Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep

PLoS One. 2019 Apr 23;14(4):e0215204. doi: 10.1371/journal.pone.0215204. eCollection 2019.


Copy number variation (CNV) is a major source of genomic structural variation. The aim of this study was to detect genomic CNV regions (CNVR) in Valle del Belice dairy sheep population and to identify those affecting milk production traits. The GO analysis identified possible candidate genes and pathways related to the selected traits. We identified CNVs in 416 individuals genotyped using the Illumina OvineSNP50 BeadChip array. The CNV association using a correlation-trend test model was examined with the Golden Helix SVS 8.7.0 tool. Significant CNVs were detected when their adjusted p-value was <0.01 after false discovery rate (FDR) correction. We identified 7,208 CNVs, which gave 365 CNVRs after aggregating overlapping CNVs. Thirty-one CNVRs were significantly associated with one or more traits included in the analysis. All CNVRs, except those on OAR19, overlapped with quantitative trait loci (QTL), even if they were not directly related to the traits of interest. A total of 222 genes were annotated within the significantly associated CNVRs, most of which played important roles in biological processes related to milk production and health-related traits. Identification of the genes in the CNVRs associated with the studied traits will provide the basis for further investigation of their role in the metabolic pathways related to milk production and health traits.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromosome Mapping
  • DNA Copy Number Variations*
  • Dairying
  • Female
  • Genome-Wide Association Study
  • Genotype
  • Lactation / genetics*
  • Quantitative Trait Loci*
  • Sheep / genetics*

Grants and funding

This work was supported by the Ministero Istruzione Università e Ricerca PON02_00451_3133441, CUP:B61C1200076005 to BP. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.