The use of next-generation sequencing (NGS) technologies for genotyping by sequencing (GBS) is becoming an increasingly important, cost-effective, and unique tool. NGS is useful for association studies and genomics-assisted breeding in a range of plant and animal species, including those with complex genomes that lack a reference sequence. It can be used for the discovery and identification of SNPs or to screen large panels of known markers.

The Ion Proton™ and Ion PGM™ Sequencers enable plant and animal researchers to use flexible, high-throughput GBS to perform fast and cost-effective studies.

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GBS: advantages of the Ion Proton™ and Ion PGM™ Sequencers
  • Allow both SNP marker confirmation and de novo marker (SNP) discovery, even in cases where there is no reference genome
  • Provide attractive, low-cost options for large numbers of samples and data points
  • Utilize highly multiplexed sequencing to scale from thousands to millions of data points per day
  • Enable 2–4 hour sequencing turnaround times to facilitate efficient planning for the next reproduction cycle
  • Deliver a high degree of accuracy of SNP calling
  • Offer versatility for many applications: de novo and targeted resequencing, transcriptome sequencing, and more

Multiplex enrichment PCR

In cases where a set of SNPs has been defined for a section of the genome, this approach uses PCR primers designed to amplify the targets of interest. View our complete solution for multiplex PCR below. Creating and ordering custom panels is easy with the Ion AmpliSeq™ Designer: a free, online assay design tool that enables custom design for any genome. Use the preloaded maize, tomato, soybean, and rice genomes to design your custom panel, or easily upload a FASTA file with your desired reference sequences for your genome of interest.

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Case study: Improving plant breeding using Ion AmpliSeq™ and Ion Torrent™ sequencing technologies for targeted resequencing and SNP analysis in tomato

High-throughput characterization of known and novel SNPs is critical for plant genotyping applications. In this study we used the Ion AmpliSeq™ panel workflow to genotype 370 SNPs from 192 matched paired tomato leaf samples (purified DNA and crude leaf lysate) on the Ion PGM™ Sequencer. The results showed a call rate of 94% and a call concordance of 99% between purified DNA and leaf lysates.

Learn more about this study in our recorded webinar ›

Genotyping by sequencing workflow
1 Construct library
Ion Torrent™ library kits

Hands-on time: 15 minutes

Ion AmpliSeq Panels on the Ion Chef System

2 Prepare template
Ion Chef™ System

Hands-on time: 15 minutes

Ion Chef System

3 Run sequence
Ion S5 or Ion S5 XL Systems

Hands-on time: 15 minutes

Ion S5 or Ion S5 XL Systems

4 Analyze data
Torrent Suite Software and Ion Reporter™ Software

Hands-on time: N/A

Torrent Suite Software


Plant genotyping by sequencing product flyer

Learn more about our plant genotyping solutions for genomics-assisted breeding programs, including Ion Torrent sequencers and Ion AmpliSeq DNA library and assay products.

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