Genome-Wide Association Studies of Somatic Cell Count in the Assaf Breed
A genome-wide association study (GWAS) was performed to identify new single nucleotide polymorphisms (SNPs) and genes associated with mastitis resistance in Assaf sheep by using the Illumina Ovine Infinium<sup>®</sup> HD SNP BeadChip (680K). In total, 6173 records from 1894 multiparous A...
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| Format: | Article |
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MDPI AG
2021-05-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/11/6/1531 |
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| author | Yasemin Öner Malena Serrano Pilar Sarto Laura Pilar Iguácel María Piquer-Sabanza Olaia Estrada Teresa Juan Jorge Hugo Calvo |
| author_facet | Yasemin Öner Malena Serrano Pilar Sarto Laura Pilar Iguácel María Piquer-Sabanza Olaia Estrada Teresa Juan Jorge Hugo Calvo |
| author_sort | Yasemin Öner |
| collection | DOAJ |
| description | A genome-wide association study (GWAS) was performed to identify new single nucleotide polymorphisms (SNPs) and genes associated with mastitis resistance in Assaf sheep by using the Illumina Ovine Infinium<sup>®</sup> HD SNP BeadChip (680K). In total, 6173 records from 1894 multiparous Assaf ewes with at least three test day records and aged between 2 and 7 years old were used to estimate a corrected phenotype for somatic cell score (SCS). Then, 192 ewes were selected from the top (<i>n</i> = 96) and bottom (<i>n</i> = 96) tails of the corrected SCS phenotype distribution to be used in a GWAS. Although no significant SNPs were found at the genome level, four SNPs (rs419096188, rs415580501, rs410336647, and rs424642424) were significant at the chromosome level (FDR 10%) in two different regions of OAR19. The SNP rs419096188 was located in intron 1 of the <i>NUP210</i> and close to the <i>HDAC11</i> genes (61 kb apart), while the other three SNPs were totally linked and located 171 kb apart from the <i>ARPP21</i> gene. These three genes were related to the immune system response. These results were validated in two SNPs (rs419096188 and rs424642424) in the total population (<i>n</i> = 1894) by Kompetitive Allele-Specific PCR (KASP) genotyping. Furthermore, rs419096188 was also associated with lactose content. |
| first_indexed | 2024-03-10T11:05:43Z |
| format | Article |
| id | doaj.art-b52ef32426dd410a813f24622f426877 |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-10T11:05:43Z |
| publishDate | 2021-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj.art-b52ef32426dd410a813f24622f4268772023-11-21T21:11:12ZengMDPI AGAnimals2076-26152021-05-01116153110.3390/ani11061531Genome-Wide Association Studies of Somatic Cell Count in the Assaf BreedYasemin Öner0Malena Serrano1Pilar Sarto2Laura Pilar Iguácel3María Piquer-Sabanza4Olaia Estrada5Teresa Juan6Jorge Hugo Calvo7Department of Animal Science, University of Uludag, Bursa 16059, TurkeyDepartamento de Mejora Genética Animal, INIA, 28040 Madrid, SpainUnidad de Producción y Sanidad Animal. Centro de Investigación y Tecnología Agroalimentaria de Aragón —Instituto Agroalimentario de Aragón (IA2) (CITA—Zaragoza University), 50059 Zaragoza, SpainUnidad de Producción y Sanidad Animal. Centro de Investigación y Tecnología Agroalimentaria de Aragón —Instituto Agroalimentario de Aragón (IA2) (CITA—Zaragoza University), 50059 Zaragoza, SpainUnidad de Producción y Sanidad Animal. Centro de Investigación y Tecnología Agroalimentaria de Aragón —Instituto Agroalimentario de Aragón (IA2) (CITA—Zaragoza University), 50059 Zaragoza, SpainUnidad de Producción y Sanidad Animal. Centro de Investigación y Tecnología Agroalimentaria de Aragón —Instituto Agroalimentario de Aragón (IA2) (CITA—Zaragoza University), 50059 Zaragoza, SpainUnidad de Producción y Sanidad Animal. Centro de Investigación y Tecnología Agroalimentaria de Aragón —Instituto Agroalimentario de Aragón (IA2) (CITA—Zaragoza University), 50059 Zaragoza, SpainUnidad de Producción y Sanidad Animal. Centro de Investigación y Tecnología Agroalimentaria de Aragón —Instituto Agroalimentario de Aragón (IA2) (CITA—Zaragoza University), 50059 Zaragoza, SpainA genome-wide association study (GWAS) was performed to identify new single nucleotide polymorphisms (SNPs) and genes associated with mastitis resistance in Assaf sheep by using the Illumina Ovine Infinium<sup>®</sup> HD SNP BeadChip (680K). In total, 6173 records from 1894 multiparous Assaf ewes with at least three test day records and aged between 2 and 7 years old were used to estimate a corrected phenotype for somatic cell score (SCS). Then, 192 ewes were selected from the top (<i>n</i> = 96) and bottom (<i>n</i> = 96) tails of the corrected SCS phenotype distribution to be used in a GWAS. Although no significant SNPs were found at the genome level, four SNPs (rs419096188, rs415580501, rs410336647, and rs424642424) were significant at the chromosome level (FDR 10%) in two different regions of OAR19. The SNP rs419096188 was located in intron 1 of the <i>NUP210</i> and close to the <i>HDAC11</i> genes (61 kb apart), while the other three SNPs were totally linked and located 171 kb apart from the <i>ARPP21</i> gene. These three genes were related to the immune system response. These results were validated in two SNPs (rs419096188 and rs424642424) in the total population (<i>n</i> = 1894) by Kompetitive Allele-Specific PCR (KASP) genotyping. Furthermore, rs419096188 was also associated with lactose content.https://www.mdpi.com/2076-2615/11/6/1531dairysheepGWASmastitissomatic cell count |
| spellingShingle | Yasemin Öner Malena Serrano Pilar Sarto Laura Pilar Iguácel María Piquer-Sabanza Olaia Estrada Teresa Juan Jorge Hugo Calvo Genome-Wide Association Studies of Somatic Cell Count in the Assaf Breed Animals dairy sheep GWAS mastitis somatic cell count |
| title | Genome-Wide Association Studies of Somatic Cell Count in the Assaf Breed |
| title_full | Genome-Wide Association Studies of Somatic Cell Count in the Assaf Breed |
| title_fullStr | Genome-Wide Association Studies of Somatic Cell Count in the Assaf Breed |
| title_full_unstemmed | Genome-Wide Association Studies of Somatic Cell Count in the Assaf Breed |
| title_short | Genome-Wide Association Studies of Somatic Cell Count in the Assaf Breed |
| title_sort | genome wide association studies of somatic cell count in the assaf breed |
| topic | dairy sheep GWAS mastitis somatic cell count |
| url | https://www.mdpi.com/2076-2615/11/6/1531 |
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