Genomics information is at the center of more and more research in biology, whether in academia, government laboratories or private industry. Independent service providers are an increasingly important part of this process, offering next-generation sequencing, genotyping and similar services to all of these researchers for a fee. Able to provide services at enormous scales using the latest tools, service providers such as Eurofins bring genotyping-by-sequencing and similar capabilities to labs that cannot maintain them on their own, making the power of genomics more accessible.
Starting with tools for testing wine authenticity, Eurofins has built a particularly strong presence in the field of plant agrigenomics, offering genetic assays that can assess plant health, identity, authenticity and overall vigor. These tools help plant breeders make sure that plant varieties they create show the attributes they desire, and track rare or valuable traits that are important for viable agriculture. Plant genetics features complications, such as extraordinarily large genomes and allopolyploidy, that are rare or nonexistent among animals, making plant agrigenomics an especially challenging field. Within that challenge, single-nucleotide polymorphisms (SNPs) are an area of increasing interest, difficult to detect with other methods because of their small size. Particularly when one is interested in numerous possible SNPs at different loci, reading and understanding them all can be beyond many practitioners and tools.
Eurofins achieves its presence here with the aid of Applied Biosystems genotyping solutions. For high-density genotyping requests, Eurofins uses the Applied Biosystems GeneTitan and associated Axiom array, but the AgriSeq NGS has proven ideal for smaller, medium-scale requests of 100 to 3,000 genes or markers per run. The AgriSeq platform has proven particularly versatile, thanks to the option to use predesigned panels or create custom panels using the Ion AmpliSeq Designer. This enables AgriSeq to serve both common requests and rare ones, including species and varieties for which gene panels do not already exist. Additionally, as Eurofins chief scientific officer Dr. Farhad Ghavami puts it, “The nice thing about these AgriSeq panels and chemistry that we’ve found is that you don’t need that much DNA,” which saves time, effort and possibility all around. Eurofins collaborates with Thermo Fisher Scientific to develop and implement custom gene panels, appreciating the fast turnaround time and comprehensive validation that this approach offers. “Our experience with AgriSeq has been excellent in different animal and plant species,” as Dr. Ghavami tells it, and Eurofins has made use of numerous pre-existing and custom AgriSeq panels.
Eurofins worked with Thermo Fisher to develop an AgriSeq genotyping-by-sequencing (GBS) panel for sunflowers at this medium scale, filling a gap in current offerings in order to help sunflower breeders make use of this modern technique as they develop and maintain new varieties as ornamental plants, for food and for seed oil. This panel was based on 5,019 SNP markers taken from three distinct sunflower varieties, providing a comprehensive overview of sunflower genetics suitable for breeding. The 700 best-performing markers, distributed uniformly through the genome and across all chromosomes, were selected for the GBS panel.
In both the long process of developing and validating this new sunflower panel and their uses of existing panels for maize, soy, canola, sunflower, pine trees, cattle, horses, sheep, dogs and swine, Dr. Farhad Ghavami and Eurofins report excellent results from their use of and collaboration with Thermo Fisher Scientific. “We chose AgriSeq because of Thermo Fisher’s support and collaboration,” Dr. Ghavami tells us. “The process for making a custom panel was really easy and user-friendly…it was a fast approach to get the panel we wanted.”
Learn more about Thermo Fisher’s AgriSeq genotyping-by-sequencing tools.