Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru
Goat farming constitutes a significant source of income for farmers in northern Peru. There is currently an absence of information about the genetics of Peruvian Creole goats that would enable us to understand their origins and genetic spread. The objective of this study was to estimate the genetic...
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| Format: | info:eu-repo/semantics/article |
| Language: | Inglés |
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Elsevier
2024
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| Online Access: | https://hdl.handle.net/20.500.12955/2495 https://doi.org/10.1016/j.livsci.2024.105473 |
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| author | Corredor Arizapana, Flor Anita Figueroa Venegas, Deyanira Antonella Estrada Cañari, Richard Burgos Paz, William Salazar Coronel, Wilian Cruz Góngora, Wilder Lobato Gálvez, Roiser Honorio Injante Silva, Pedro Hugo Godoy Padilla, David José Barrantes Bravo, Christian Alfredo Ganoza Roncal, Jorge Juan Cruz Luis, Juancarlos Alejandro Arbizu Berrocal, Carlos Irvin |
| author_browse | Arbizu Berrocal, Carlos Irvin Barrantes Bravo, Christian Alfredo Burgos Paz, William Corredor Arizapana, Flor Anita Cruz Góngora, Wilder Cruz Luis, Juancarlos Alejandro Estrada Cañari, Richard Figueroa Venegas, Deyanira Antonella Ganoza Roncal, Jorge Juan Godoy Padilla, David José Injante Silva, Pedro Hugo Lobato Gálvez, Roiser Honorio Salazar Coronel, Wilian |
| author_facet | Corredor Arizapana, Flor Anita Figueroa Venegas, Deyanira Antonella Estrada Cañari, Richard Burgos Paz, William Salazar Coronel, Wilian Cruz Góngora, Wilder Lobato Gálvez, Roiser Honorio Injante Silva, Pedro Hugo Godoy Padilla, David José Barrantes Bravo, Christian Alfredo Ganoza Roncal, Jorge Juan Cruz Luis, Juancarlos Alejandro Arbizu Berrocal, Carlos Irvin |
| author_sort | Corredor Arizapana, Flor Anita |
| collection | Repositorio INIA |
| description | Goat farming constitutes a significant source of income for farmers in northern Peru. There is currently an absence of information about the genetics of Peruvian Creole goats that would enable us to understand their origins and genetic spread. The objective of this study was to estimate the genetic diversity of Creole goats from northern Peru using SNP markers. This study involved the collection of 192 male Creole goats from three key goat production geographical departments in northern Peru. These goat samples were genotyped using the GGPGoat70k SNP panel. To explore the genetic influence of other breeds on Peruvian Creole goats, our dataset was combined with previously published SNP genotypes. External data set includes multiple breeds genotypes sampled from Argentina, Brazil, Spain, and Alpine breed from Italy, France, and Switzerland. After quality control 52,832 autosomal SNPs were used to assess genetic diversity in the Peruvian goats. For the population structure analysis of the merged data 20,513 common SNPs were used. Estimations for expected heterozygosity (He), observed heterozygosity (Ho), and inbreeding coefficient (FIS) were computed for the Peruvian groups. AMOVA, principal component analysis and ADMIXTURE were conducted to evaluate the population structure in the two data sets, Peru and merged. The results revealed a considerable genetic diversity, with Ho values ranging from 0.40 to 0.41 for the Peruvian sampling groups, and inbreeding coefficient was notably low for Peruvian goat. The population structure analysis demonstrated a distinction (p < 0.05) from other breeds. These findings suggest a level of genetic differentiation of the Peruvian goat population among other breeds, although further research is needed considering samples from other Peruvian areas. We expect this study will contribute to define genetic management strategies to prevent the loss of genetic diversity in Peruvian goat populations and for upcoming advancements in this field. |
| format | info:eu-repo/semantics/article |
| id | INIA2495 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Elsevier |
| publisherStr | Elsevier |
| record_format | dspace |
| spelling | INIA24952024-05-06T17:53:26Z Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru Corredor Arizapana, Flor Anita Figueroa Venegas, Deyanira Antonella Estrada Cañari, Richard Burgos Paz, William Salazar Coronel, Wilian Cruz Góngora, Wilder Lobato Gálvez, Roiser Honorio Injante Silva, Pedro Hugo Godoy Padilla, David José Barrantes Bravo, Christian Alfredo Ganoza Roncal, Jorge Juan Cruz Luis, Juancarlos Alejandro Arbizu Berrocal, Carlos Irvin Genetic resources Genomics Genotyping Creole goat https://purl.org/pe-repo/ocde/ford#4.02.01 Genetic resources Recurso genético Genomics Genómica Genotyping Genotipado Caprinos Goats Goat farming constitutes a significant source of income for farmers in northern Peru. There is currently an absence of information about the genetics of Peruvian Creole goats that would enable us to understand their origins and genetic spread. The objective of this study was to estimate the genetic diversity of Creole goats from northern Peru using SNP markers. This study involved the collection of 192 male Creole goats from three key goat production geographical departments in northern Peru. These goat samples were genotyped using the GGPGoat70k SNP panel. To explore the genetic influence of other breeds on Peruvian Creole goats, our dataset was combined with previously published SNP genotypes. External data set includes multiple breeds genotypes sampled from Argentina, Brazil, Spain, and Alpine breed from Italy, France, and Switzerland. After quality control 52,832 autosomal SNPs were used to assess genetic diversity in the Peruvian goats. For the population structure analysis of the merged data 20,513 common SNPs were used. Estimations for expected heterozygosity (He), observed heterozygosity (Ho), and inbreeding coefficient (FIS) were computed for the Peruvian groups. AMOVA, principal component analysis and ADMIXTURE were conducted to evaluate the population structure in the two data sets, Peru and merged. The results revealed a considerable genetic diversity, with Ho values ranging from 0.40 to 0.41 for the Peruvian sampling groups, and inbreeding coefficient was notably low for Peruvian goat. The population structure analysis demonstrated a distinction (p < 0.05) from other breeds. These findings suggest a level of genetic differentiation of the Peruvian goat population among other breeds, although further research is needed considering samples from other Peruvian areas. We expect this study will contribute to define genetic management strategies to prevent the loss of genetic diversity in Peruvian goat populations and for upcoming advancements in this field. 2024-05-06T17:53:24Z 2024-05-06T17:53:24Z 2024-04-24 info:eu-repo/semantics/article Corredor-Arizapana, F. A.; Figueroa-Venegas, D. A.; Estrada-Cañari, R.; Burgos-Paz, W.; Salazar-Coronel, W.; Cruz-Góngora, W.; Lobato-Gálvez, R. H.; Injante-Silva, P. H.; Godoy-Padilla, D. J.; Barrantes-Bravo, C. A.; Ganoza-Roncal, J. J; Cruz-Luis, J. A.; & Arbizu-Berrocal, C. I. (2024). Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru. Livestock Science, 283, 105473. doi: 10.1016/j.livsci.2024.105473 1871-1413 https://hdl.handle.net/20.500.12955/2495 https://doi.org/10.1016/j.livsci.2024.105473 eng urn:issn:1871-1413 Livestock Science info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc/4.0/ application/pdf application/pdf Elsevier NL Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
| spellingShingle | Genetic resources Genomics Genotyping Creole goat https://purl.org/pe-repo/ocde/ford#4.02.01 Genetic resources Recurso genético Genomics Genómica Genotyping Genotipado Caprinos Goats Corredor Arizapana, Flor Anita Figueroa Venegas, Deyanira Antonella Estrada Cañari, Richard Burgos Paz, William Salazar Coronel, Wilian Cruz Góngora, Wilder Lobato Gálvez, Roiser Honorio Injante Silva, Pedro Hugo Godoy Padilla, David José Barrantes Bravo, Christian Alfredo Ganoza Roncal, Jorge Juan Cruz Luis, Juancarlos Alejandro Arbizu Berrocal, Carlos Irvin Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru |
| title | Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru |
| title_full | Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru |
| title_fullStr | Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru |
| title_full_unstemmed | Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru |
| title_short | Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru |
| title_sort | genome wide single nucleotide polymorphisms reveal the genetic diversity and population structure of creole goats from northern peru |
| topic | Genetic resources Genomics Genotyping Creole goat https://purl.org/pe-repo/ocde/ford#4.02.01 Genetic resources Recurso genético Genomics Genómica Genotyping Genotipado Caprinos Goats |
| url | https://hdl.handle.net/20.500.12955/2495 https://doi.org/10.1016/j.livsci.2024.105473 |
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