Agrigenomics Videos and Webinars

Paul Flynn, Head of R&D, Weatherbys Scientific

Transitioning from STR to SNP molecular markers to perform parentage verification is becoming an ever more discussed topic within the global Equine community. A key area that requires exploration is ensuring maintenance of test integrity when moving to SNP based parentage. Due to its highly accurate and reproducible results, targeted GBS is becoming an increasingly favored technology for SNP genotyping.

Wim van Haeringen, PhD, CEO, VHLGenetics

As a pioneer with a successful history of applying molecular technologies to animal genotyping, VHLGenetics is again leading the way with the application of genotyping by sequencing (GBS). VHL will present the output of a collaborative effort with Thermo Fisher Scientific on feline, canine, and bovine GBS panels for detecting genetic variants and conducting parentage testing.

Maarten de Groot, Chief Financial Officer, VHLGenetics

Recent advances in targeted next-generation sequencing technologies are creating new opportunities for service labs to expand the breadth of variants evaluated in a single, low-cost test.

Elinor K. Karlsson, PhD, Assistant Professor, Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School; Director of Vertebrate Genomics, Broad Institute of Harvard and MIT

Most dogs throughout the world are mixed-breed dogs, yet past genetic studies in dogs have focused on purebreds. In part, this reflected technological limitations, as the genotyping panels available were designed for purebred dog populations.

Guilherme Neumann, Humboldt University of Berlin, Germany

German Black Pied (DSN) cattle are an endangered ancestral breed of Holstein and an important reservoir of genetic diversity for Holstein breeding. The team at Humboldt University of Berlin had been using generic 50K bovine chips but these were missing important DSN variation and so they partnered with Thermo Fisher Scientific to create an Axiom Genotyping Array that delivered high haplotype and functional variant coverage. Their strategy of combining variants from existing commercial arrays with de novo SNP discovery is an excellent case study of optimized design of breeding and conservation tools.

Brenda Mae Murdoch PhD, Assistant Professor, Animal and Veterinary Science, University of Idaho

Genomic tools have enabled the acquisition of information to aid and accelerate the rate of genetic improvement of agricultural livestock species. With price still a limiting factor to widespread utilization in the U.S. sheep industry, there is a need for a lower density panel that reports markers for Mendelian and other well-known traits relevant to sheep production.

Emily Rose, Sequencing Lab Supervisor, GeneSeek-Neogen

Bacterial classifications and phylogenetic studies have been largely improved by the targeted amplicon sequencing of the hypervariable regions within the 16S rRNA gene, which is represented in all bacteria. However, limiting the classification investigation to 16S sequencing can still lead to difficulty in discerning closely related organisms down to the species level. To aid in the pursuit of accurately identifying bacterial species and serotypes (strains), Thermo Fisher Scientific has recently created the Applied Biosystems Axiom Microbiome Array as an effective assay to distinguish thousands of microorganisms at the species and even serotype level.

A number of global dynamics are changing the agriculture and food ecosystem. The simplicity, accessibility, and ease of use of molecular technologies and next-generation sequencing are reshaping the animal and plant breeding sciences. Thermo Fisher Scientific products and services offer high quality, innovative life science solutions for every plant and animal research or breeding lab.

Aaron Larsen, Chief Science Officer, United Bio Research, Inc.

The targeted genotyping-by-sequencing (GBS) approach using the AgriSeq workflow streamlines the process of developing custom assays and provides the flexibility to quickly modify or combine existing assays.

Ali Pirani, Manager, Bioinformatics, Microarray, Thermo Fisher Scientific

The success of genome-wide association studies has paralleled the development of efficient genotyping technologies. An apt high-throughput genotyping platform can enable marker-assisted breeding, association mapping, and genomic selection.

Wim van Haeringen, PhD, CEO, VHLGenetics

As a pioneer with a successful history of applying molecular technologies to animal genotyping, VHLGenetics is again leading the way with the application of genotyping by sequencing (GBS). VHL will present the output of a collaborative effort with Thermo Fisher Scientific on feline, canine, and bovine GBS panels for detecting genetic variants and conducting parentage testing.

Through the use of Ion AmpliSeq™ custom panels, GeneSeek—a Neogen Corporation subsidiary—has designed a primer pool that is able to target ~4,000 SNP loci which allows certain traits such as tenderness and parentage to be identified in cattle. Within this process, GeneSeek has modified the Ion AmpliSeq protocol in order to sequence at least 192 samples in one run.

Donagh Berry, Quantitative genetics research officer, Teagasc

Axiom genotype panel was developed to provide high-quality genotype calls, at a low cost, to facilitate the generation of considerable information for use by sheep producers and the sheep sector as a whole.

Donagh Berry, Principal Investigator in Quantitative Genetics, Teagasc

Sheep, because of their relatively low unit value and lack of widespread use of artificial insemination and single-sire mating, differ from many other farmed species in their requirements for low-cost genomic technologies.

Tom Scott, CEO, Informa Agribusiness Intelligence IEG

The world’s agriculture market is dynamic and subject to constant change. Investments in agricultural technologies and innovations are driven by the underlying economics of commodities and the markets they support. This session will provide both short- and long-term perspectives on the impact of mega-trends, trade, industry consolidation, and other market drivers on innovation and technology in agriculture. 

Farhad Ghavami, PhD, Chief Scientific Officer (CSO), Agrigenomics, Eurofins BioDiagnostics Inc.

The advent of next-generation sequencing technologies and the ongoing reduction of sequencing costs have made genotyping-by-sequencing (GBS) a common practice for genotyping in plant and animal breeding. Among different methods of GBS, amplicon-based GBS is an accurate and economical method that can expedite any QTL mapping projects and genomic selection programs.

Gaspar Malone, PhD, Biotechnology Research Manager, GDM Seeds

Molecular markers have allowed breeding companies to enhance the plant selection accuracy year by year. However, a high cost and restricted throughput of some technologies have become a challenge to meet the need of companies. Targeting genotyping-by-sequencing (T-GBS) has appeared as a good alternative, proving to be a low cost and ultra–high-throughput method while allowing breeding companies to optimize their breeding selection pipelines to help reduce time and cost.

A number of global dynamics are changing the agriculture and food ecosystem. The simplicity, accessibility, and ease of use of molecular technologies and next-generation sequencing are reshaping the animal and plant breeding sciences. Thermo Fisher Scientific products and services offer high quality, innovative life science solutions for every plant and animal research or breeding lab.

Hans Peter Koelewijn, Scientist, Genetics, BAYER Vegetable Seeds

Bayer Vegetable Seeds identified a need for a platform that would result in greater throughput, higher marker density, and a fast turnaround time to advance their breeding program.

Dr. Dario Grattapaglia, Senior Research Scientist and Project Leader, Brazilian Agricultural Research Corporation (Embrapa)

The identification of new sources of genetic variation is a key component of any long-term breeding strategy to increase the productivity, resilience, and sustainability of crop varieties. Over six million crop accessions are currently being conserved worldwide in still largely untapped gene banks. High-throughput, low-cost, and robust SNP genotyping technologies are necessary to unlock this wealth of diversity and release the data in an organized and user-friendly fashion to allow adoption by germplasm curators and breeders.

Dr. Carlos Azambuja, Director, GENIA

The barley industry requires strict control of varieties; Genia was asked to develop a method to enable the determination of varietal purity as well as to identify and quantify the components of varietal mixtures.

Ali Pirani, Manager, Bioinformatics, Microarray, Thermo Fisher Scientific

The success of genome-wide association studies has paralleled the development of efficient genotyping technologies. An apt high-throughput genotyping platform can enable marker-assisted breeding, association mapping, and genomic selection.

Sugar beet is one of the world’s most important crops, currently supplying around 20% of the sugar consumed worldwide. The development of varieties that require less technical inputs for cultivation is one of the main research goals in sugar beet. To achieve this, sugar beet breeding is focusing on genetic improvement programs assisted by SNP (single nucleotide polymorphisms) molecular markers.

Genotyping by sequencing (GBS) is a cost-effective alternative for obtaining a large number of markers across a large sample size, but markers are randomly distributed throughout the genome. Alternately, enrichment coupled with next-generation sequencing is a cost-effective strategy for obtaining sequence information for loci of interest across a large sample.

Tom Scott, CEO, Informa Agribusiness Intelligence IEG

The world’s agriculture market is dynamic and subject to constant change. Investments in agricultural technologies and innovations are driven by the underlying economics of commodities and the markets they support. This session will provide both short- and long-term perspectives on the impact of mega-trends, trade, industry consolidation, and other market drivers on innovation and technology in agriculture. 

Jason Nichols, Senior Team Leader, Molecular Analytics, Syngenta Crop Protection, LLC

The application of genotypic data to support molecular breeding of commercial crop species faces myriad challenges including cost pressure, demands for ever shorter turn-around times, species and genome complexity, etc. Recently, Syngenta has adopted the Applied Biosystems Axiom 384 HT Array platform for the majority of our crops’ needs for medium density fingerprinting. In parallel, and for select crops and applications where a lower density, more agile platform is required, we have also implemented the Applied Biosystems Eureka Genotyping platform.

Tom Osborn, Director of Molecular Breeding Technology, Monsanto

Genotyping at Monsanto has been transformed through a series of technology innovations to the current state of automated workflows that deliver high-volume genetic data for key decisions in product advancement. Some recent innovations utilizing genome-wide selection and data from genotyping by sequencing have led to our ability to conduct yield testing in the lab. The success of this new workflow is dependent on collaborations with internal and external technology partners to deliver scalable, low-cost, and rapid lab processes.