Plant and animal genotyping

Discovery and screening tools to aid in breeding decisions

A male researcher holding a digital tablet, taking notes near a river; a farmland with buildings and cows testing on a grassy open area, blurry in the background.

From genomic variants to physical traits

Animal and plant genotyping has become a mainstay of modern agricultural research. Illumina microarrays enable high-throughput screening of known genomic markers to inform selection and breeding decisions. Array-based studies can also be used to discover novel associations between SNP (single nucleotide polymorphism) markers and traits or diseases.

Plant and animal genotyping applications

Custom arrays

Not every nonhuman organism has been extensively genetically investigated, resulting in an absence of commercial genotyping arrays for certain plant and animal species. We offer custom microarrays that can be designed with all the discovered markers for species of interest, enabling genotyping studies to identify variants associated with desired phenotypic traits. Through ongoing work with major agrigenomics consortia, our technology is being used to identify new, relevant markers in a wide range of species.

Copy number variation studies

A common form of natural diversity, copy number variation (CNV) is also heritable. It appears to play an important role in agrigenomics. CNV differences can correlate to health and production traits, and contribute to phenotypic diversity. In animal and plant genotyping studies, the distribution of high-density probes can be used to identify CNV breakpoints and ultimately accelerate genomic improvements. Studies are ongoing to determine if the impact of CNVs is the result of differences in copy number for key genomic segments, structural modification of the genome, or a combination of both.

Fine mapping and candidate gene region genotyping

Microarray-based animal and plant genotyping can be used to create fine map traits and/or test a genotype-phenotype hypothesis. Quantitative trait loci (QTL) analyses can be performed on the results to characterize how differential gene expression might contribute to phenotypic variation.

Whole-genome association studies

Association mapping across an entire animal or plant genome provides insight into the genetic location and architecture of linking traits to species’ adaption (eg, to a wide variety of environmental conditions). The results of these studies support whole-genome selection applications (eg, fingerprinting, net merit, marker-assisted breeding) that enhance the value of commercial crops and herds. Illumina microarrays offer focused content, custom capabilities, and convenient add-on content capabilities.

Featured animal and plant genotyping stories

Animal genotyping customer stories

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Improved breeding plans for beef cattle

Learn how genomic selection has increased gains in beef cattle through improved breeding plans, the ability to select for specific genes, and a quicker, better understanding of a bull’s genetic value.

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How genomic testing improves dairy cattle herds

General manager of the Canadian Dairy Network Brian Van Doormaal discusses how genomic testing can better define the value of milking cows and improve dairy herds.

Featured products for plant and animal genotyping

Ordering the iScan System

Order an iScan System today. Speak to a representative for information on pricing, availability, and more.

Infinium XT iSelect-96 Kit

A comprehensive microarray solution that enables production-scale genotyping of up to 100,000 single- or multi-species custom variants for non-human, and 50,000 custom variants for human.

See more agrigenomics content

The user-friendly "Recommended Links" feature allows you to easily find content and products relevant to agricultural genomics and/or other fields of interest. You can access this option from the top of any illumina.com page.

Explore resources and tools

We offer training and everything else for your workflow, from start to finish. From learning about our technology to making sense of your data, purchasing what you need, and getting support, we'll set you up for success.

Additional resources

Agrigenomics genotyping portfolio

Illumina Infinium genotyping arrays combine cutting-edge technology with a proven track record of quality and reliability for agricultural research and breeding applications.

Polyploid organism genotyping

GenomeStudio Software now contains a polyploid clustering module for analyzing species with the most complicated genomes.

Custom genotyping options

The broadest range of marker density and the most flexible content for any genome, in any species.

Speak to a specialist

Interested in learning more about agrigenomics?