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

Short communication: Accounting for nuclear and mito genome in dairy cattle breeding - a simulation study

“…Our initial simulations of mDNA, indicated that we need larger N e for mDNA than for nDNA (despite an order of magnitude larger mutation rate in mDNA) to obtain a number of segregating sites in mDNA in line with the observed variation both within and across cattle populations (Dorji et al 2021; Brajkovic et al, 2023;). As expected, we noticed that the lower the diversity among the mDNA, the smaller the impact of accounting for mDNA in breeding value estimation, in line with Boettcher et al (1996).…”

“…Note that n m was smaller than the number of distinct maternal founder lineages in pedigree. We calculated the mDNA genomic relationship matrix as G m = M m M m T / k , where M m = W m – P m with W m an n m × n s matrix of 0s (for ancestral allele) and 1s (for mutation) for n m distinct mDNA and n s polymorphic loci (we assume we know all these loci by sequencing mDNA within pedigrees; Brajkovic et al, 2023), P m a matrix of mutation frequencies, k = , and p l the mutation frequency at locus l . To speed up simulations, we fixed variance components to simulated values during the burn-in phase (see the next paragraphs).…”

“…We set mDNA effective population size to 1,000 in the most recent generation. We increased the historical effective population sizes from MacLeod et al (2013) (see GitHub) to obtain over 1,000 polymorphic loci in line with literature (Brajkovic et al, 2023;Dorji et al, 2021). We chose all polymorphic loci (on average 1,084 across 10 replicates) in the mDNA as SNP markers.…”

“…The maternal inheritance of mDNA enables tracking maternal lineages from founders via pedigrees (Schutz et al, 1992). Spehar et al (2017) estimated that variation between pedigree maternal lineages accounted for 2-3% of the phenotypic variance for milk yield in the Croatian Holstein population, while a genomic analysis in the same population accounted for up to 5% of the phenotypic variance (Brajkovic et al, 2023). An earlier simulation study accounting for variation between maternal lineages suggested an increase in the accuracy of estimated breeding values for cows by 0.01 when the maternal lineages accounted for 2.5% of the phenotypic variance and 0.04 when accounted for 10% (Boettcher et al, 1996).…”

“…García-Ruiz et al, 2016), which is a molecule of ~3Gb (e.g., Srirattana and St. John, 2017). In contrast, variation in the mDNA, which spans only ~16kbp (e.g., Srirattana and St. John, 2017), is associated with 1-5% of the phenotypic variation (Bell et al, 1985;Brajkovic et al, 2023;Schutz et al, 1992). These proportions indicate that dairy breeding could benefit from accounting for mDNA variation.…”