Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs

Next-Generation Snow Leopard Population Assessment Tool: Multiplex-PCR SNP Panel for Individual Identification From Faeces

In recent years, numerous single nucleotide polymorphism (SNP) panel methods to genotype non-invasive faecal samples have been developed. However, none of these existing methods fit all of the criteria necessary to make a SNP panel broadly usable for conservation projects in any country-cost effective, streamlined lab protocol and user-friendly open-source bioinformatics protocols for panel design and analysis. Here, we present such a method and display its utility by developing a multiplex PCR SNP panel for conducting individual ID of snow leopards, Panthera uncia, from faecal samples. The SNP panel we present consists of 144 SNPs and utilises next-generation sequencing technology. We validate our SNP panel with paired tissue and faecal samples from zoo individuals, showing a minimum of 96.7% accuracy in allele calls per run. We then generate SNP data from 235 field-collected faecal samples from across Pakistan to show that the panel can reliably identify individuals from low-quality faecal samples of unknown age and is robust to contamination. We also show that our SNP panel has the capability to identify first-order relatives among sampled zoo individuals and provides insights into the geographic origin of samples. This SNP panel will empower the snow leopard research community in their efforts to assess local and global snow leopard population sizes. More broadly, we present a SNP panel development method that can be used for any species of interest for which adequate genomic reference data is available.

Rewilded horses in European nature conservation - a genetics, ethics, and welfare perspective

In recent decades, the integration of horses (Equus ferus) in European rewilding initiatives has gained widespread popularity due to their potential for regulating vegetation and restoring natural ecosystems. However, employing horses in conservation efforts presents important challenges, which we here explore and discuss. These challenges encompass the lack of consensus on key terms inherent to conservation and rewilding, the entrenched culture and strong emotions associated with horses, low genetic diversity and high susceptibility to hereditary diseases in animals under human selection, as well as insufficient consideration for the social behaviour of horses in wild-living populations. In addition, management of wild-living horses involves intricate welfare, ethics and legislative dimensions. Anthropocentric population-control initiatives may be detrimental to horse group structures since they tend to prioritise individual welfare over the health of populations and ecosystems. To overcome these challenges, we provide comprehensive recommendations. These involve a systematic acquisition of genetic information, a focus on genetic diversity rather than breed purity and minimal veterinary intervention in wild-living populations. Further, we advise allowing for natural top-down and bottom-up control - or, if impossible, simulating this by culling or non-lethal removal of horses - instead of using fertility control for population management. We advocate for intensified collaboration between conservation biologists and practitioners and enhanced communication with the general public. Decision-making should be informed by a thorough understanding of the genetic makeup, common health issues and dynamics, and social behaviour in wild-living horse populations. Such a holistic approach is essential to reconcile human emotions associated with horses with the implementation of conservation practices that are not only effective but also sustainable for the long-term viability of functional, biodiverse ecosystems, while rehabilitating the horse as a widespread wild-living species in Europe.

Reduced-Cost Genotyping by Resequencing in Peanut Breeding Programs Using Tecan Allegro Targeted Resequencing V2

The identification of informative molecular markers is useful for linkage mapping and can benefit genome-wide association studies by providing fine-scale information about sequence variations. However, high-throughput genotyping approaches are not cost-effective for labs that require frequent use, such as breeding programs that need to perform genotyping on large populations with hundreds of individuals. The number of single nucleotide polymorphism markers generated by those approaches can be far more than needed for most breeding programs; instead, breeders focus on the use of at most hundreds of polymorphic molecular markers for analysis. To help make use of molecular markers a routine tool for breeding programs, we aim to develop a cost-effective genotyping system by using the Tecan Allegro Targeted Resequencing V2 kit. This provides a customized probe design, which indicates that all the DNA fragments synthesized are known targets. SNPs obtained from previous peanut next-generation sequencing data were pre-filtered and selected as targets. These SNP targets were polymorphic among different tetraploid accessions and were selected to be distinguishable from paralogs. A total of 5154 probes were designed to detect 2770 SNP targets and were tested on 48 accessions, which include some closely related sister lines from a breeding population. The results indicated that genotyping by a targeted resequencing approach reduced the cost from around USD 28 (SNP chip and GBS) to USD 18 per sample, while providing polymorphic markers with accurate SNP calls. With this cost-effective genotyping platform, pre-selected SNP markers can be used effectively and routinely for more breeding programs.

Development of a high-density sub-species-specific targeted SNP assay for Rocky Mountain bighorn sheep (Ovis canadensis canadensis)

Due to their abundance and relative ease of genotyping, single nucleotide polymorphisms (SNPs) are a commonly used molecular marker for contemporary population genetic and genomic studies. A high-density and cost-effective way to type SNP loci is Allegro targeted genotyping (ATG), which is a form of targeted genotyping by sequencing developed and offered by Tecan genomics. One major drawback of this technology is the need for a reference genome and information on SNP loci when designing a SNP assay. However, for some non-model species genomic information from other closely related species can be used. Here we describe our process of developing an ATG assay to target 50,000 SNPs in Rocky Mountain bighorn sheep, using a reference genome from domestic sheep and SNP resources from prior bighorn sheep studies. We successfully developed a high accuracy, high-density, and relatively low-cost SNP assay for genotyping Rocky Mountain bighorn sheep that genotyped ~45,000 SNP loci. These loci were relatively evenly distributed throughout the genome. Furthermore, the assay produced genotypes at tens of thousands of SNP loci when tested on other mountain sheep species and subspecies.