A genome-wide analysis of copy number variation in Murciano-Granadina goats
Abstract Background In this work, our aim was to generate a map of the copy number variations (CNV) segregating in a population of Murciano-Granadina goats, the most important dairy breed in Spain, and to ascertain the main biological functions of the genes that map to copy number variable regions....
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | deu |
| Published: |
BMC
2020-08-01
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| Series: | Genetics Selection Evolution |
| Online Access: | http://link.springer.com/article/10.1186/s12711-020-00564-4 |
| _version_ | 1818850971358330880 |
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| author | Dailu Guan Amparo Martínez Anna Castelló Vincenzo Landi María Gracia Luigi-Sierra Javier Fernández-Álvarez Betlem Cabrera Juan Vicente Delgado Xavier Such Jordi Jordana Marcel Amills |
| author_facet | Dailu Guan Amparo Martínez Anna Castelló Vincenzo Landi María Gracia Luigi-Sierra Javier Fernández-Álvarez Betlem Cabrera Juan Vicente Delgado Xavier Such Jordi Jordana Marcel Amills |
| author_sort | Dailu Guan |
| collection | DOAJ |
| description | Abstract Background In this work, our aim was to generate a map of the copy number variations (CNV) segregating in a population of Murciano-Granadina goats, the most important dairy breed in Spain, and to ascertain the main biological functions of the genes that map to copy number variable regions. Results Using a dataset that comprised 1036 Murciano-Granadina goats genotyped with the Goat SNP50 BeadChip, we were able to detect 4617 and 7750 autosomal CNV with the PennCNV and QuantiSNP software, respectively. By applying the EnsembleCNV algorithm, these CNV were assembled into 1461 CNV regions (CNVR), of which 486 (33.3% of the total CNVR count) were consistently called by PennCNV and QuantiSNP and used in subsequent analyses. In this set of 486 CNVR, we identified 78 gain, 353 loss and 55 gain/loss events. The total length of all the CNVR (95.69 Mb) represented 3.9% of the goat autosomal genome (2466.19 Mb), whereas their size ranged from 2.0 kb to 11.1 Mb, with an average size of 196.89 kb. Functional annotation of the genes that overlapped with the CNVR revealed an enrichment of pathways related with olfactory transduction (fold-enrichment = 2.33, q-value = 1.61 × 10−10), ABC transporters (fold-enrichment = 5.27, q-value = 4.27 × 10−04) and bile secretion (fold-enrichment = 3.90, q-value = 5.70 × 10−03). Conclusions A previous study reported that the average number of CNVR per goat breed was ~ 20 (978 CNVR/50 breeds), which is much smaller than the number we found here (486 CNVR). We attribute this difference to the fact that the previous study included multiple caprine breeds that were represented by small to moderate numbers of individuals. Given the low frequencies of CNV (in our study, the average frequency of CNV is 1.44%), such a design would probably underestimate the levels of the diversity of CNV at the within-breed level. We also observed that functions related with sensory perception, metabolism and embryo development are overrepresented in the set of genes that overlapped with CNV, and that these loci often belong to large multigene families with tens, hundreds or thousands of paralogous members, a feature that could favor the occurrence of duplications or deletions by non-allelic homologous recombination. |
| first_indexed | 2024-12-19T06:57:36Z |
| format | Article |
| id | doaj.art-679e57422883430797d535e981525e9b |
| institution | Directory Open Access Journal |
| issn | 1297-9686 |
| language | deu |
| last_indexed | 2024-12-19T06:57:36Z |
| publishDate | 2020-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-679e57422883430797d535e981525e9b2022-12-21T20:31:29ZdeuBMCGenetics Selection Evolution1297-96862020-08-0152111010.1186/s12711-020-00564-4A genome-wide analysis of copy number variation in Murciano-Granadina goatsDailu Guan0Amparo Martínez1Anna Castelló2Vincenzo Landi3María Gracia Luigi-Sierra4Javier Fernández-Álvarez5Betlem Cabrera6Juan Vicente Delgado7Xavier Such8Jordi Jordana9Marcel Amills10Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de BarcelonaDepartamento de Genética, Universidad de CórdobaCentre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de BarcelonaDepartamento de Genética, Universidad de CórdobaCentre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de BarcelonaAsociación Nacional de Criadores de Caprino de Raza Murciano-Granadina (CAPRIGRAN)Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de BarcelonaDepartamento de Genética, Universidad de CórdobaGroup of Research in Ruminants (G2R), Department of Animal and Food Science, Universitat Autònoma de Barcelona (UAB)Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de BarcelonaCentre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de BarcelonaAbstract Background In this work, our aim was to generate a map of the copy number variations (CNV) segregating in a population of Murciano-Granadina goats, the most important dairy breed in Spain, and to ascertain the main biological functions of the genes that map to copy number variable regions. Results Using a dataset that comprised 1036 Murciano-Granadina goats genotyped with the Goat SNP50 BeadChip, we were able to detect 4617 and 7750 autosomal CNV with the PennCNV and QuantiSNP software, respectively. By applying the EnsembleCNV algorithm, these CNV were assembled into 1461 CNV regions (CNVR), of which 486 (33.3% of the total CNVR count) were consistently called by PennCNV and QuantiSNP and used in subsequent analyses. In this set of 486 CNVR, we identified 78 gain, 353 loss and 55 gain/loss events. The total length of all the CNVR (95.69 Mb) represented 3.9% of the goat autosomal genome (2466.19 Mb), whereas their size ranged from 2.0 kb to 11.1 Mb, with an average size of 196.89 kb. Functional annotation of the genes that overlapped with the CNVR revealed an enrichment of pathways related with olfactory transduction (fold-enrichment = 2.33, q-value = 1.61 × 10−10), ABC transporters (fold-enrichment = 5.27, q-value = 4.27 × 10−04) and bile secretion (fold-enrichment = 3.90, q-value = 5.70 × 10−03). Conclusions A previous study reported that the average number of CNVR per goat breed was ~ 20 (978 CNVR/50 breeds), which is much smaller than the number we found here (486 CNVR). We attribute this difference to the fact that the previous study included multiple caprine breeds that were represented by small to moderate numbers of individuals. Given the low frequencies of CNV (in our study, the average frequency of CNV is 1.44%), such a design would probably underestimate the levels of the diversity of CNV at the within-breed level. We also observed that functions related with sensory perception, metabolism and embryo development are overrepresented in the set of genes that overlapped with CNV, and that these loci often belong to large multigene families with tens, hundreds or thousands of paralogous members, a feature that could favor the occurrence of duplications or deletions by non-allelic homologous recombination.http://link.springer.com/article/10.1186/s12711-020-00564-4 |
| spellingShingle | Dailu Guan Amparo Martínez Anna Castelló Vincenzo Landi María Gracia Luigi-Sierra Javier Fernández-Álvarez Betlem Cabrera Juan Vicente Delgado Xavier Such Jordi Jordana Marcel Amills A genome-wide analysis of copy number variation in Murciano-Granadina goats Genetics Selection Evolution |
| title | A genome-wide analysis of copy number variation in Murciano-Granadina goats |
| title_full | A genome-wide analysis of copy number variation in Murciano-Granadina goats |
| title_fullStr | A genome-wide analysis of copy number variation in Murciano-Granadina goats |
| title_full_unstemmed | A genome-wide analysis of copy number variation in Murciano-Granadina goats |
| title_short | A genome-wide analysis of copy number variation in Murciano-Granadina goats |
| title_sort | genome wide analysis of copy number variation in murciano granadina goats |
| url | http://link.springer.com/article/10.1186/s12711-020-00564-4 |
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