphisms markers recommended by International Society of Animal Genetics and the International Committee for Animal Recording, using Next Gen Sequencing sequencing. Parameters such as number of usable loci, loci polymorphism, observed heterozygosis (Hob) and expected (He), average molecular diversity per loci (DML), distance between populations, fixation index that estimates the coefficient of inbreeding (Fis) and genetic differentiation value between populations (Fst). Of the total loci used, an average of 186 usable alleles were observed: maximum of 187 in the Guabala breed and a minimum of 183 in the Brahman. An average of 174 polymorphic loci with a maximum of 184 in crossed genotypes and a minimum of 149 in the Guabala breed. The values of Hob, He and DML were 0,378, 0,439 and 0,438, respectively. The molecular Analysis of Variance (AMOVA) showed a percentage of variation between populations of 19,25 and Fst index of 0,19. The percentage of variation and Fst between the Panamanian Creole and Zebu breeds were 5,22% and 0,22, respectively and the percentage of variation between Creole and Taurine breeds was 1,82% with genetic differentiation value (Fst) of 0,163, respectively. The Fis values ranged from 0,00302 (Guaymi) to 0,04333 (Holstein); negative values of Fis were observed for Senepol and Guabala breeds, so a Wahlund effect is presumed. The tree of circular distances showed a similar behavior to those reported in a previous work carried out with microsatellites, as was observed in the AMOVA and Fst in the populations. Preliminary results suggest that the single nucleotide polymorphism markers used have potential for genetic diversity studies and it is recommended to extend the study to more breeds and numbers of animals. El objetivo de este trabajo fue evaluar un panel reducido de 200 marcadores de polimorfismo de nucleótido simple recomendados por la Sociedad Internacional de Genética Animal y el Comité Internacional de Registro de Animales, mediante secuenciación de siguiente generación. Se utilizaron parámetros como número de loci utilizables, polimorfismo de loci, heterocigosis observada (Hob) y esperada (He), diversidad molecular media por loci (DML), distancia entre poblaciones, índice de fijación que estima el coeficiente de endogamia (Fis) y valor de diferenciación genética entre poblaciones (Fst). Del total de loci utilizados, se observó un promedio de 186 alelos utilizables; máximo de 187 en la raza Guabalá y un mínimo de 183 en la Brahman. Una media de 174 loci polimórficos con un máximo de 184 en genotipos cruzados y un mínimo de 149 en la raza Guabalá. Los valores de Hob, He y DML fueron 0,378, 0,439 y 0,438, respectivamente. El Análisis Molecular de Varianza (AMOVA) mostró un porcentaje de variación entre poblaciones de 19,25 e índice Fst de 0,19. El porcentaje de variación y Fst entre las razas criollas panameñas y cebuinas fueron de 5,22% y 0,22, respectivamente y el porcentaje de variación entre razas criollas y taurinas fue 1,82 con índice de diferenciación genética Fst de 0,163, respectivamente. Los valores de endogamia (Fis) oscilaron entre 0,00302 (Guaymí) a 0,04333 (Holstein); valores negativos de Fis se observaron en la raza Senepol y Guabalá por lo que se presume un efecto Wahlund. El árbol de distancias circulares mostró un comportamiento similar a los reportados en trabajos realizados con microsatélites al igual que lo observado en el AMOVA y Fst en las poblaciones. Los resultados preliminares apuntan a que los marcadores de polimorfismo de nucleótido simple utilizados tienen potencial para estudios de diversidad genética y se recomienda ampliar el estudio a más razas y números de animales. Instituto de Innovación Agropecuaria de Panamá 2020-12-08 info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Artículo revisado por pares application/pdf http://www.revistacienciaagropecuaria.ac.pa/index.php/ciencia-agropecuaria/article/view/298 Ciencia Agropecuaria; Núm. 31 (2020): CIENCIA AGROPECUARIA; 19-36 2414-3278 0258-6452 spa http://www.revistacienciaagropecuaria.ac.pa/index.php/ciencia-agropecuaria/article/view/298/237 |