Single nucleotide polymorphisms in Bison bison identified by the GGP Bovine 50K SNP assay

Alexandru Eugeniu Mizeranschi, Ion Adrian Oprea, Stelian Acatincăi, Radu Ionel Neamț, Ciprian Valentin Mihali, Daniela Elena Ilie

Abstract


The vulnerable populations of bison had gone through a drastic reduction in population size, have undergone a very high level of inbreeding and have been through severe bottlenecks. Using a panel of Single Nucleotide Polymorphisms (GGP Bovine 50K SNP arrays, Neogen) developed across the entire bovine (Bos taurus) genome, we have carried out agenome variability screening on a bison (Bison bison) population in Romania. Eight males were included in the analysis. As part of SNP quality control filtering, one individual with a call rate below 80% was removed from the study. From a total of 47,843 SNPs only 4474 were polymorphic (9.35% from the total) and 7 individuals (out of a total of 8) were left after PLINK's quality control filtering. The total call rate of genotyped samples was 90.11% for the filtered dataset. A secondary PLINK run was performed on the 4474 filtered SNPs to find the ones whose HWE p-value fell below 0.05 and 100 markers were highlighted in this way. The results showed a larger number of polymorphic SNPs compared with previous studies from the literature. In addition, the data obtained using the GGP Bovine 50K SNP arrays may facilitate the design of breeding strategies that can be applied for decreasing unwanted inbreeding effects in the vulnerable bison populations.

Keywords


GGP Bovine 50K; Bison bison; single-nucleotide polymorphism

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References


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