Plant Breeding for the future using the Applied Biosystems Axiom and Eureka Genotyping Platforms

Population increases and environmental changes have increased the need for efficient and directed plant breeding. As the world’s climate shifts in response to decades of pollution, the world’s agricultural heartlands are beginning to visibly change in character, and these changes mean that plant cultivars that previously excelled in one place are seeing reduced yields and increased pest attack. Breeding plants to better cope with the changes to their environments stands to make water-hungry crops like almonds better suited to the increasingly arid regions that grow them and help coastal crops resist the increasing issues of saltwater intrusion and flooding, among others. The seed industry is pushing hard to increase rates of genetic gain and reduce cycle times at each step of the breeding process. Modern tools like marker-assisted selection represent a key innovation, adding much-needed precision to this venerable practice. Syngenta, a global agriculture company with a mission to bring solutions – be it seeds, chemistry, or digital tools to help with decision making – to growers around the world, is using Thermo Fisher Scientific genotyping platforms to provide necessary genetic data for its breeding pipeline to rapidly select for new varieties with improved yield potential.


Population increases and environmental changes have increased the need for efficient and directed plant breeding. As the world’s climate shifts in response to decades of pollution, the world’s agricultural heartlands are beginning to visibly change in character, and these changes mean that plant cultivars that previously excelled in one place are seeing reduced yields and increased pest attack. Breeding plants to better cope with the changes to their environments stands to make water-hungry crops like almonds better suited to the increasingly arid regions that grow them and help coastal crops resist the increasing issues of saltwater intrusion and flooding, among others. The seed industry is pushing hard to increase rates of genetic gain and reduce cycle times at each step of the breeding process. Modern tools like marker-assisted selection represent a key innovation, adding much-needed precision to this venerable practice. Syngenta, a global agriculture company with a mission to bring solutions – be it seeds, chemistry, or digital tools to help with decision making – to growers around the world, is using Thermo Fisher Scientific genotyping platforms to provide necessary genetic data for its breeding pipeline to rapidly select for new varieties with improved yield potential.

Jason Nichols is a Team Leader in Syngenta’s Molecular Analytics group at its Research Triangle Park, North Carolina facility, whose mission is to provide the genomic information and molecular technologies that his internal colleagues in product discovery and development depend on. Thermo Fisher Scientific’s Applied Biosystems Axiom and Eureka platforms have been extremely helpful to this mission. These platforms provide low- to medium-density genotypic data for fixed panels of single-nucleotide polymorphisms (SNPs) and molecular variants, supporting early genomic selection in favor of traits of interest across a range of crops. Axiom and Eureka provide advantages in terms of cost and turn-around time that contribute to our ability to conduct low-medium density genotyping at the scale (i.e., volumes of samples) needed to meet Syngenta’s molecular breeding targets. Syngenta finds these platforms particularly ideal for their use because, as Jason puts it, “both are available as end-to-end services, through the same vendor and location, and they are able to take in footprints that we create, rather than requiring us to submit targets and coordinates against a reference genome that may or may not be relevant, and report data in a format that we are used to.”

This combination of advantages makes these two platforms ideal for Syngenta as they move into the future of seed breeding, toward ever more successful selection of varieties with improved traits. “Shorter turnaround times open up new applications,” Jason explains, and “Eureka especially has quite a short turnaround time, and that’s enabled us to apply it to more demanding applications.” Thermo Fisher Scientific’s open and collaborative environment helps companies like Syngenta continually optimize and customize their processes and panels, leading to more effective results all around.