Mitochondrial genome variability of 205 Arabian endurance horses

Abstract

Objectives:The objectives of this study were to propose a new strategy to call genetic variants in mitochondrial genome, and determine whether some variants are associated to endurance performance.Methodology:DNA was isolated from peripheral blood and mtDNA was amplified by 5 overlapping amplicons and then sequenced by Illumina Miseq. We chose a reference genome (GenBank ID : JN398380.1) that we « circularized » to improve terminals' alignments. After quality filtering and alignment, GATK (v3.5) was used to detect SNPs, indels and heteroplasmy. Association between SNPs and performance in endurance was tested using mixed model with fixed SNP Effect and random additive genetic effect with relationship matrix.Results:We got 590 variable positions of which 72% were known through studies of mitochondrial variability in horses [1,2]. 80% of the protein coding variants are silent and the transition/transversion ratio is 22.5. We observed 1.5% of non-haploid genotype. We graphically described the variants and the observed heteroplasmy in terms of localization, diversity, potential effects along the mitochondrial genome. Our preliminary analysis do not allow to associate some of the variants to performance.Conclusions:Despite a very strong conservative selection, 590 variants were identified on mtDNA of endurance horses.