Abstract
Locally adapted cattle herds such as Curraleiro Pé Duro (CDP) are rustic and adapted to the tropics and are able to survive in extreme environmental conditions such as the Brazilian Semi-Arid region. The study aimed to identify copy number variants (CNVs) possibly related to CPD adaptive traits. A total of 126 CPD animals were genotyped using the Illumina Bovine50K Genotyping BeadChip (Illumina Inc., San Diego, CA). To reduce false positives, the LRR of each SNP was adjusted for the GC content of 1 Mb window surrounding the SNP and PennCNV software was applied to 29 autosomes to detect CNVs. All samples with standard deviation of LRR > 0.30, standard deviation of BAF > 0.001, wave factor > 0.05, samples with > 150 CNVs and CNVs presenting length < 50kb were discarded for downstream analysis. BEDtools suite was used to map CNVs onto genes using the BioMart tool (Bos taurus UMD 3.1 assembly). Gene lists were mapped onto curated biological process and gene categories using the PANTHER classification system. 635 CNVs were identified after quality control of the autosomal chromosomes (51 deletions and 584 insertions). The CNVs length ranged from 50.6 kb (BTA20) up to 1,362 kb (BTA7) with a mean and median of 179.4 kb and 148.8 kb, respectively, corresponding to 0.03% of the bovine genome. The CNVs identified were overlapping with 339 genes, which we can highlight GRIK2 (BTA9:48476204), PCDH18 (BTA17:20336068), IGF2 (BTA4:32077891) previously reported in the literature as involved with flight time (temperament), rectal temperature and reproduction, respectively. The functional enrichment analysis demonstrated that the main enriched pathways (P < 0.05) were regulation of biogenesis (GO:0071840) and catalytic activities (GO 0005198). The CNVs identified as potentially related to adaptive traits may be used to select animals of higher adaptive value to a tropical environment.