Biology subjects

Schoenebeck, J.

Publications and source records attributed to Schoenebeck, J..

3 recordsLinked to original sources

bioRxiv2025

Evaluating genotyping strategies for a small managed population with simulation

BackgroundCollecting genomic information is crucial to advance breeding for complex traits such as health, welfare, and behaviour in domesticated populations. For that purpose, different data collection scenarios can be envisioned based on the number of individuals, the number of markers, and the genotyping technology. This study developed a simulation framework, based on a service dog population, aiming to identify an optimal and cost-effective genotyping strategy that would support the implementation of genomic selection, investigation of the genetic architecture of traits of interest, and track loci of interest. MethodsWe simulated a population based on the existing pedigree, using the gene drop method in AlphaSimR. The existing pedigree was extended with additional progeny generations to evaluate the outcomes of different genotyping strategies in the future. We generated genotype data based on existing high-coverage whole-genome sequences (WGS) for the current breeding dogs and evaluated different scenarios for genotyping the progeny. The genotyping options considered SNP arrays of various densities and WGS callsets produced from different sequencing depths. We then phased and imputed the genotype data to high-coverage WGS using AlphaPeel. ResultsAll scenarios were compared based on individual imputation accuracy against the simulated true whole-genome genotype. Averaged over five generations of simulated progeny, low-pass sequencing (0.5 to 2X depth) achieved accuracies of 0.998 to 0.999. The accuracy of SNP array genotyping (25K to 710K markers) was lower, with means of 0.911 to 0.938. ConclusionsOur simulation was tailored to identify the most cost-effective and efficient strategy for downstream use in genomic selection and genetic research into traits and loci of interest. Low-pass sequencing outperformed SNP array genotyping in imputation accuracy of whole-genome genotypes as expected. Additionally, low-pass sequencing technology was the most affordable genotyping approach currently available for dogs. Thus, it appears to be the optimal choice for balancing the goals of regimented breeding programmes such as those that produce service dogs. This simulation framework could also be adapted to address other objectives for breeding organisations working with small populations.

genomics↗

bioRxiv2024

Genomic insights into red squirrels in Scotland reveals loss of heterozygosity associated with extreme founder effects

Remnant populations of endangered species often have complex demographic histories associated with human impact. This can present challenges for conservation as the genetic status of these populations are often a-typical of natural populations, and may require bespoke management. The Eurasian red squirrel, Sciurus vulgaris (L., 1758), is endangered in the UK. Scotland represents a key stronghold, but Scottish populations have been subjected to intense anthropogenic influence, including wide-spread extirpations, reintroductions and competition from an invasive species. This study examined the genetic legacy of these events through whole genome resequencing of 106 red squirrels. Using SNP and genotype likelihood datasets, previously undetected population structure and patterns of gene-flow were uncovered. One off-shore island, three mainland Scottish populations, and a key east-coast migration corridor were observed. An abrupt historical population bottleneck related to extreme founder effects has led to a severe and prolonged depression in genome-wide heterozygosity, which is amongst the lowest reported for any species. Current designated red squirrel conservation stronghold locations do not encompass all existing diversity. These findings highlight the genetic legacies of past anthropogenic influence on long-term diversity in endangered taxa. Continuing management interventions and regular genetic monitoring are recommended to safeguard and improve future diversity.

genomics↗

bioRxiv2019

A Highly Conserved Shh Enhancer Coordinates Hypothalamic and Craniofacial Development

Enhancers that are conserved deep in evolutionary time regulate characteristics held in common across taxonomic classes. Here, deletion of the highly conserved Shh enhancer SBE2 (Shh brain enhancer 2) markedly reduced Shh expression within the embryonic brain specifically in the rostral diencephalon; however, no abnormal anatomical phenotype was observed due to compensatory low levels of expression mediated by a second enhancer. In contrast, a further reduction of Shh levels, achieved by crossing the SBE2 deletion with the Shh null allele, disrupted brain and craniofacial tissue; thus, linking SBE2 regulated Shh expression to multiple defects and further enabling the study of the effects of differing levels of Shh on embryogenesis. Development of the hypothalamus, derived from the rostral diencephalon, was disrupted along both the anterior-posterior (AP) and the dorsal-ventral (DV) axes. Expression of DV patterning genes and subsequent neuronal population induction were particularly sensitive to Shh expression levels, demonstrating a novel morphogenic context for Shh. The role of SBE2, which is highlighted by DV gene expression, is to step-up expression of Shh above the minimal activity of the second enhancer, ensuring the necessary levels of Shh in a regional-specific manner. We also show that low Shh levels in the diencephalon disrupted neighbouring craniofacial development, including mediolateral patterning of the bones along the cranial floor and viscerocranium. Thus, SBE2 contributes to hypothalamic morphogenesis and ensures there is coordination with the formation of the adjacent midline cranial bones that subsequently protects the neural tissue.

developmental biology↗