Genetic Variants with Potential Loss of Function in Gyr, Girolando, and Guzerat Cattle Breeds By Re-Sequencing

The aim of this study was to detect, by whole-genome re-sequencing, SNVs (single nucleotide variants) and indels (insertion/deletions) and annotate them into functional categories in order to identify functionally relevant variants in three important cattle breeds in Brazil: Gyr and Girolando (dairy production), and Guzerat (dual-purpose). A total of approximately 2.7 billion reads from an Illumina HiSeq2000 sequencer generated for each animal 10.9 to 16.4-fold genome coverage. Sequencing reads were mapped to the UMD 3.1 bovine genome assembly using the Burrows-Wheeler Aligner tool (v.0.7.10-r789). Picard tools (v.1.54) were used to eliminate PCR duplicates and the variant calling was conducted with Freebayes. The resulting variant list were filtered by vcffilter in order to remove SNVs and indels with quality scores lower than 30 or coverage lower than 7. A total of 25,020,024 SNVs (16,743,392 from Guzerat, 15,941,804 from Gyr, and 13,286,669 from Girolando) and 3,249,148 indels (1,975,563 from Guzerat, 1,833,387 from Gyr, and 1,413,047 from Girolando) were detected in the DNA samples. A total of 13,253, 13,817, and 12,480 genes showed genetic variation in Guzerat, Gyr, and Girolando, respectively, of which 64.84% of genes with SNVs and 31.29% of genes with indels were shared among all breeds. The functional enrichment analysis by DAVID (v.6.8) tool revealed 24, 27, and 28 enriched KEGG pathways (FDR < 10%) in Guzerat, Gyr, and Girolando, respectively, of which 14 pathways were common to all breeds, three pathways were significantly over-represented only in Guzerat (arachidonic acid metabolism, Fc gamma R-mediated phagocytosis, and aldosterone-regulated sodium reabsorption), six pathways only in Gyr (alanine, aspartate and glutamate metabolism, inflammatory mediator regulation of TRP channels, thyroid hormone synthesis, pancreatic secretion, central carbon metabolism in cancer, and choline metabolism in cancer), and eight pathways only in Girolando (amino sugar and nucleotide sugar metabolism, inositol phosphate metabolism, vascular smooth muscle contraction, tight junction, regulation of actin cytoskeleton, amoebiasis, small cell lung cancer, and dilated cardiomyopathy). Although the genetic variants identified were distributed throughout the genomes, a large number of novel variants were clustered in specific genes. A total of 61 genes were identified with novel variants common in all breeds, while 349, 404, and 206 genes were identified as enriched with novel variants exclusively in the Guzerat, Gyr, and Girolando breeds, respectively. These genes are related to many biological processes, providing valuable information about genomic variants that may be responsible for variation in economically important traits among these breeds.