Genome-wide association study of fiber diameter in alpacas
The aim of this study was the identification of candidate genomic regions associated with fiber diameter in alpacas. DNA samples were collected from 1011 female Huacaya alpacas from two geographical Andean regions in Peru (Pasco and Puno), and three alpaca farms within each region. The samples were...
| Autores principales: | , , , , , |
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| Formato: | Artículo |
| Lenguaje: | Español |
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MDPI
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/20.500.12955/2389 https://doi.org/10.3390/ani13213316 |
| _version_ | 1855490452546912256 |
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| author | More, Manuel Veli Rivera, Eudosio Amancio Cruz, Alan Gutiérrez, Juan Pablo Gutiérrez, Gustavo Ponce de León, F. Abel |
| author_browse | Cruz, Alan Gutiérrez, Gustavo Gutiérrez, Juan Pablo More, Manuel Ponce de León, F. Abel Veli Rivera, Eudosio Amancio |
| author_facet | More, Manuel Veli Rivera, Eudosio Amancio Cruz, Alan Gutiérrez, Juan Pablo Gutiérrez, Gustavo Ponce de León, F. Abel |
| author_sort | More, Manuel |
| collection | Repositorio INIA |
| description | The aim of this study was the identification of candidate genomic regions associated with fiber diameter in alpacas. DNA samples were collected from 1011 female Huacaya alpacas from two geographical Andean regions in Peru (Pasco and Puno), and three alpaca farms within each region. The samples were genotyped using an Affymetrix Custom Alpaca genotyping array containing 76,508 SNPs. After the quality controls, 960 samples and 51,742 SNPs were retained. Three association study methodologies were performed. The GWAS based on a linear model allowed us to identify 11 and 35 SNPs (−log10(p-values) > 4) using information on all alpacas and alpacas with extreme values of fiber diameter, respectively. The haplotype and marker analysis method allowed us to identify nine haplotypes with standardized haplotype heritability higher than six standard deviations. The selection signatures based on cross-population extended haplotype homozygosity (XP-EHH) allowed us to identify 180 SNPs with XP-EHH values greater than |3|. Four candidate regions with adjacent SNPs identified via two association methods of analysis are located on VPA6, VPA9, VPA29 and one chromosomally unassigned scaffold. This study represents the first analysis of alpaca whole genome association with fiber diameter, using a recently assembled alpaca SNP microarray. |
| format | Artículo |
| id | INIA2389 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Español |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | INIA23892023-12-04T22:04:26Z Genome-wide association study of fiber diameter in alpacas More, Manuel Veli Rivera, Eudosio Amancio Cruz, Alan Gutiérrez, Juan Pablo Gutiérrez, Gustavo Ponce de León, F. Abel GWAS SNP Genotyping Fiber diameter Alpaca https://purl.org/pe-repo/ocde/ford#4.02.01 Genome-Wide Association Studies Estudios Single Nucleotide Polymorphisms Polimorfismos de nucleótido único Genotyping Genotipado Alpaca Alpacas The aim of this study was the identification of candidate genomic regions associated with fiber diameter in alpacas. DNA samples were collected from 1011 female Huacaya alpacas from two geographical Andean regions in Peru (Pasco and Puno), and three alpaca farms within each region. The samples were genotyped using an Affymetrix Custom Alpaca genotyping array containing 76,508 SNPs. After the quality controls, 960 samples and 51,742 SNPs were retained. Three association study methodologies were performed. The GWAS based on a linear model allowed us to identify 11 and 35 SNPs (−log10(p-values) > 4) using information on all alpacas and alpacas with extreme values of fiber diameter, respectively. The haplotype and marker analysis method allowed us to identify nine haplotypes with standardized haplotype heritability higher than six standard deviations. The selection signatures based on cross-population extended haplotype homozygosity (XP-EHH) allowed us to identify 180 SNPs with XP-EHH values greater than |3|. Four candidate regions with adjacent SNPs identified via two association methods of analysis are located on VPA6, VPA9, VPA29 and one chromosomally unassigned scaffold. This study represents the first analysis of alpaca whole genome association with fiber diameter, using a recently assembled alpaca SNP microarray. 2023-12-04T22:04:25Z 2023-12-04T22:04:25Z 2023-10-25 info:eu-repo/semantics/article More, M.; Veli, E.; Cruz, A.; Gutiérrez, J. P.; Gutiérrez, G.; & Ponce de León, F. A. (2023). Genome-wide association study of fiber diameter in alpacas. Animals, 13(21), 3316. doi: 10.3390/ani13213316 2076-2615 https://hdl.handle.net/20.500.12955/2389 https://doi.org/10.3390/ani13213316 spa urn:issn:2076-2615 Animals info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ application/pdf application/pdf MDPI CH Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
| spellingShingle | GWAS SNP Genotyping Fiber diameter Alpaca https://purl.org/pe-repo/ocde/ford#4.02.01 Genome-Wide Association Studies Estudios Single Nucleotide Polymorphisms Polimorfismos de nucleótido único Genotyping Genotipado Alpaca Alpacas More, Manuel Veli Rivera, Eudosio Amancio Cruz, Alan Gutiérrez, Juan Pablo Gutiérrez, Gustavo Ponce de León, F. Abel Genome-wide association study of fiber diameter in alpacas |
| title | Genome-wide association study of fiber diameter in alpacas |
| title_full | Genome-wide association study of fiber diameter in alpacas |
| title_fullStr | Genome-wide association study of fiber diameter in alpacas |
| title_full_unstemmed | Genome-wide association study of fiber diameter in alpacas |
| title_short | Genome-wide association study of fiber diameter in alpacas |
| title_sort | genome wide association study of fiber diameter in alpacas |
| topic | GWAS SNP Genotyping Fiber diameter Alpaca https://purl.org/pe-repo/ocde/ford#4.02.01 Genome-Wide Association Studies Estudios Single Nucleotide Polymorphisms Polimorfismos de nucleótido único Genotyping Genotipado Alpaca Alpacas |
| url | https://hdl.handle.net/20.500.12955/2389 https://doi.org/10.3390/ani13213316 |
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