Agrigenomics arrays

Barley 50K Consortium

The Barley 50K consortia array features ~44,000 SNPs derived from exome capture data of 170 carefully selected barley accessions. It covers genetic variation that exists among a wide range of European germplasm. This array was designed by the James Hutton Institute, referring to the most recently released barley pseudomolecules genome assembly.

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Barley 50K SNP Platform (James Hutton Institute)
Development and evaluation of a barley 50k iSelect SNP array

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Cotton 30K Array

The Cotton 30K Array features 27,349 SNPs. Applications include genetic diversity analysis, genetic mapping, QTL analysis, candidate gene discovery, marker assisted selection, genomic selection, and genome sequence assembly.
This array includes a subset of the International Cotton Consortium, which had 70,000 markers developed with SNPs from Gossypium hirsutum, G. barbadense, G. tomentosum, and G. mustelinum. Small numbers of attempted bead types are devoted to G. longicalyx and G. armourianum. Intraspecific SNPs were discovered and validated on germplasm lines that include Australian, US, Indian, and Chinese varieties of Gossypium hirsutum.

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Development of a cotton SNP chip from international consortium-based collaborations

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Pulses Array

This array features ~30,000 SNPs total, with 10,000 each for lentil and field pea, and 5,000 each for chickpea and lupin. Applications include genomic selection, population genetics, genome-wide association studies, and imputation to whole-genome.

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USDA Multispecies Array (for barley, oat, soy, and wheat)

The USDA Multispecies Array, also known as the Small Grains Array, features ~3,000 SNPs each for barley, oat, soy, and wheat. Applications include genomic selection, genetic diversity, fingerprinting, purity assessment/QC, and imputation. The array content was selected by key opinion leaders at the USDA from the soy 6K, wheat 9K, barley 50K, and oat 3K legacy consortia arrays.

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A multi species, low cost, genome-wide genotyping platform for molecular breeding in small grains

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Sorghum Consortium

The Sorghum consortia array features ~50,000 SNPs covering over 97% of S. bicolor genes with a SNP on average every 13.5 kb. This array allows researchers to detect common/rare variants across global sorghum populations at a low cost. It includes ~34,000 genes from S. bicolor reference, ~8,500 SNPs for breeding, ~22,700 SNPs from exonic genes, ~4,200 SNPs within 5 kb up/downstream of remaining genes, and additional targets identified by key opinion leaders.

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A genomic resource for the development, improvement, and exploitation of sorghum for bioenergy

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Wheat and Barley Array

This array features ~40,000 markers. Applications include genomic selection, genetic diversity, fingerprinting, purity assessment/QC, imputation, marker-assisted selection, and trait mapping.

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Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars

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Honeybee Array

This array features ~70,000 SNPs for genome-wide association studies on honeybee. Applications include gene discovery, genetic diversity, genome-wide association studies for complex traits, and genomic selection.

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BovineHD and BovineSNP50 BeadChips

These off-the-shelf BeadChip arrays enable researchers to interrogate genetic variation across the genome for any breed of cattle. Illumina worked with a variety of consortia to develop these arrays, which feature SNP loci representing the genetic diversity of three populations of beef and dairy cattle, including Bos taurus taurus (Btt), Bos taurus indicus (Bti), and several Bti x Btt breeds, as well as temperate and tropically adapted breeds within these groupings.

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BovineHD BeadChip: This comprehensive genome-wide genotyping array features 777,962 SNPs that uniformly span the entire bovine genome. The array was developed in collaboration with USDA-ARS, UNCEIA-INRA, Pfizer Animal Genetics, and the University of Missouri.

BovineSNP50 BeadChip: This award-winning array features 54,609 informative SNP probes evenly spaced across the entire bovine genome. The array was developed in collaboration with USDA-ARS, USDA-MARC, University of Missouri, and the University of Alberta.

Camel Array

This array features ~56,000 markers. Applications include genome-wide association studies, genomic selection, population genetics, carrier screening, and parentage verification.

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Dog Array

This array features ~172,000 markers. Applications include genome-wide association studies (for complex traits), monogenic trait screening, parentage verification, genetic diversity, breed purity/composition, and imputation.

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Horse Array

This array features ~76,000 SNPs. Applications include genomic selection, parentage verification, genetic diversity, breed purity/composition, whole-genome imputation, and SNP-to-STR imputation.

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Goat Array

This array features ~79,000 markers. Applications include genomic selection, genome-wide association studies (for complex traits), monogenic trait screening, parentage verification, genetic diversity, breed purity/composition, and imputation.

The array was developed by the International Goat Genome Consortium. Several datasets generated by the consortium were considered in SNP discovery, including de novo sequencing of goat genome scaffolds, SNP discovery sequencing data from next-generation sequencing, and sequencing data from expressed (EST) sequences. SNPs for goat genotyping were annotated using expressed sequences together with data from the ovine genome. Candidate goat SNPs were validated for Alpine, Angora, Boer, Creole, Jinlan, Katjang, Saanen, Savanna, and Skopelos breeds. The community has provided a cluster file suitable for quick automated analysis of all project sizes. This array is suitable as base content for over 30,000 add-on markers for a customized goat genotyping array.

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Design and characterization of a 52K SNP chip for goats

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Sheep Array

This array features ~52,000 markers. Applications include genome-wide association studies (for complex traits), monogenic trait screening, parentage verification, genetic diversity, genomic selection, and imputation.

In the sheep industry, the most important animals are the "sires to breed sires" — the animals that produce the males that are used across the industry. By genotyping thousands of sires, researchers can evaluate a vast number of variants for economically important traits. To develop an ovine BeadChip, Illumina worked with the International Sheep Genomics Consortium (ISGC), comprising leading researchers from AgResearch, Baylor University, UCSC, and Australia's Commonwealth Scientific and Industrial Research Organization (CSIRO).

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Pig Array

This array features ~75,000 markers. Applications include genome-wide association studies (for complex traits), monogenic trait screening, parentage verification, genetic diversity, breed purity/composition, and imputation.

To develop a porcine BeadChip array, Illumina collaborated with the International Porcine SNP Chip Consortium, comprising researchers from Wageningen University, Danish Institute of Agricultural Science, USDA-ARS, USMARC, Roslin Institute, University of Illinois, Iowa State University, INRA, University of Missouri, and Cambridge University.

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