Copy Number Variants (CNV) Mapping and Association Analysis in the Autochthonous Italian Valdostana Red Pied Cattle Population

CNV have been recently mapped in several cattle population. They are an important source of genomic structural variation, found to affect phenotypic expression of complex traits. The Valdostana Red-Pied population, an autochthonous double purpose Italian cattle breed, did not undergo a strong selection, as the Holstein and the Brown Swiss, and thus can deliver valuable information on structural variation and its association with complex traits. CNVs have been mapped from the log R ratio (LRR) obtained genotyping 143 bulls with the Illumina BovineHD bead chip. Data were edited for quality control with SVS v8.1.0 (Golden Helix) for derivative LRR spread, genomic wave and chromosomal abnormalities. Univariate approach of CNAM optimal segmenting algorithm was used to identify a total of 2467 CNVs segments in 108 sires for a total of 253 CNV regions on all autosomes. Association analysis has been developed on productive and functional traits. CNVs found here confirm regions identified on chromosomes 12 (70-75 Mb) and 23 (MHC region) in the Italian Brown Swiss and in hortologous regions in Capra Hircus  Ovis Aries and Sus Scrofa. The smallest CNV (0.5 Kb) was  on chromosome 1, the largest (773Kb) on chromosome 12, the remaining spanning from 2.6 Kb to 760 Kb. Data was generated as part of the FP7 project QUANTOMICS contract n. 222664-2.