Exploring the Origin and Relatedness of Maternal Lineages Through Analysis of Mitochondrial DNA in the Holstein Horse

Abstract

Maternal lineages are important for the breeding decision in the Holstein horse breed. To investigate the genetic diversity of the maternal lineages and the relationships between founder mares, the maternal inherited mitochondrial genome (except the repetitive part of the non-coding region) of 271 mares representing 75 lineages was sequenced. The sequencing predominantly revealed complete homology in the nucleotide sequences between mares from one lineage with exceptions in 13 lineages, where differences in one to three positions are probably caused by de novo mutations or alternate fixation of heteroplasmy. We found 78 distinct haplotypes that have not yet been described in other breeds. Six of these occurred in two or three different lineages indicating a common ancestry. Haplotypes can be divided into eight clusters with all mares from one lineage belonging to the same cluster. Within a cluster, the average number of pairwise differences ranged from zero to 16.49 suggesting close maternal relationships between these mares. The results showed that the current breeding population originated from at least eight ancestral founder mares.

Mitochondrial DNA Variation Contributes to the Aptitude for Dressage and Show Jumping Ability in the Holstein Horse Breed

“…The sequencing was performed in 36 reactions using the ABI 3130xl Genetic Analyzer and the BigDye ® Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, Foster City, CA, USA). A more detailed description of the methods can be found in the work of [5].…”

“…A total of 467 polymorphic sites were found, but only the 101 non-synonymous substitutions previously reported in the work of [5] were considered for the evaluation.…”

“…Within a lineage, identical mtDNA haplotypes were found in all mares with respect to the non-synonymous substitutions [5], which is in accordance with results from studies in other breeds [6,7]. Based upon these findings, we enlarged our sample size by including both sequenced and non-sequenced mares belonging to one of the maternal lineages analyzed in our previous study [5], assuming that the non-sequenced mares have the same mitochondrial haplotype of non-synonymous variants as the sequenced mares of the same lineage. Using the resulting sample, we investigated the involvement of mitochondrial variants with regard to the performance of Holstein mares.…”

“…Since aerobic energy production takes place in mitochondria, it is reasonable to assume that variation in mitochondrial genes could possibly have an effect on athletic performance. Therefore, we recently analyzed mtDNA sequences from 271 Holstein mares belonging to 75 maternal lineages [5]. We were able to show that considerable molecular variation among mitochondrial genomes of different maternal lineages exists in Holstein horses and identified a total of 78 haplotypes that could be assigned to eight distinct haplogroups.…”

“…On the other hand, EBVs were estimated across all German warmblood breeds on behalf of the Fédération Équestre Nationale (FN) based on the results from sport and breeding events. A detailed description of the breeding value estimation can be found in the work of [5,8,9] Supplementary File S1.…”