ArticleGenetics, selection, evolution : GSE2020
A genome-wide analysis of copy number variation in Murciano-Granadina goats.
Article in Genetics, selection, evolution : GSE, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 13 citations in OpenAlex.
- Structural variant landscapes reveal convergent signatures of evolution in sheep and goats.Genome biology · 2024Article
- Structural variations in livestock genomes and their associations with phenotypic traits: a review.Frontiers in veterinary science · 2024Review
- Detection of genome-wide copy number variation in Murrah buffaloes.Animal biotechnology · 2023Article
- Identification of copy number variation in Tibetan sheep using whole genome resequencing reveals evidence of genomic selection.BMC genomics · 2023Article
- Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits.Frontiers in veterinary science · 2023Review
- Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing.Frontiers in genetics · 2022Article
- Genome Scan for Variable Genes Involved in Environmental Adaptations of Nubian Ibex.Journal of molecular evolution · 2021Article
- A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes.BMC genomics · 2021Article
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Authors and funding
11 authors at 2 institutions in 3 countries.
Funding
Abstract
backgroundIn 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.
resultsUsing 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
conclusionsA 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.
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