Mapping copy number variation in Murciano-Granadina goats

Abstract

Copy number variation (CNV) plays an important role in phenotypic diversity and evolutionary adaptation in livestock. In this study, we have searched for caprine CNV regions (CNVRs) by using Goat SNP50 BeadChip data from 1,036 Murciano-Granadina goats. Two softwares, PennCNV and QuantiSNP, have been employed to call CNVs in this resource population. The CNVRs were defined as genomic regions containing CNV that overlap at least 30% by 2 callers. The CNV scan resulted in the identification of 486 CNVRs that were consistently detected with PennCNV and QuantiSNP. Interestingly, one of the CNVRs mapped to the casein cluster, so it would be worth to investigate its association with milk composition. Indeed, one of the null alleles of the CSN1S1 gene involves a partial deletion of this locus and causes a marked decrease in milk protein content. Moreover, another CNVR mapped to the ASIP gene, which has been reported to be associated with white color in sheep and goats. To further validate the presence of the ASIP CNVR, a qPCR assay was developed to estimate its copy number in several goat populations. We have found evidence of the presence of structural variation in the ASIP locus in goat populations, such as Murciano-Granadina, which have a solid non-white color.