Modern genomics studies generate vast amounts of sequencing data, but researchers still face a familiar challenge: how do you accurately determine which allele has been inherited from which parent?
A recent study published in Genetics Selection Evolution provides an excellent example of how targeted genotyping can support complex genomic investigations. Researchers studying genomic imprinting in pigs used the PACE®-IR 2× Genotyping Master Mix to genotype a variant within the important IGF2 locus, helping them establish parental inheritance patterns and validate findings from their wider genomic analysis.
The challenge: identifying parental inheritance
The study investigated parent-of-origin gene expression, a phenomenon where genes are expressed differently depending on whether they are inherited from the mother or father.
To analyse these effects accurately, researchers must first determine which allele each offspring inherited from each parent. While whole-genome sequencing and RNA sequencing can identify candidate genes and expression patterns, targeted genotyping is often required to confirm inheritance at specific loci.
This is particularly important when studying genes such as IGF2, one of the best-known imprinted genes in pigs and a locus associated with growth and production traits.
Why the researchers used PACE®
To genotype a variant within the IGF2 region, the research team selected PACE® (PCR Allelic Competitive Extension) technology.
PACE® offers several advantages for this type of work:
- Accurate SNP discrimination
- Simple assay design using unlabelled primers
- Cost-effective screening of large sample sets
- Compatibility with standard qPCR instrumentation
- Flexible deployment from small validation studies to large-scale breeding programmes
In the study, PACE® genotyping was used to establish inheritance patterns at the target variant, providing information needed for downstream analyses of parent-of-origin expression.
The researchers subsequently confirmed the PACE® results using Sanger sequencing, demonstrating confidence in the genotyping data.
Beyond genomic imprinting: where else can this approach be applied?
Although this study focused on genomic imprinting, the challenge it addresses is common across many areas of genetics and breeding research.
Researchers frequently need to:
Validate sequencing discoveries
Genome-wide sequencing studies often identify candidate variants associated with important traits. Before these findings can be investigated further, researchers need a reliable and affordable method to genotype larger populations.
PACE® provides a practical route from discovery to validation.
Track inheritance in breeding programmes
Whether working in livestock, aquaculture, crop breeding or horticulture, understanding which alleles are passed from parents to offspring is fundamental to genetic improvement programmes.
PACE® enables rapid genotyping of informative markers across breeding populations.
Confirm candidate trait-associated markers
When a SNP is associated with disease resistance, productivity, growth, quality traits or other commercially important characteristics, breeders often need a scalable way to screen large numbers of individuals.
PACE® allows researchers to convert sequencing discoveries into routine marker assays.
Support parentage and lineage studies
Establishing inheritance patterns is critical in many applications, from livestock breeding and conservation genetics to aquaculture and plant breeding.
The same genotyping approach used in this study can be applied to confirm parentage, track genetic lineages and monitor breeding outcomes.
Turning genomic discoveries into actionable data
Large-scale sequencing technologies continue to transform genetics research, but targeted genotyping remains an essential part of the workflow.
This study demonstrates how PACE® can support researchers by providing accurate genotype information at key loci, helping bridge the gap between genome-wide discovery and biological validation.
Whether the goal is understanding genomic imprinting, validating trait-associated markers or tracking inheritance in breeding populations, PACE® offers a flexible and cost-effective solution for generating the genotypic data needed to move research forward.
Ready to turn your genomic discoveries into reliable genotyping assays?
Whether you’re validating trait-associated markers, tracking inheritance patterns, or scaling breeding programmes, PACE® provides a flexible, accurate, and cost-effective solution for targeted genotyping.
Reference
- Perret M. et al. (2026). A comprehensive genome-wide scan for parent-of-origin expressed genes in the pig clarifies the conservation landscape of genomic imprinting. Genetics Selection Evolution.
