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...
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MDPI AG
2023-10-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/13/21/3316 |
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| author | Manuel More Eudosio Veli Alan Cruz Juan Pablo Gutiérrez Gustavo Gutiérrez F. Abel Ponce de León |
| author_facet | Manuel More Eudosio Veli Alan Cruz Juan Pablo Gutiérrez Gustavo Gutiérrez F. Abel Ponce de León |
| author_sort | Manuel More |
| collection | DOAJ |
| 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 (−log<sub>10</sub>(<i>p</i>-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. |
| first_indexed | 2024-03-11T11:34:55Z |
| format | Article |
| id | doaj.art-a7f8ec53df1543ee9a90c415da9295d2 |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-11T11:34:55Z |
| publishDate | 2023-10-01 |
| publisher | MDPI AG |
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| series | Animals |
| spelling | doaj.art-a7f8ec53df1543ee9a90c415da9295d22023-11-10T14:57:41ZengMDPI AGAnimals2076-26152023-10-011321331610.3390/ani13213316Genome-Wide Association Study of Fiber Diameter in AlpacasManuel More0Eudosio Veli1Alan Cruz2Juan Pablo Gutiérrez3Gustavo Gutiérrez4F. Abel Ponce de León5Facultad de Agronomía y Zootecnia, Universidad Nacional de San Antonio Abad del Cusco, Cusco 08006, PeruCentro Experimental La Molina, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, PeruFacultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, PeruDepartamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, SpainFacultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, PeruFacultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, PeruThe 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 (−log<sub>10</sub>(<i>p</i>-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.https://www.mdpi.com/2076-2615/13/21/3316GWASSNPgenotypingfiber diameteralpaca |
| spellingShingle | Manuel More Eudosio Veli Alan Cruz Juan Pablo Gutiérrez Gustavo Gutiérrez F. Abel Ponce de León Genome-Wide Association Study of Fiber Diameter in Alpacas Animals GWAS SNP genotyping fiber diameter alpaca |
| 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 |
| url | https://www.mdpi.com/2076-2615/13/21/3316 |
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