Retriever and Pointer: Software to Evaluate Inbreeding and Genetic Management in Captive Populations

Evaluation of breeding strategies to reduce the inbreeding rate in the Friesian horse population: Looking back and moving forward

In the past, small population sizes and unequal ancestor contributions have resulted in high inbreeding rates (ΔF) in the Friesian horse. Two decades ago, the studbook implemented a mating quota and started publishing individual kinships and reduced ΔF below 1% per generation. However, since then, the breeding population size has decreased and this raises the question whether current breeding strategies are sufficient to keep ΔF below desired rates. The aim of this study was to (1) reflect on past inbreeding trends and their main determinants, using pedigree analysis and (2) evaluate the effectiveness of the current and additional breeding strategies using stochastic simulations. We estimated the current ΔF (2013-2022) at 0.72% per generation. While the total contribution of the top 10 sires to the number of offspring per year has decreased from 75% in 1980 to 35% in 2022, this was mainly due to an increased number of approved studbook sires, and not due to more equalized contributions among sires. Of the simulated breeding strategies, selecting only breeding stallions with a below average mean kinship (i.e., "mean kinship selection") was most effective to decrease ΔF (from 0.66% to 0.33%). Increasing the number of breeding sires only had an effect when also a mating quota was applied. However, its effect remained limited. For example, a ~1.5 fold increase, combined with a mating quota of 80 offspring per sire per year, reduced ΔF from 0.55% to 0.51%. When increasing the number of breeding mares, a practically unfeasible large increase was needed for a meaningful reduction in ΔF (e.g. twice as many mares were needed to reduce ΔF from 0.66% to 0.56%). Stratified mating quotas, a novel approach in which we assigned each sire a mating quota (of 60, 80, 100 or 120 offspring per year) based on its mean kinship to recently born foals, resulted in a lower ΔF (0.43%) than a general mating quota of 90 offspring per sire per year (0.55%). Overall, while the current ΔF is below 1%, we recommend to implement additional strategies to further reduce ΔF below 0.5% in the Friesian horse population. For this breed and similar populations, we recommend to focus on breeding strategies based on kinship levels to effectively reduce ΔF.

Evaluation of Genetic Diversity in Dog Breeds Using Pedigree and Molecular Analysis: A Review

Domestic dogs are important for many economic and social reasons, and they have become a well-known model species for human disease. According to research, dog breeds exhibit significant levels of inbreeding and genetic diversity loss, decreasing the population’s ability to adapt in certain conditions, and indicating the need of conservation strategies. Before the development of molecular markers, pedigree information was used for genetic diversity management. In recent years, genomic tools are frequently applied for accurate estimation of genetic diversity and improved genetic conservation due to incomplete pedigrees and pedigree errors. The most frequently used molecular markers include PCR-based microsatellite markers (STRs) and DNA sequencing-based single-nucleotide polymorphism markers (SNP). The aim of this review was to highlight genetic diversity studies on dog breeds conducted using pedigree and molecular markers, as well as the importance of genetic diversity conservation in increasing the adaptability and survival of dog breed populations.

Unique genetic signature and selection footprints in Dutch population of German Longhaired Pointer dogs

The German Longhaired Pointer (GLP) breed is a versatile pointer dog breed. In the current study, we investigated the genetic diversity of these dogs based on SNP array data and compared it to 11 other pointer setter breeds. The results show that GLPs have a relatively low level of inbreeding among these pointer breeds. In addition, with the availability of pedigree information of the GLPs, we demonstrate that the correlation between pedigree-based inbreeding and genotype-based inbreeding coefficients was high (R = 0.89 and 0.85). By investigating population structure between these 12 pointer setter breeds we showed that GLP is a breed distinct from other pointers and shares common ancestry with a few other pointing breeds. Finally, we identified selection signatures in GLPs using the runs of homozygosity islands method. The most significant runs of homozygosity island was detected on chromosome 30 harboring the genes RYR3, FMN1, and GREM1. The RYR3 gene plays a role in skeletal muscle contraction while the FMN1 and GREM1 genes are involved in limb development. The selection on these three genes could have contributed to the excellent athletic performance of GLPs, which is an extremely important characteristic for this hunting dog.

Using the Unity Game Engine to Develop a 3D Simulated Ecological System Based on a Predator–Prey Model Extended by Gene Evolution

In this paper, we present a novel implementation of an ecosystem simulation. In our previous work, we implemented a 3D environment based on a predator–prey model, but we found that in most cases, regardless of the choice of starting parameters, the simulation quickly led to extinctions. We wanted to achieve system stabilization, long-term operation, and better simulation of reality by incorporating genetic evolution. Therefore we applied the predator–prey model with an evolutional approach. Using the Unity game engine we created and managed a closed 3D ecosystem environment defined by an artificial or real uploaded map. We present some demonstrative runs while gathering data, observing interesting events (such as extinction, sustainability, and behavior of swarms), and analyzing possible effects on the initial parameters of the system. We found that incorporating genetic evolution into the simulation slightly stabilized the system, thus reducing the likelihood of extinction of different types of objects. The simulation of ecosystems and the analysis of the data generated during the simulations can also be a starting point for further research, especially in relation to sustainability. Our system is publicly available, so anyone can customize and upload their own parameters, maps, objects, and biological species, as well as inheritance and behavioral habits, so they can test their own hypotheses from the data generated during its operation. The goal of this article was not to create and validate a model but to create an IT tool for evolutionary researchers who want to test their own models and to present them, for example, as animated conference presentations. The use of 3D simulation is primarily useful for educational purposes, such as to engage students and to increase their interest in biology. Students can learn in a playful way while observing in the graphical scenery how the ecosystem behaves, how natural selection helps the adaptability and survival of species, and what effects overpopulation and competition can have.