Genotyping by Amplicon Sequencing (GBAS)

Our genotyping by amplicon sequencing (GBAS) service is tailored to support breeding programs, R&D efforts, and quality control needs. Through targeted sequencing of specific genetic regions, this method offers precise genotypic data essential for selecting desirable traits, optimizing breeding processes, and verifying crop integrity.

Whether you’re enhancing a new variety or evaluating genetic purity, our GBAS service can help. We offer pre-existing QC and breeding panels on various crops and can also develop custom panels to meet your specific needs.

Genotyping by Skim Sequencing (skimGBS)

Genotyping by skim sequencing (skimGBS) is a cost-effective, high-resolution genotyping method that utilizes low-coverage whole-genome sequencing. Skim sequencing allows plant breeders to obtain data on a greater number of single nucleotide polymorphisms (SNPs) without the need to develop panels in advance or use pre-existing fixed panels.

The abundance of SNPs facilitates several applications including, but not limited to, genetic mapping, QTL mapping, recombination characterization, gene conversion identification, genome-wide association studies (GWAS), genomic selection (GS), and assessment of chromosome dosage, deletions, and aneuploidy. With skim sequencing, we can also identify genetic differences between parent lines directly, without prior targets, knowledge, or panel development, and evaluate segregating lines to pinpoint these differences.

Pathogen Whole Genome Sequencing

Pathogen whole genome sequencing empowers researchers with a comprehensive understanding of the genetic basis for pathogenicity and virulence, providing valuable insights for developing targeted diagnostics and effective disease management strategies.

Our full-service laboratory can go from samples to pathogen isolation to genome sequencing, all under one roof. Our high-throughput sequencing capabilities enable the generation of high-quality, complete, or near-complete genome sequences for a wide range of plant pathogens, including viruses, bacteria, and fungi – even from complex samples such as seeds. Access to the genomic data of plant pathogens can help in providing a more complete picture of genes involved in pathogenicity and host-pathogen interactions, as well as an understanding of pathogen diversity and lineage in production systems, leading to the development of more effective and targeted disease control strategies.

Comprehensive Plant Pathogen Detection and Analysis by HTS

Comprehensive Plant Pathogen Detection and Analysis by HTS is a cutting-edge service that utilizes high-throughput sequencing to analyze the complete nucleic acid content (both RNA and DNA) of your sample. Unlike traditional methods, this approach requires no prior knowledge of the suspected pathogen, enabling the detection of both known and novel disease agents. It provides comprehensive data for further analysis, such as pathogen characterization and epidemiology.

This service is ideal for disease diagnostics, large-scale surveys, certification of plant material, and quarantine monitoring.

16S and ITS HTS for Plant, Seed, and Soil Health Diagnostics

Bacterial 16S and fungal internal transcribed spacer (ITS) sequencing provide rapid and sensitive identification of bacterial and fungal pathogens impacting plant, seed, and soil health, informing targeted disease management strategies. This service utilizes high-throughput sequencing (HTS) to analyze any unique 16S rRNA genes in bacteria and ITS regions in fungi within a sample, without targeting specific organisms. Unlike traditional methods that sequence a single organism from a colony or similar sample, this approach (which can be culture-free) enables the detection of multiple organisms simultaneously, even at low abundance.

This approach is particularly valuable for diagnosing diseases caused by complex microbial communities, as seen in soil-borne diseases and those involving multiple pathogens, where traditional methods may be limited. 16S and ITS HTS can uncover pathogens present at low levels in plant tissues, seeds, or soil, enabling early detection and intervention to prevent disease outbreaks.

Targeted Amplicon Sequencing Panels

Targeted amplicon sequencing panels offer a cost-effective and highly sensitive solution for diagnosing specific plant diseases, enabling the detection of multiple pathogens in a single test. By using carefully designed primer sets that target specific pathogens, this approach provides a focused analysis, reducing costs compared to whole-genome sequencing while maintaining high sensitivity. Multiplexing numerous specific primer sets in a single reaction allows for the simultaneous detection of a wide range of pathogens, at a low cost.

This technology enables the detection of pathogens present at low levels in plant tissues, seeds, or soil, facilitating early detection and targeted intervention strategies.

Targeted amplicon sequencing panels are ideal for routine diagnostics, clean plant programs, and monitoring programs, where cost-effective strategies are critical.