AgriSeq Targeted Genotyping by Sequencing

Innovative solutions that help accelerate plant and animal breeding programs

Discover the power of Applied Biosystems AgriSeq targeted genotyping by sequencing (GBS) solutions, designed to revolutionize the field of molecular breeding for agricultural applications. With our advanced genomic technologies, we offer a cost-effective and high-throughput approach to the analysis of genetic variation in plant and animal populations, helping breeders and researchers accelerate their programs and deliver improved species efficiently. Explore the possibilities and harness the potential of AgriSeq GBS for your agricultural genotyping needs.

Spotlight

AgriSeq Pre-Designed genotyping by sequencing panels enable your lab to quickly begin genotyping plants and animals with minimal prep work.

Up to 2.6M 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 2.6 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 1.3 million 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 ~2-3 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.

AgriSeq pre-designed made-to-order (MTO) panels

High-throughput analysis of plant and animal genotypes via flexible and cost-effective technology

AgriSeq high-density panels, ranging from 3K to 5K SNPs in size, are specifically designed to screen breeding populations for the most relevant SNPs with exceptional minor allele frequency and marker performance. Whether you need routine screening or other downstream genomic applications, these panels are a versatile solution.

Key features of AgriSeq ready-to-use panels include:

  • Reproducible genotyping of ISAG-recommended markers for all species with high call rates
  • Customizable approach to combine with compatible parentage, traits or disorders, or additional markers of interest

Available AgriSeq pre-designed panels

AgriSeq Panel Description

Number of SNPs

Plant Panels

USDA Wheat 5K

5,000

Strawberry 4.5K

4,500

Maize QA/QC

160

Maize Trait

259

Lettuce QA/QC/Trait

215

Sunflower

700

Chickpea

5,000

Groundnut

5,000

Pearl Millet

4,000

Cotton

4,500

Tomato 5K

5,000

Pepper 5K

5,000

Barley 3.5K

3,500

Maize 3.6K

3,600

Animal Panels

ISAG Bovine Parentage

554

ISAG Equine Parentage & Traits/Disorders

950

Canine Traits & Disorders

154

Canine Parentage & ID

394

Feline Parentage & Traits/Disorders

165

Caprine

450

Ovine

400

Pacific Oyster

592

Coho Salmon

434

Chinook Salmon

599

Sockeye Salmon

598

Eulachon (Candlefish)

580

AgriSeq Canine Traits and Disorders Panel

The AgriSeq Canine Traits and Disorders Panel contains 154 markers targeting clinically important genetic traits and disorders in canines. The panel includes 97 SNPs and complex markers such as 6 MNPs, 13 insertions, and 38 deletions. Most of these markers are common to all breeds, while some are breed specific for certain traits and conditions. The performance of the panel was verified using orthogonal testing, robustness testing, and field testing with diverse DNA samples from canine oral swabs. The panel enables multiplexed simultaneous genotyping of 154 markers to deliver reliable genotyping results for 136 genetic disorders and 18 traits using the AgriSeq targeted GBS workflow. The CanFam 3.1 reference genome is used for the analysis.

AgriSeq Canine SNP Parentage and Identification 

Panel Contains 379 SNPs and 2 deletion markers designed to deliver reliable genotyping results for parentage The AgriSeq Canine SNP Parentage and Identification Panel contains 379 SNPs and 2 deletion markers designed to deliver reliable genotyping results for parentage determination and identity verification of canines by targeted GBS. The panel enables multiplexed simultaneous genotyping using the AgriSeq targeted GBS workflow. The performance of the panel was verified using orthogonal testing, robustness testing, and field testing with diverse DNA samples from canine oral swabs. The panel was also qualified using the 2019 ISAG/ICAR 2nd SNP Typing Canine Comparison samples. The CanFam 3.1 reference genome is used for the analysis.

Figure 1. Performance of AgriSeq canine panels. Call rates were calculated for both panels after testing >180 diverse DNA field samples from canine oral swabs with the AgriSeq workflow. The mean call rate for the AgriSeq Canine Traits and Disorders Panel was 99.1% (A), and for the AgriSeq Canine SNP Parentage and Identification Panel was 99.2% (B), demonstrating the high performance obtained from customer samples.

AgriSeq Feline Parentage and ID Plus Traits and Disorders Panel 

The AgriSeq Feline Parentage and Identification Plus Traits and Disorders (PITD) Panel is a combined panel for determining parentage and identification (111 SNP markers) plus targeting 64 clinically important traits and disorders (43 SNP, 1 MNP, 4 insertion, and 16 deletion markers) in felines by targeted GBS. The performance of the panel was verified using orthogonal testing, robustness testing, and field testing with diverse DNA samples from feline oral swabs (Figure 4). The 111 SNP parentage and ID markers were also qualified using the 2019 ISAG/ICAR 2nd SNP Typing Feline Comparison samples. The comprehensive AgriSeq Feline PITD Panel is designed to deliver reliable genotyping results for parentage determination, including identity verification and prediction of 42 genetic disorders and 22 traits that are clinically important. When desired, additional custom markers referencing the Felis_catus_8.0 can be added if compatible.

Figure 2. Performance of AgriSeq Feline panel. A total of 258 feline oral swab DNA samples were tested either in duplicate or in quadruplicate with the AgriSeq workflow using the AgriSeq Feline PITD kit. The call rate, the number of markers generating a genotype call for each sample, was calculated for all samples with at least 100x mean read depth, the minimum recommended. The mean call rate was 99.3% and all samples had call rates >92.5%, demonstrating the high performance obtained from field samples.

Bovine ISAG SNP Parentage Panel (2013) 

The Applied Biosystems Bovine ISAG SNP Parentage Panel (2013) contains primers targeting the 200 ISAG-recommended SNPs available for simple multiplexed analysis using the AgriSeq targeted GBS workflow. The ISAG has standardized a set of 100 core SNPs and 100 additional SNPs with sufficient minor allele frequency (MAF) and genomic spacing for accurate bovine parentage determination across a wide range of breeds (Figure 5). You can download SNP information from the ISAG website [3]. Qualified using the 2015 ISAG/ICAR 3rd SNP Typing Bovine Comparison samples, our comprehensive Bovine ISAG Parentage Panel is designed to deliver reliable genotyping results for animal parentage testing. The Bos taurus reference genome is needed for analysis of the Bovine ISAG SNP Parentage Panel and can be obtained by contacting our technical support specialists.

Figure 3. Performance of AgriSeq Bovine panel. Evaluation of 96 diverse bovine gDNA samples from the United States Department of Agriculture (USDA), representing 19 different breeds with the Bovine ISAG SNP Parentage Panel (2013), with 4 replicates each. All 384 individually barcoded libraries were pooled onto a single Ion 540™ Chip and sequenced on the Ion S5™ XL System. All but one of the samples tested gave a mean sample call rate of >95%. The mean call rate across all samples was 98.5%.

Bovine_no caption

Easy data summarization and visualization

Ion Torrent™ AgriSum Tool Kit (AST) plug-in aggregates data from the coverageAnalysis and variantCaller plugins for easy review of data. AST displays overall sequencing run summary metrics for easy review, enabling quality control or troubleshooting, if needed.  Additionally, AST converts TVC data into genotype Martix, TOP, and TOP/BOTTOM formats for further analysis applications.

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.

 

IonCode Barcode Adapters

IonCode Barcode Adapters are a family of products that provides 1536 unique barcode adapters designed for optimal performance with Ion Torrent semiconductor sequencers. When used in combination with the AgriSeq HTS Library, users can pool up to 1536 amplicon libraries and then conduct multiplexed sequencing analysis, which helps increase lab efficiency and reduce sequencing costs per sample.

Ordering information