Abstract:

High-density SNP arrays are available and routinely used for genetic improvement of livestock populations. At the same time, mitogenome SNPs have rarely been used. In this study, we empirically evaluated 331 mitogenome SNPs included in the GGP Bovine 100K SNP array developed in collaboration with NEOGEN Genomics (Lincoln, NE, USA). Here we present a pipeline for the potential use of mitogenome SNPs with some examples: (1) classification of haplogroups with emphasis on rare ones (I, P, Q, R and T5); (2) pedigree verification; (3) pedigree and haplotype imputation; (4) deleterious mutation detection; (5) mitogenomic and nuclear diversity; and (6) standard mitogenome classification and phylogenetics. In summary, 317 mitogenome SNPs have been successfully validated and contribute as additional information to autosomal markers in population genomic analyses. We believe that our study will help to promote the use of mitogenome information in cattle breeding and biodiversity management.