Mitogenome information in cattle breeding and conservation genetics: Developments and possibilities of the SNP chip

Abstract

In contrast to nuclear markers routinely used for genomic selection, mitogenome information has been underutilized for breeding and biodiversity management of cattle populations. Our main goal was to promote the efficient use of mitogenome SNPs contained in commercial high-throughput SNP arrays. In collaboration with NEOGEN Genomics (Lincoln, NE, USA), we integrated 310 SNPs into the commercial GGP Bovine 100K SNP array. In doing so, we demonstrated how mitogenome SNPs can be used in high-throughput arrays to (i) analyze population structure and diversity, (ii) classify bovine haplogroups and identify introgression and/or upgrading, (iii) screen and identify pedigree defects, (iv) impute mitogenome information on maternal lineages to increase statistical power in estimating the effects of mitogenome variation on quantitative production traits, and (v) identify deleterious mutations found in humans. In addition, we have developed protocols and pipelines integrated with the Magellan v2.0 software to enable efficient and routine use of mitogenome information in cattle breeding and genetic diversity management. Finally, we have highlighted some other interesting opportunities for the use of mitogenome information in the near future.