Copy number variation in the genome of four South American camelid species

Abstract

Copy number variation (CNV), a type of structural genomic variant, has been widely studied in humans, plants, and livestock. CNVs may contribute to phenotypic variation and traits of economic importance. Evaluating CNVs in domestic populations and their wild ancestors can reveal genetic changes associated with phenotypic differences that have emerged during domestication. In this study, whole-genome data from sixteen alpacas, six llamas, one guanaco, and one vicuna were used to investigate CNVs. A total of 4,247 CNVs were identified through genome-wide analysis. Functional analysis of Gene Ontology (GO) groups indicated that CNVs in alpacas are mainly related to immune-related genes, olfactory receptor genes, and keratinization. Species-level differences were observed, with the vicuna showing the least variation and the alpaca the most. This study provides the first CNV map for camelids and contributes to expanding knowledge of CNV diversity across the four South American camelid species.