Genetic diversity and population structure of a Peruvian cattle herd using SNP data
New-generation sequencing technologies, among them SNP chips for massive genotyping, are useful for the effective management of genetic resources. To date, molecular studies in Peruvian cattle are still scarce. For the first time, the genetic diversity and population structure of a reproductive nucl...
| Autores principales: | , , , , , , , , , |
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| Formato: | info:eu-repo/semantics/article |
| Lenguaje: | Inglés |
| Publicado: |
Frontiers Media S.A.
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/20.500.12955/2126 https://doi.org/10.3389/fgene.2023.1073843 |
| _version_ | 1855028712641134592 |
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| author | Corredor Arizapana, Flor Anita Figueroa Venegas, Deyanira Antonella Estrada Cañari, Richard Salazar Coronel, Wilian Quilcate Pairazamán, Carlos Enrique Vásquez Pérez, Héctor Vladimir Gonzales Malca, Jhony Alberto Maicelo Quintana, Jorge Luis Medina Morales, Percy Edilberto Arbizu Berrocal, Carlos Irvin |
| author_browse | Arbizu Berrocal, Carlos Irvin Corredor Arizapana, Flor Anita Estrada Cañari, Richard Figueroa Venegas, Deyanira Antonella Gonzales Malca, Jhony Alberto Maicelo Quintana, Jorge Luis Medina Morales, Percy Edilberto Quilcate Pairazamán, Carlos Enrique Salazar Coronel, Wilian Vásquez Pérez, Héctor Vladimir |
| author_facet | Corredor Arizapana, Flor Anita Figueroa Venegas, Deyanira Antonella Estrada Cañari, Richard Salazar Coronel, Wilian Quilcate Pairazamán, Carlos Enrique Vásquez Pérez, Héctor Vladimir Gonzales Malca, Jhony Alberto Maicelo Quintana, Jorge Luis Medina Morales, Percy Edilberto Arbizu Berrocal, Carlos Irvin |
| author_sort | Corredor Arizapana, Flor Anita |
| collection | Repositorio INIA |
| description | New-generation sequencing technologies, among them SNP chips for massive genotyping, are useful for the effective management of genetic resources. To date, molecular studies in Peruvian cattle are still scarce. For the first time, the genetic diversity and population structure of a reproductive nucleus cattle herd of four commercial breeds from a Peruvian institution were determined. This nucleus comprises Brahman (N = 9), Braunvieh (N = 9), Gyr (N = 5), and Simmental (N = 15) breeds. Additionally, samples from a locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N = 9), were incorporated. Female individuals were genotyped with the GGPBovine100K and ma les with the BovineHD. Quality control, and the proportion of polymorphic SNPs, minor allele frequency, expected heterozygosity, observed heterozygosity, and inbreeding coefficient were estimated for the five breeds. Admixture, principal component analysis (PCA), and discriminant analysis of principal components (DAPC) were performed. Also, a dendrogram was constructed using the Neighbor-Joining clustering algorithm. The genetic diversity indices in all breeds showed a high proportion of polymorphic SNPs, varying from 51.42% in Gyr to 97.58% in AFB. Also, AFB showed the highest expected heterozygosity estimate (0.41 ± 0.01), while Brahman the lowest (0.33 ± 0.01). Besides, Braunvieh possessed the highest observed heterozygosity (0.43 ± 0.01), while Brahman the lowest (0.37 ± 0.02), indicating that Brahman was less diverse. According to the molecular variance analysis, 75.71% of the variance occurs within individuals, whereas 24.29% occurs among populations. The pairwise genetic differentiation estimates (FST) between breeds showed values that ranged from 0.08 (Braunvieh vs. AFB) to 0.37 (Brahman vs. Braunvieh). Similarly, pairwise Reynold’s distance ranged from 0.09 (Braunvieh vs. AFB) to 0.46 (Brahman vs. Braunvieh). The dendrogram, similar to the PCA, identified two groups, showing a clear separation between Bos indicus (Brahman and Gyr) and B. taurus breeds (Braunvieh, Simmental, and AFB). Simmental and Braunvieh grouped closely with the AFB cattle. Similar results were obtained for the population structure analysis with K = 2. The results from this study would contribute to the appropriate management, avoiding loss of genetic variability in these breeds and for future improvements in this nucleus. Additional work is needed to speed up the breeding process in the Peruvian cattle system. |
| format | info:eu-repo/semantics/article |
| id | INIA2126 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Frontiers Media S.A. |
| publisherStr | Frontiers Media S.A. |
| record_format | dspace |
| spelling | INIA21262023-04-21T19:57:00Z Genetic diversity and population structure of a Peruvian cattle herd using SNP data Corredor Arizapana, Flor Anita Figueroa Venegas, Deyanira Antonella Estrada Cañari, Richard Salazar Coronel, Wilian Quilcate Pairazamán, Carlos Enrique Vásquez Pérez, Héctor Vladimir Gonzales Malca, Jhony Alberto Maicelo Quintana, Jorge Luis Medina Morales, Percy Edilberto Arbizu Berrocal, Carlos Irvin Cattle breeds Genotypes Diversity Genomics Next generation sequencing https://purl.org/pe-repo/ocde/ford#4.04.01 Cattle breeds Species diversity Genomics High-throughput sequencing Population structure Single nucleotide polymorphism New-generation sequencing technologies, among them SNP chips for massive genotyping, are useful for the effective management of genetic resources. To date, molecular studies in Peruvian cattle are still scarce. For the first time, the genetic diversity and population structure of a reproductive nucleus cattle herd of four commercial breeds from a Peruvian institution were determined. This nucleus comprises Brahman (N = 9), Braunvieh (N = 9), Gyr (N = 5), and Simmental (N = 15) breeds. Additionally, samples from a locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N = 9), were incorporated. Female individuals were genotyped with the GGPBovine100K and ma les with the BovineHD. Quality control, and the proportion of polymorphic SNPs, minor allele frequency, expected heterozygosity, observed heterozygosity, and inbreeding coefficient were estimated for the five breeds. Admixture, principal component analysis (PCA), and discriminant analysis of principal components (DAPC) were performed. Also, a dendrogram was constructed using the Neighbor-Joining clustering algorithm. The genetic diversity indices in all breeds showed a high proportion of polymorphic SNPs, varying from 51.42% in Gyr to 97.58% in AFB. Also, AFB showed the highest expected heterozygosity estimate (0.41 ± 0.01), while Brahman the lowest (0.33 ± 0.01). Besides, Braunvieh possessed the highest observed heterozygosity (0.43 ± 0.01), while Brahman the lowest (0.37 ± 0.02), indicating that Brahman was less diverse. According to the molecular variance analysis, 75.71% of the variance occurs within individuals, whereas 24.29% occurs among populations. The pairwise genetic differentiation estimates (FST) between breeds showed values that ranged from 0.08 (Braunvieh vs. AFB) to 0.37 (Brahman vs. Braunvieh). Similarly, pairwise Reynold’s distance ranged from 0.09 (Braunvieh vs. AFB) to 0.46 (Brahman vs. Braunvieh). The dendrogram, similar to the PCA, identified two groups, showing a clear separation between Bos indicus (Brahman and Gyr) and B. taurus breeds (Braunvieh, Simmental, and AFB). Simmental and Braunvieh grouped closely with the AFB cattle. Similar results were obtained for the population structure analysis with K = 2. The results from this study would contribute to the appropriate management, avoiding loss of genetic variability in these breeds and for future improvements in this nucleus. Additional work is needed to speed up the breeding process in the Peruvian cattle system. 2023-03-31T22:15:14Z 2023-03-31T22:15:14Z 2023-03-10 info:eu-repo/semantics/article Corredor F., Figueroa D., Estrada R., Salazar W., Quilcate C., Vásquez H., Gonzales J., Maicelo J., Medina P., & Arbizu C. (2023) Genetic diversity and population structure of a Peruvian cattle herd using SNP data. Frontiers in genetics, 14. doi: 10.3389/fgene.2023.1073843 1664-8021 https://hdl.handle.net/20.500.12955/2126 https://doi.org/10.3389/fgene.2023.1073843 eng urn:issn:1664-8021 Frontiers in Genetics info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ application/pdf application/pdf Frontiers Media S.A. CH Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
| spellingShingle | Cattle breeds Genotypes Diversity Genomics Next generation sequencing https://purl.org/pe-repo/ocde/ford#4.04.01 Cattle breeds Species diversity Genomics High-throughput sequencing Population structure Single nucleotide polymorphism Corredor Arizapana, Flor Anita Figueroa Venegas, Deyanira Antonella Estrada Cañari, Richard Salazar Coronel, Wilian Quilcate Pairazamán, Carlos Enrique Vásquez Pérez, Héctor Vladimir Gonzales Malca, Jhony Alberto Maicelo Quintana, Jorge Luis Medina Morales, Percy Edilberto Arbizu Berrocal, Carlos Irvin Genetic diversity and population structure of a Peruvian cattle herd using SNP data |
| title | Genetic diversity and population structure of a Peruvian cattle herd using SNP data |
| title_full | Genetic diversity and population structure of a Peruvian cattle herd using SNP data |
| title_fullStr | Genetic diversity and population structure of a Peruvian cattle herd using SNP data |
| title_full_unstemmed | Genetic diversity and population structure of a Peruvian cattle herd using SNP data |
| title_short | Genetic diversity and population structure of a Peruvian cattle herd using SNP data |
| title_sort | genetic diversity and population structure of a peruvian cattle herd using snp data |
| topic | Cattle breeds Genotypes Diversity Genomics Next generation sequencing https://purl.org/pe-repo/ocde/ford#4.04.01 Cattle breeds Species diversity Genomics High-throughput sequencing Population structure Single nucleotide polymorphism |
| url | https://hdl.handle.net/20.500.12955/2126 https://doi.org/10.3389/fgene.2023.1073843 |
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