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.
Targeted custom research panels optimized for specific targets or genomic content of interest.
Speed and simplicity for targeted and small genome sequencing.
An on-premises software solution for creating sequencing runs, monitoring run status, and analyzing data.
AgResearch uses genotyping by sequencing to overcome cost and resource hurdles associated with genomic selection of minor livestock species, such as the Meredith Dairy goat herd.Read Interview
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.
Click on the below to view products for each workflow step.
An easy-to-use online software tool that provides dynamic feedback to optimize probe designs.AmpliSeq for Illumina Custom Panels
Create custom targeted sequencing panels optimized for content of interest.
Speed and simplicity for targeted and small genome sequencing.NextSeq 550 System
Flexible power for whole-genome, transcriptome, and targeted resequencing.HiSeq 4000 System
Power and efficiency for large-scale genomics.
Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.Platform Comparison Tool
Compare sequencing platforms and identify the best system for your lab and applications.Sequencing Reagents
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.
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