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Innovative solutions that help accelerate plant and animal breeding programs

Molecular breeding can significantly reduce the cost and time required to deliver improved plant and animal species for agricultural use. Advancements in genomic technologies are accelerating these breeding programs by enabling higher-throughput genotyping across large populations than ever before. Applied Biosystems AgriSeq targeted genotyping by sequencing (GBS) solutions are our latest innovation that helps our customers economically deliver high-throughput plant and animal genotypes.

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Up to 1.6M genotypes per day for pennies or less per genotype

The AgriSeq targeted GBS solution utilizes a highly efficient multiplexed PCR chemistry where hundreds to thousands of markers can be targeted and uniformly amplified in a single reaction. The amplicon libraries can then be barcoded and pooled for simultaneous sequencing of hundreds of samples on the Ion Torrent suite of next-generation sequencing (NGS) instruments. At a cost of pennies or less per genotype, AgriSeq targeted GBS is capable of generating up to 1.6 million genotypes per day from high-quality NGS data. Whether you’re looking to achieve more accurate marker-assisted breeding selection, or to improve your livestock parentage discrimination and trait monitoring, our solutions can help advance your plant and animal breeding programs.

Scalable genotyping

AgriSeq genotyping is performed on the Ion Torrent NGS platform and is validated for 100–5,000 markers per sample. Using the Ion 540 chip, AgriSeq genotyping can produce up to 800,000 unique genotype results per chip at an average read depth of 100x to achieve maximal genotype call rates. Combinations of different panels and species can also be processed on the same run.

Reproducible results

Deliver high marker call rates with greater reproducibility across diverse sample sets to help ensure accurate selection. Marker call rates can exceed 96% with >99% inter- and& intra-run reproducibility, and AgriSeq targeted GBS data maintains a high concordance (>99%) when compared to the orthogonal genotyping technologies such as DNA microarrays.

Fast, simple workflow

Includes library generation, automated template prep, sequencing, and data analysis, which can be completed in ~2 days with <4 hours of hands-on time, enabling a single operator to process up to four 96- or 384-well plates per day. The Ion Chef System automates template preparation and chip loading, requiring only 15 min of hands-on time, followed by an overnight run.

Custom panel designs, validation and pilot projects

Agricultural genomics can be challenging for a number of reasons, including sequence complexity, high genetic diversity, and limited sequence availability. We offer end-to-end project management services through panel design, wet-lab validation, and data analysis to help ensure delivery of high-performance panels for your project. These low cost, proof of concept pilot projects are a great way to confirm the value of AgriSeq targeted GBS for your research.


Bovine ISAG SNP Parentage Panel (2013)

Our parentage panel contains primers targeting the 200 ISAG recommended SNPs available for simple multiplexed analysis using the AgriSeq targeted GBS chemistry. Qualified using the Eureka 2015 ISAG/ICAR 3rd SNP Typing Bovine Comparison samples, our comprehensive panel delivers reliable genotyping results for animal parentage testing.

  • Reproducible genotyping of 200 ISAG-recommended markers, with >98% genotyping call rate across breeds
  • Simple, high-throughput workflow—up to 768 unique animals can be pooled per chip
  • Customizable approach to combine with compatible trait or markers that detect genetic defects

Resources

Videos

Tom Osborn, Monsanto's Director of Molecular Breeding Technology, explains how genotyping has been transformed through a series of technology innovations to the current state of automated workflows.

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