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. Results: Using a dataset that comprised 1036 Murciano-Granadina goats genotyped with the Goat SNP50 Bead-Chip, 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 (foldenrichment = 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 nonallelic homologous recombination.

Genome-wide Analysis of CNVs in Three Populations of Tibetan Sheep using Whole-genome Resequencing

“…The enrichment of nutrient metabolism terms, including nitrogen metabolism, citrate cycle, and bile secretion, was important for the digestion of nutrients in TS, especially in the cold season. Similar results showing the enrichment of CNVRharboring genes in ABC transporters were also reported in humans [38,39], cattle [10,40,41] and goats [42]. In mammals, ABC transporters can carry a broad array of endogenous metabolites, such as amino acids, peptides, and sugars, across lipid membranes, which facilitate the absorption and utilization of these nutrients.…”

“…Notably, the olfactory transduction pathway was signi cantly enriched speci cally in OTSs. Enrichment of the olfactory transduction pathway has been reported in cattle [11,16,43,44], yaks [45], sheep [18, 28, 46] and goats [42]. It has been revealed to in uence food consumption [47] and as a factor to assess feed e ciency and performance in crossbred beef cattle [48] and residual feed intake in pigs [49].…”

GWAS for genetics of complex quantitative traits: Genome to pangenome and SNPs to SVs and k‐mers

“…In these two studies in goats, GWAS was used for identification of CNVs associated with traits like coat color and sensory perception. [114,115] It is thus apparent that enormous activity on the use of CNVs in livestock has already been witnessed; this activity is likely to increase in future.…”

Genome Scan for Variable Genes Involved in Environmental Adaptations of Nubian Ibex

“…To account for variable regions that are not exclusive to Nubian ibex, we downloaded the genome coordinates of CNVs that have been identified in goat populations (Di Gerlando et al 2020;Guan et al 2020) and extracted overlapping sites using bedtools intersect (Quinlan and Hall 2010). Copy number variable regions overlapping (> 10%) with domestic goat CNV sites were excluded from further analysis.…”

“…Altogether, 367 CNVs were detected across the Nubian ibex genomes. Twenty-seven ( 27) CNVs identified across the Nubian ibexes reported previously in domestic goat genomes (Di Gerlando et al 2020;Guan et al 2020) were discarded since they reflect polymorphisms in/across goat species. Although only three Nubian ibexes were investigated, the samples were derived from unrelated individuals representing different geographical populations (South Africa, Egypt and Saudi Arabia).…”