Abstract
Simple SummaryMitochondria are commonly known as “the powerhouse of the cell”, influencing the fitness, lifespan and metabolism of eukaryotic organisms. In our study we examined mitochondrial and nuclear genomic diversity in two high yielding strains of laying hens. We tested if the mitochondrial genome affects functional traits such as body weight and phosphorus utilization. We discovered a surprisingly low mitochondrial genetic diversity and an unequal distribution of the haplotypes among both strains, leading to limitations of robust links to phenotypic traits. In contrast, we found similar levels of nuclear genome diversity in both strains. Our study explores the potential influence of the mitochondrial genome on phenotypic traits and thus contributes to a better understanding of the function of this organelle in laying hens. Further, we focus on its usefulness as a genetic marker, which is often underestimated in breeding approaches, given the different inheritance mechanism compared to the nuclear genome.Mitochondria are essential components of eukaryotes as they are involved in several organismic key processes such as energy production, apoptosis and cell growth. Despite their importance for the metabolism and physiology of all eukaryotic organisms, the impact of mitochondrial haplotype variation has only been studied for very few species. In this study we sequenced the mitochondrial genome of 180 individuals from two different strains of laying hens. The resulting haplotypes were combined with performance data such as body weight, feed intake and phosphorus utilization to assess their influence on the hens in five different life stages. After detecting a surprisingly low level of genetic diversity, we investigated the nuclear genetic background to estimate whether the low mitochondrial diversity is representative for the whole genetic background of the strains. Our results highlight the need for more in-depth investigation of the genetic compositions and mito-nuclear interaction in individuals to elucidate the basis of phenotypic performance differences. In addition, we raise the question of how the lack of mitochondrial variation developed, since the mitochondrial genome represents genetic information usually not considered in breeding approaches.
Highlights
The domestic chicken is the most popular and widely distributed domestic fowl worldwide [1] and it is a stable source of protein, including meat and eggs [2]
Even though the whole mitochondrial genome has been used in many studies of domesticated animals such as goats [10], horses [11] and pigs [12], most studies of the chicken relied on partial mitochondrial sequences or the protein coding sequences [1] and studies covering the whole mt genome are underrepresented
The mapped reads had a mean coverage of approximately 300×, with 0.02% of the nucleotides covered by less than 5 reads
Summary
The domestic chicken is the most popular and widely distributed domestic fowl worldwide [1] and it is a stable source of protein, including meat and eggs [2]. In contrast to the advances made by high-throughput nuclear genotype analyses in chicken [3,4], the insights into mitochondrial (mt) genome diversity are rather sparse. For many animals it is known that mt genome diversity can have a remarkable impact on a variety of traits, such as meat quality in pigs [5] and the metabolic capacity of dairy cows [6]. Previous studies have shown that mutations in the mitochondrial genome can have strong physiological effects. This includes the adaptation to high altitudes of the Tibetan chicken [7,8] and economically important traits such as egg quality and body weight [9]. Given the importance of the genetic background on organismic physiological performance, beside the nuclear genome, the in-depth study of mitochondrial genomes and their variation are of utmost interest
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