Copy number variation in the genome of Nellore cattle

Abstract Text: The aim of this work was to study the distribution of CNVRs (regions of copy number variation) in the genome of Nelore cattle. A total of 3,022 animals (females and males) finished in feedlot conditions were used. For genotyping, a panel with more than 777,000 SNP markers (High -Density Bovine BeadChip) was used. Samples with Call rate lower than 90% were excluded. The PennCNV algorithm (Wang et al., 2007) was used for CNVs detection. In order to maintain the quality of the samples, samples with LRR (Log R ratio) standard deviation above 0.30, BAF (frequency of allele B) higher than 0.05 and waviness factor higher than 0.01, were excluded from the analyses (Liu et. al, 2013), reducing the number of animals to 1,561. The regions of CNVs (CNVRs) were generated by overlapping 73,073 CNVs identified by the CNVRuler program (Kim et al., 2012). Initially, different CNVs length were considered with a minimum size of 10kb, 50kb and all sizes , which resulted in 4,459, 1,365 and 6,399 CNVRs respectively. When all CNV sizes were considered, the average CNVRs length was 36.4 kb, ranging from 0.65 to 1,310 kb. There was a higher incidence of CNVRs at BTA1 (483), BTA6 (381) and BTA2 (380).The chromosomes that showed lower incidence of CNV regions were BTA25 (85), BTA27 (104) and BTA28 (117). Considering the CNVs of all sizes,  35.7 %, 41.0 % and 23.3 % of the CNVRs were copy gain, copy loss and both (gain and loss in the same region), respectively. The 6,399 CNV regions estimated in the present study coverage approximately 8.80 % of the bovine genome (UMD_3.1, 2,649,685,063 bp). This study confirms the existence of large structural variations in the genome of Nelore cattle and it would support the genetic improvement of this breed and elucidate the genetic mechanisms involved in the expression of productive traits.

Keywords: CNV, CNVR, Nelore