Agrigenomics is an emerging and ever-more-important field of biology, linking the examination of entire genomes to agricultural outcomes that can affect the lives of vast populations of people. Thermo Fisher Scientific is at the forefront of animal and plant genomics tools, design and data collection, in particular via its Axiom Genotyping Solution, AgriSeq targeted genotyping by sequencing (GBS) and associated services.
Agricultural genomics can be challenging for a variety of reasons, including sequence complexity, high genetic diversity and limited sequence availability. Although reference genomes are increasingly widely available for numerous species of agricultural interest, many questions in agricultural science are best approached with custom tools, in particular custom genotyping panels tailored to the species of interest and intended inquiry. Thermo Fisher Scientific offers end-to-end project management services through panel design, wet-lab validation and data analysis to help ensure delivery of high-performance custom genomics panels for any project. Thermo Fisher Scientific works closely with customers to identify the appropriate reference genomes and other pre-existing information. We make sure that both researcher and service provider have the same understanding of the custom panel’s ultimate use. The earlier in the process Thermo Fisher Scientific can be involved, the more effective the resulting panel will be.
The AgriSeq panel design team has worked on over 100 custom panels designed to provide genomics data for crops, vegetables, trees, livestock and companion animals, fish, shrimp and flies, among other organisms. AgriSeq panels are flexible, allowing the addition of markers even after the panel is otherwise complete. This flexibility even extends to surveying multiple types of variants, such as SNPs and indels, in a single panel and to indel mutations of highly divergent size.
The AgriSeq team is constantly developing new tools and data pipelines. Research is ongoing to improve the inclusion of long indel mutations and other difficult-to-sequence genetic variants into AgriSeq panels. Software development to improve the availability of results to researchers is also an active and ongoing endeavor, including the creation of new plugins to collate and summarize complex genotype data. Development is also ongoing on a web tool to allow customers to pre-check their markers before submitting them to the designers, allowing markers to reach the designers pre-validated and save valuable time for all parties.
AgriSeq genotyping technology offers many advantages to researchers. AgriSeq technology can not only improve reads of hotspot positions, but works to generate more novel calls, often two to three times the number the customer requested, allowing for more in-depth research than anticipated. AgriSeq’s versatility allows an AgriSeq panel to be designed for 50 markers or 5,000, allowing this tool to serve goals as diverse as checking for predisposition to specific diseases and genomic selection, or exploratory studies.
Whether your intended application is parentage, breeding, SNP detection or something else entirely, AgriSeq next-generation sequencing tools can help you collect the information you need. Contact AgriSeq’s team for more information.