Agriculture is one of the key innovations in human development. The option to stay in one place rather than range widely in search of naturally occurring food made cities possible, and the formation of farming as a specialty created the possibility of lives beyond bare subsistence. Ever since, humans have been breeding new and improved varieties of food plants, enlarging the edible parts and improving the disease resistance of corn, wheat, cassava, soybeans and dozens of other plant species around the world. Plant breeding can be a tricky process, however, because plants often have mating biology (such as wind pollination, which obscures parentage) that is difficult to manipulate to human advantage, and some engineered varieties are complex hybrids of multiple related species, or are sterile and cannot be cross-bred at all. Such a field of agriculture is ideal for informative modern tools such as next-generation sequencing and targeted genotyping-by-sequencing (GBS). Firms such as GDM Seeds represent the realization of that promise.
GDM Seeds is an Argentinian plant-breeding company specializing in soybean research, development and commercialization, trying to refine and enhance the world’s soybean crop wherever soybeans are grown. With soybeans representing a large fraction of global agriculture, any advance in yield, disease resistance, tolerance to changing environmental conditions or other traits stands to help feed millions upon millions of people, both directly and through refined products such as soybean oil. Dr. Gaspar Malone is GDM’s manager of biotechnology research, and has recently incorporated Thermo Fisher Scientific’s AgriSeq genotyping-by-sequencing solution into GDM Seeds’s development process.
Bringing genomics technologies into a plant-breeding operation is a large and expensive endeavor, incorporating technologies such as ultra-high-throughput genotyping, molecular-assisted backcrossing, genome-wide selection, and more, each aimed at a different facet of the problem. It is necessary to screen thousands of samples to get a full understanding of the genetics at work and choose individuals for propagation or further research that will breed true, and the large size of many plant genomes makes plant genomics information harder to obtain than an otherwise similar animal sequence. These operations necessarily require a decision between marker-assisted methods that generate a small amount of information about a large number of samples, or genotyping-by-sequencing methods that generate a large amount of information but cannot process large numbers of samples as easily. AgriSeq represents a bridge between the specificity of marker-assisted selection and the vast range of genome-wide selection, allowing the examination of a huge number of well-chosen markers to verify large quantities of specific information about numerous samples, addressing a gap between the other methods available to Dr. Malone and GDM Seeds. As he puts it, “AgriSeq has shown to be a revolution for marker-assisted selection in crop breeding companies, offering an ultra-high-throughput genotyping output.”
Dr. Malone has been using AgriSeq technology since 2016, starting with the Ion S5 and Ion Chef platforms and moving on to the Ion S5 XL and updated, early-access barcodes. Using these advanced gene chips enables a single GDM technician to make over 700 sequencing libraries a day, each processed using two different SNP (single-nucleotide polymorphism) panels to test a huge number of loci for differences of interest. Dr. Malone hopes to expand GDM’s operations still farther, to up to 200,000 samples per year by 2021. Dr. Malone was able to get these devices set up and running quickly and without incident and maintains a fruitful partnership with Thermo Fisher Scientific to keep these devices and panels up, running and regularly improved. “The main impact we expect from AgriSeq technology is to place our company at the forefront of the best of genotyping technology,” Dr. Malone explains.
For more information on how the AgriSeq genotyping solution and devices such as the Ion GeneStudio S5 can help your lab achieve its goals, use our contact form to speak with our agrigenomics team.
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