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International Consortium Designs Illumina SNP Chip for Cotton Breeding Research, Crop Improvement

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NEW YORK (GenomeWeb) – An international team of researchers has developed a new SNP array that could enable the breeding of more sustainable and more marketable cotton.

Working together with Illumina, the group, dubbed the Cotton SNP Chip Consortium, designed a 24-sample, iSelect custom BeadChip containing fixed content of 70,000 markers, with the option for users to include another 20,000 markers of their choosing as add-on content. Members of the consortium hope that the chip will allow them to identify markers related to valuable traits that will lead to improved cotton yield and higher-quality crops.

"I think this array is going to be transformative as a technology product," said David Stelly, a professor in the department of soil and crop sciences at Texas A&M University. "I think it is going to help push cotton breeding and research forward globally," he told BioArray News. "What we really want to do is make cotton production more sustainable, more eco-friendly, more resistant to drought and heat stress, and yet we also want to be able to make the end product more marketable," he added.

Stelly and his doctoral student Amanda Hulse worked together with a number of partners to design the new chip, including the University of California, Davis; Brigham Young University; the US Department of Agriculture's Agricultural Research Service; the Commonwealth Scientific and Industrial Research Organization in Australia; the Center for International Cooperation in Agronomic Research for Development in France; and the Council of Scientific and Industrial Research Organization's National Botanical Research Institute in India. The work was supported in part by the trade organization Cotton Incorporated.

The fixed content on the chip primarily targets Gossypium hirsutum, or upland cotton, SNPs, but also contains markers that target inter-specific SNPs for G. barbadense, G. tomentosum, G. mustelinum, G. armourianum, and G. longicalyx.

"Upland cotton is the species that is used for 95 percent of the world's production of cotton and is monetarily the most important species," Stelly said. "We realized early on that having a large amount of hirsutum SNPs would be very important to the average breeder, because [he] is going to need … a chip that he can run on parent [lines] and identify sets of SNPs that would be of particular interest to a specific cross," he said.

Hulse told BioArray News that the option to add on 20,000 SNPs should interest private companies and public researchers who are not willing to make internally identified SNPs available as fixed, public content. Stelly and Hulse estimated that the new chip's users would be evenly split between academics and private industry, though industry might run more samples on the array. Stelly said the ability to carry out high-volume studies using such custom content could make the chip attractive to private industry in particular.

"Typically, all of the companies have some SNPs in hand already," said Stelly. "They are using TaqMan or KASP assays, but they can import those SNPs over to the chip," he said. "They might also have RNA-seq data that are related to some traits of interest – insect resistance or cotton seed oil flavor, for example," Stelly continued. "There is a whole wide array of topics that a person can address using this type of technology," he said, "and if you have enough samples to run, this is a logical way to do it: just add some markers to the chip."

Since the new array became available earlier this year, the Cotton SNP Chip Consortium's sites at Texas A&M and CSIRO have been running initial samples on the tool to create cluster file data that can be used later to enable automated genotype calling. Once the cluster file data is generated, the chip will likely be used in a wide variety of studies, Stelly predicted, due in part to the usability of the array platform.

"I think its going to have a very big footprint," Stelly said of the chip. "Its use will snowball because it is going to be easy to use with a quick turnaround time that does not require a lot of in-house infrastructure, and that makes a big difference to most users," he said. "These are people who want the data, the results, but don't want to mess around with the technology any more than they have to."

Within Stelly's lab, the array will be used to continue studies of wild germplasm, part of a larger effort to increase diversity within upland cotton.

"One area of our work has to do with creating chromosome substitution lines where we replace an entire chromosome from the cultivated upland blue jean cotton with a corresponding chromosome from another polyploid species, such as G. barbadense, Pima cotton," Stelly said. "We can now use the array as a tool to look for single gene effects or epistatic gene effects, and to systematically explore where those changes occur and if they [affect] traits of economic importance," he said.

It will also be used within cotton genome sequencing projects, according to Stelly. "The chip will have some ramifications there, because the markers make a nice place to land sequence scaffolds," he noted.

As the top cotton-producing countries worldwide include China, India, the US, Brazil, Uzbekistan, and Pakistan, the chip is also likely to find use in cotton breeding programs abroad. Stelly gave Pakistan as an example of a cotton-producing country where roughly a quarter of gross national product is tied to the crop. He said that the Pakistani cotton industry has been devastated in recent years by a new strain of cotton leaf curl virus and suggested that the new SNP chip could enable local breeders to identify markers associated with resistance to the disease.

"Groups like that are almost necessarily going to have to look at tools like this because it is such an easy tool to use," said Stelly. "There are other ways to do genotyping, and they may look efficient and inexpensive up front, but when you really get down to the nitty gritty, they really don't fit as well as the Illumina cotton SNP chip will in terms of being able to get large amounts of data back quickly," he added.

'A lot of life left'

For Illumina, the new cotton SNP chip is just one of 40-plus consortium-designed arrays for agricultural research. At the same time, company representatives see its availability as further evidence of the agricultural research market bolstering its microarray business, even as next-generation sequencing continues to dominate discussion within the life sciences industry, as well as drive Illumina's revenues.

"Ironically, the rapid expansion of next-generation sequencing is driving the creation of content for the array business," said Kirk Malloy, general manager of Illumina's Life Sciences Business Unit. "Next-generation sequencing really drove discovery, and the proportion of arrays increased as people created custom chips for genomic selection," Malloy told BioArray News recently.

Illumina first began catering to the agricultural research market with the launch of its 54,000-marker Infinium BovineSNP50 BeadChip in 2008. Since then, it has introduced additional arrays containing a similar amount of markers for ovine, canine, porcine, and maize studies, as well as a 770,000-marker, high-density array for bovine studies and a 170,000-marker chip for canine research. While using genotyping arrays to guide breeding of high-value livestock such as cattle seemed like an obvious choice for breeders, Malloy said that crop researchers are also increasingly seeing the value in moving to microarrays.

"The economic driver is a bit different for crops, but it's still all about yield, which is just as significant for those who need to decide which crops to plant," said Malloy.

Mike Thompson, Illumina's associate director of global sales, concurred with Malloy's assessment of the industry. "There is a lot of life left in the array business, and there are a lot of business entities working on the technology and pumping a lot of samples through that business," he told BioArray News. He added that the cotton industry has "high expectations for what this new chip will do for them."

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