Historically, array-based approaches to single nucleotide polymorphism (SNP) screening have been the method of choice in analyzing and associating traits with regions of the genome for many plants and animals. As sequencing costs continue to decline, researchers are developing new approaches that leverage next-generation sequencing (NGS) for genotyping.
Genotyping by sequencing, or next-generation genotyping, is a genetic screening method for discovering novel plant and animal SNPs and performing genotyping studies. For some applications, such as genotype screening and genetic mapping, sequence-based genotyping provides a lower-cost alternative to arrays for studying genetic variation.
Genotyping by sequencing is cost-effective for populations with complex genomes or limited available resources. Techniques include amplicon-based targeted sequencing, hybridization-based enrichment sequencing, and restriction enzyme reduced representation sequence-based genotyping.
Various sequence-based genotyping approaches have been developed.1–4 Enrichment methods are useful for plants, which often contain duplicated areas of the genome. Restriction enzyme methods are advantageous for species where there is no prior knowledge of the genome.
Sequence to high depth with custom or predesigned panels.
Speed and simplicity for targeted and small genome sequencing.
An on-premises software solution for creating sequencing runs, monitoring run status, and analyzing data.
New Zealand–based research group uses GBS to overcome cost and resource hurdles associated with genomic selection for orphan crops and minor livestock species.Read Interview
Scientists developed Genotyping-in-Thousands by Sequencing (GT-Seq) to genotype thousands of fish simultaneously.Read Interview
The authors of this study used a genotyping by sequencing method based on transcript sampling to study crops with varying ploidy levels.View Publication
For some applications, sequence-based genotyping provides a lower-cost alternative to microarrays in performing genetic variation studies. This application spotlight describes the advantages and limitations of several genotyping by sequencing methods.Access PDF
Illumina sequencing by synthesis (SBS) chemistry is the most widely adopted NGS technology, generating approximately 90% of global sequencing data.*
Illumina offers integrated sequencing workflows that simplify the entire process, from library preparation to data analysis and biological interpretation.
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Achieve consistent genotyping performance from content designed by Illumina Concierge services. Inquire about Illumina Concierge services.Nextera XT DNA Library Prep Kit
Library preparation for small genomes (bacteria, archaea, viruses), amplicons, and plasmids in less than 90 minutes.
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Speed and simplicity for targeted and small genome sequencing.NextSeq 2000 System
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Find kits that include sequencing reagents, flow cells, and/or buffers tailored to each Illumina sequencing system.
An on-premises software solution for creating sequencing runs, monitoring run status, and analyzing data.BaseSpace BWA Aligner App
Aligns samples (consisting of FASTQ files) to a reference genome.BaseSpace Whole-Genome Sequencing App
Quickly extracts biological information from whole-genome sequences, using Isaac alignment and variant calling.
The Illumina genomics computing environment for NGS data analysis and management.BaseSpace Correlation Engine
A growing library of curated genomic data to support researchers in identifying disease mechanisms, drug targets, and biomarkers.
For small genomes (eg, Drosophila) or high-profile research species (eg, Arabidopsis), genotyping and variant screening can be completed using standard whole-genome sequencing or resequencing methods relative to a reference. Low-depth sequencing can be used for phylogenetic or comparative analyses.Learn More
NGS technology can benefit agricultural studies of plants and animals, whether it is used for de novo sequencing, transcriptome analysis, genotyping by sequencing, or metagenomics. Learn more about plant and animal sequencing.
The application of genomics in commercial agriculture is helping breeders and researchers perform trait screening, parentage testing, and more. Learn more about commercial agriculture and genomics.
*Data calculations on file. Illumina, Inc., 2015