Mitochondrial DNA single nucleotide polymorphism associated with weight estimated breeding values in Nelore cattle (Bos indicus)

We sampled 119 Nelore cattle (Bos indicus), 69 harboring B. indicus mtDNA plus 50 carrying Bos taurus mtDNA, to estimate the frequencies of putative mtDNA single nucleotide polymorphisms (SNPs) and investigate their association with Nelore weight and scrotal circumference estimated breeding values (EBVs). The PCR restriction fragment length polymorphism (PCR-RFLP) method was used to detect polymorphisms in the mitochondrial asparagine, cysteine, glycine, leucine and proline transporter RNA (tRNA) genes (tRNA, tRNA, tRNA, tRNA and tRNA). The 50 cattle carrying B. taurus mtDNA were monomorphic for all the tRNA gene SNPs analyzed, suggesting that they are specific to mtDNA from B. indicus cattle. No tRNA or tRNA polymorphisms were detected in any of the cattle but we did detect polymorphic SNPs in the tRNA, tRNA and tRNA genes in the cattle harboring B. indicus mtDNA, with the same allele observed in the B. taurus sequence being present in the following percentage of cattle harboring B. indicus mtDNA: 72.46% for tRNA, 95.23% for tRNA and 90.62% for tRNA. Analyses of variance using the tRNA SNP as the independent variable and EBVs as the dependent variable showed that the G → T SNP was significantly associated (p < 0.05) with maternal EBVs for weight at 120 and 210 days (p < 0.05) and animal’s EBVs for weight at 210, 365 and 455 days. There was no association of the tRNA SNP with the scrotal circumference EBVs. These results confirm that mtDNA can affect weight and that mtDNA polymorphisms can be a source of genetic variation for quantitative traits.