Association between copy number variation regions in the Nellore cattle genome and meat tenderness
The present study aimed to analyze the association between the copy number variation regions (CNVR) with meat tenderness of 737 Nellore bulls. The animals were finished in feedlot and slaughtered at approximately two years of age. Samples from the Longissimus dorsi muscle with 2.5 cm (thickness) were collected to obtain the meat tenderness using a Warner-Bratzler shear force device. A panel with 777,962 SNPs markers (High-Density Bovine BeadChip) was used to genotype the animals. Samples with call rate below 90% were excluded. The parameters used to estimate the CNVs were: Log R Ratio (LRR) and B Allele Frequency (BAF). For quality control, samples with standard deviation values for LRR <0.30, BAF <0.05 and waving factor <0,01 were eliminated. The CNVR were appointed as the CNV’s overlaps in the samples, that were located by the CNVRuler software. The shear force data were adjusted for the effects of farm and year of birth, and management groups at birth, weaning and yearling. The model included the state of CNV as a fixed effect and the age of animal at slaughter as a covariate. The average shear force obtained was 5.51 kgf. A total of 4504 CNVRs with an average size of 36.59 kb were detected. There were 10 CNVRs with MAF greater than 0.05, and among them only 2 significant (P<0.05) associated with meat tenderness (CNVR_1491, CNVR_1130). The CNVR_1491, located on chromosome 7, is in an intergenic region, possibly serving as an indirect marker. This CNVR is between two regions, the first is not characterized and the second is a pseudogene of transcription factors for heat shock proteins, therefore the significant p-value for this region is an indication that these genes may be influencing this trait. All these LOC regions are "like" regions, areas that have partial or total similarity to genes in other genome regions. The CNVR_1130, located on chromosome 5, is in theory a intergenic region. There were four regions within this CNVR, two are not characterized and the other two are "like" sequences of the gene associated with butyrophilin protein subfamily 1 member A1, which participates in the formation of fat droplets in milk cattle. Theoretically, this gene may influence the subcutaneous fat thickness and therefore affect meat tenderness. The meat tenderness should be improved in Zebu cattle, and the CNVRs are a tool that can be used to genetic improve this trait.
Keywords: Chromosomal region, CNVR, shear force.