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Affymetrix to Launch High-Density Chicken Array in Q2 for Genomic Selection, GWAS


This story has been updated to include comments from an Affymetrix executive.

By Justin Petrone

Affymetrix will in June launch a new microarray designed to help guide chicken researchers and breeders.

The 600,000-marker chip was developed in collaboration with the Roslin Institute at the University of Edinburgh and expands the vendor's menu of high-density arrays for the agricultural research market.

David Burt, chair of comparative genomics at the Roslin Institute, said that the 600,000 markers on the new chip were selected from a set of 20 million SNPs to meet the density of Affy's format. The array was developed by Affy, Roslin, and other partners with support from the UK's Biotechnology and Biological Sciences Research Council, which awarded Burt and fellow researchers £507,743 ($783,349) in 2010 to produce the genotyping array.

Burt spoke with BioArray News at the Plant and Animal Genome Conference, held in San Diego last week.

According to Burt, the new array can be used by both researchers and breeders for a number of applications.

"On one hand it can be used by researchers … to look at resistance to different diseases, for instance," Burt said. "More importantly it has been designed for [use by] the poultry industry, which consists of the meat side, the broilers, and the egg layers," he said.

Application areas include genome selection, using a few hundred thousand markers to account for variation in a particular trait, and genome-wide association studies to identify a particular gene or mutation that underlies a phenotype in chicken, like growth rate or a defect.

Burt said that he expects global demand for the new chip. "The poultry industry is worldwide, everywhere," he said. "I would expect thousands and thousands of these chips to be used all over the world. So this chip should do quite well."

A company executive agreed. "With industry estimates of over 50 billion chickens in the world, we expect significant demand for the high density chicken genotyping chip both for basic and applied research as well as genomic selection," said Jasmine Gruia-Gray, vice president of global marketing at Affy.

"Interested parties can build arrays tailored to their needs by choosing content from our database of 1.2 million high performing SNPs derived from the chicken screen we ran with our collaborators at Roslin and commercial breeders, Gruia-Gray told BioArray News this week.

Traditionally, the poultry industry has used phenotype information and family pedigree records to identify families and individuals that will be used to breed, Burt said. Genetic selection has been successful based on those principles, but it has become more sophisticated over time.

"Breeders wanted to be able to select for more traits, but that approach has probably reached a limit," said Burt. Over the past twenty years, the industry has evolved from using "very cumbersome" restriction fragment length polymorphisms to satellites to, more recently, SNPs. Next-generation sequencing has also provided researchers with the ability to discover more SNPs, Burt said.

Affy's new chicken array will be available for use on its automated GeneTitan platform. Burt said that the Roslin Institute recently acquired a GeneTitan to support its studies. "We were able to do 48 cartridges at a time" using Affy's original platform. "With GeneTitan we can do 96" arrays, he said, as the instrument can process plates of 96 arrays mounted on pegs.

"It is very fast," Burt added. "Within a few days you can generate a hundred million genotypes," he said. "Handling that information is the next challenge for us."

Burt said that the poultry industry has used microarrays for years, including a whole-genome expression chip commercialized by Affymetrix and custom genotyping arrays manufactured by Illumina. Looking forward, he said he is eager to see an exome array become available for chicken studies, but provided no timeline for when that might occur.

The new chicken array will join several high-density genotyping arrays commercialized by Affy for agbio researchers. Last year, the firm released high-density SNP chips for bovine and rice studies (BAN 1/18/2011).

Gruia-Gray said that Affy plans to launch other high-density and lower-density arrays in the future that "cover a spectrum of plant and animal genomics applications," including both livestock and crops.

"We are also looking at other arrays based on our recent announcement of the partnership with BGI," she said.

Affy and BGI last week announced a deal that will see the life sciences tool vendor and the Chinese genomics organization co-develop and co-market microarrays for agricultural applications. The first arrays from the collaboration could become available in the second quarter (BAN 1/17/2012).

Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [.] com