FrenchSeq, the DNA sequence for AXIOM selection.

Mastering DNA means mastering the future of breeding. For several decades, AXIOM has relied on genomics to refine its selection choices and push back the limits of precision. The reference tool: the DNA chip, which analyzes up to 700,000 variations (or SNPs) per animal. A tried-and-tested technology, but one that is now reaching its limits in the face of the explosion in sequencing capacity.

A new era is dawning: that of access to complete genome information, i.e. several million data sets per individual. This revolution paves the way for even finer, faster and potentially more sustainable selection.

AXIOM, a pioneer in the use of sequencing for its fundamental research work, is now taking the next step: making this technology available on a large scale, on a routine basis, to reinforce current tools or even replace them. This paradigm shift involves overcoming a number of scientific and technical hurdles.

This is what the FrenchSeq project is all about: turning sequencing into a concrete lever for the pork industry. Developing French know-how, from raw DNA to the use of information in selection indexes, the detection of genes of interest or anomalies. An ambitious research challenge, but also a strategic industrial challenge for the entire industry.

Context

Genomics, a pillar of AXIOM breeding for over 10 years

For over 10 years, genomics has been an essential tool, fully integrated into AXIOM’s selection work. Using genomic chips, AXIOM identifies genetic variations between individuals of the same breed by analyzing SNPs (single nucleotide polymorphisms), regularly spaced differences in DNA.

AXIOM can then accurately select those individuals that inherit the best characteristics. This represents between 50,000 and 70,000 pieces of information analyzed per animal. At the same time, AXIOM has been investing for several years in the creation of reference genomes, sequenced in their entirety, giving access to all the information in the genome, i.e. several million data per individual, far beyond SNPs.

Anticipating the future: towards routine use of sequencing

AXIOM’s challenge is to anticipate the future by developing the tools needed to use sequencing as a routine part of its selection scheme. This technology will offer a much richer level of information than current methods.

This level of knowledge opens the way to new selection levers, such as the finer identification of genes of interest or the early detection of genetic anomalies. To date, no swine laboratory or genetic scheme has the tools to integrate large-scale sequencing for routine use.

The concrete benefits of the FrenchSeq project

FrenchSeq: building comprehensive, 100% French genomics expertise

The FrenchSeq project represents a major strategic lever for AXIOM, strengthening its technological sovereignty in a field where the genome chip market is still dominated by a single player and where competition is very limited. For AXIOM, reducing this dependence is essential in order to secure its long-term selection scheme.

AXIOM’s development relies on leading French partners such as GDBiotech and INRAE, guaranteeing not only national scientific expertise, but also logistical and regulatory advantages. Legislation on DNA ownership varies from country to country, and working in France gives AXIOM greater protection for its genetic data. What’s more, the proximity of our teams facilitates operational management, a considerable advantage in a context where transporting biological samples can be complex.

A sequencing chain mastered from start to finish

The first stage of development is DNA sequencing. Although AXIOM does not carry out the laboratory biology itself, the company ensures that it controls and supports the development of key technologies with French partners. This is an important step in mastering the research and selection chain for AXIOM lines.

As part of the FrenchSeq project, the analysis was carried out from the collection of the DNA from the farm to the complete reading of the sequence. It is essential that each technical step is carried out with a high level of precision, in order to collect the highest quality DNA sequence possible. The industrialization of these processes also implies cost optimization, a prerequisite for routine use.

Sequencing depth,
a lever for optimization

Sequencing depth determines data accuracy, like the scale of a map: the higher the depth, the finer the detail… but the higher the cost:

• Shallow: sufficient for routine analyses, such as on-chip genotyping, but less accurate.
• High depth: essential for fundamental research on targeted areas of the genome, but more expensive

AXIOM has a vast database, with sufficient reference animals, sequenced at depths of up to 64x (a commonly accepted quality depth is equal to 16x). Thanks to this resource, the FrenchSeq project has been able to develop imputation tools, capable of efficiently and accurately going from 1x to over 30x.

This work, the fruit of a year and a half of bioinformatics research, is based on the optimal choice of algorithms and software. Thanks to these advances, AXIOM and its French partners now have the technical capacity to switch from on-chip genotyping to full sequencing, if necessary.

Perspectives and applications of the complete sequence

The use of complete genomic sequences opens up major prospects for pig breeding, far beyond the current capabilities of genomic chips.

Better targeting of genes of interest

The technical limitation of genomic microarrays is that it is not possible to integrate all the areas of the genome likely to be of strategic importance. As a result, certain regions have to be analyzed separately, adding time and cost. With the complete sequence, every DNA position can be examined, providing a comprehensive view of the animal’s genetic status.

Work on the FrenchSeq project has made it possible to assess the performance of the various existing methods for targeted analysis of genes of interest, identifying their advantages, limitations and conditions for automation. The quality of AXIOM’s reference genomes is a decisive asset, making it possible to carry out precise searches for any area of interest, subject to the availability of suitable computing resources.

Integrating crossbred animals into genomic analyses

DNA microarrays have also shown their limitations on crossbred animals.
The sequence enables more precise phasing of the paternal and maternal origins of DNA segments, even in the absence of complete genealogical information. This breakthrough paves the way for the use of “omics” tools on meat pigs, often bred by polyspermy (several fathers in the same dose), by tracing genetic links with their ancestors.

Early detection of genetic abnormalities thanks to AI

Every animal is born with a number of mutations, most often without consequence, but sometimes causing major defects (infertility, developmental disorders, etc.). Routine use of the sequence, coupled with artificial intelligence models, could enable automatic, early detection of these anomalies. This would make it possible to eliminate carrier animals from the selection process at a very early stage, without the need for additional analyses such as karyotyping.

In this way, mastery of the complete sequence is not limited to replacing genomic chips: it opens the way to finer, faster selection, better adapted to the challenges of performance, health and genetic diversity.

Conclusion

FrenchSeq marks a major step forward for AXIOM and the French pork industry. At the interface between cutting-edge research and field applications, this project has enabled us to reach a technological milestone: making sequencing available for routine use, as a credible alternative to SNP chips.

Beyond the gains in precision and data richness, FrenchSeq positions AXIOM as an autonomous player, capable of controlling the entire chain – from sample to valorized information. This is a strategic advance, opening up new opportunities for detecting anomalies, exploring areas of genetic interest, and making effective use of genomics in crossbred animals.
It is also a model of successful transfer between scientific innovation and operational challenges, based on a strong partnership dynamic on a national scale.
With FrenchSeq, AXIOM confirms its role as a pioneer, ready to take swine genomics into a new era.