Identification of CNVs (Copy Number Variants) Associated to Multiple Reproduction and Dairy Production Traits in Gyr (Bos indicus) Cattle

In the last decade, several different methods have been developed to identify genomic regions involved with dairy cattle fertility and productive traits. The aim of this study was to investigate common CNVs sassociated with those traits in Gyr cattle (Bos primigenius indicus). A total of 462 Gyr bulls were genotyped using the Illumina BovineHD Genotyping BeadChip. The de-regressed PTAs for age at first calving (AFC), milk, fat, protein and total solids yield at 305 days, fat, protein and total solids percentage, were used as pseudo-phenotypes for genome-wide association studies. The copy number analysis module implemented in SNP & Variation Suite v8.3 (Golden Helix, Inc., Bozeman), under the multivariate option, was used to segment chromosomes with a significance level of p = 0.01 for full pairwise permutations (n = 1,000). A single CNV regression was employed to identify CNVs associated with each one of the traits. It was considered as significant CNVs, those which presented FDR-corrected significance level of p-value < 0.05. A total of 32 CNVs were detected to affect at least one trait, with 21 regions affecting at least three traits. A genomic region located on chromosome 2 affect all traits, except AFC (BTAU2:4934647). This specific region overlap two QTLs already described in QTLdb as associated with dairy traits (milk fat yield (EBV) - QTL 9943 and milk protein percentage - QTL 3531) suggesting this region as an important candidate for functional exploration and selection in indicine breeds.