29 Mitochondrial haplotype variation and its association with feed efficiency in beef cattle.

Abstract The mitochondrion, an organelle inherited exclusively from the mother, is responsible for generating approximately 90% of total cellular energy and harbors a unique genome (mtDNA). This genome is composed of 13 essential protein-coding genes involved in oxidative phosphorylation, which is vital to ATP production. The electron transport system encompasses five complexes, four of which are encoded by the mtDNA. Despite their critical role, mtDNA influence on growth and feed efficiency in cattle is underexplored. Investigating variation in the mtDNA may provide insight into its role in feed efficiency, growth performance, and overall productivity of beef cattle. Data from 531 beef steers (composite Simmental, Red Angus, and Gelbvieh) from a primarily closed herd at UNL was used to identify mitochondrial variation and its potential impact on average daily gain (ADG) and dry matter intake (DMI). Low pass sequencing (0.38X average autosomal coverage) was performed on 531 steers, achieving an average of 55X coverage of the mtDNA. Mitochondrial haplotypes on an additional 66 steers were determined from known maternal relationships for a total sample of 597. Data were trimmed and mapped (BWA-MEM) to the ARS-UCD2.0 cattle genome. Variants were called (GATK) and impacts were predicted (Ensembl VEP). Among all samples, nineteen nonsynonymous variants were identified; twelve variants were in Complex I genes (ND1-ND6), two in Complex III (CYTB), four in Complex IV (COX1-COX3), and one in Complex V (ATP6, ATP8). These variants were distributed into 17 haplotypes. A comprehensive evaluation of the mitochondrial haplotypes and their association with feed efficiency traits was conducted. Dry matter intake (DMI) and average daily gain (ADG) were measured for each animal using a GrowSafe system. Average DMI was 12.74±2.94 kg/d (n = 597) and ADG was 2.10±0.34 kg/d (n = 524). A linear mixed model was implemented to assess the impact of mitochondrial haplotype on ADG and DMI. The model accounted for age at harvest, mitochondrial haplotype, contemporary group (birth year and harvest cohort), and a genomic relationship matrix, constructed from approximately 90,000 autosomal single nucleotide polymorphisms. A suggestive association (P = 0.065) between mitochondrial haplotype and DMI indicates mitochondrial variation may influence feed intake in these steers. Increasing sample size from haplotypes represented by fewer animals is needed to better understand their effects. No association between ADG and mtDNA haplotypes was observed, suggesting that mitochondrial variation did not have a direct influence on growth rate in these animals. Future investigations of these relationships will include additional samples from within and outside of the UNL herd and will incorporate other growth and carcass metrics for a more comprehensive analysis of the relationships between growth performance and mitochondrial genotypes. These findings provide the first evidence that the mitochondrial genome plays a role in beef cattle growth efficiency.