A genome-wide analysis of copy number variation in Murciano-Granadina goats
Guan, Dailu (Centre de Recerca en Agrigenòmica)
Martinez, Amparo (Universidad de Córdoba. Departamento de Genética)
Castelló Farré, Anna (Centre de Recerca en Agrigenòmica)
Landi, Vincenzo (Universidad de Córdoba. Departamento de Genética)
Luigi Sierra, Maria Gracia (Centre de Recerca en Agrigenòmica)
Fernández Álvarez, Javier (Asociación Nacional de Criadores de Caprino de Raza Murciano-Granadina)
Cabrera Pane, Betlem (Centre de Recerca en Agrigenòmica)
Delgado Bermejo, Juan Vicente (Universidad de Córdoba. Departamento de Genética)
Such i Martí, Francesc Xavier (Universitat Autònoma de Barcelona. Grup de Recerca en Remugants (G2R))
Jordana i Vidal, Jordi (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Amills i Eras, Marcel (Centre de Recerca en Agrigenòmica)
Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments

Data:	2020
Resum:	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.
Ajuts:	Ministerio de Ciencia e Innovación AGL2016‑76108‑R Ministerio de Economía y Competitividad SEV‑2015‑0533 Ministerio de Economía y Competitividad BES‑2017‑079709
Nota:	Altres ajuts: CERCA Programme/Generalitat de Catalunya
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Publicat a:	Genetics, selection, evolution, Vol. 52 (August 2020) , art. 44, ISSN 1297-9686

DOI: 10.1186/s12711-020-00564-4
PMID: 32770942

10 p, 1.3 MB

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