Illumina Ovine SNP Chip to Spur New Round of Association Studies

llumina Ovine SNP Chip to Spur New Round of
Association Studies
January 27, 2009
By Justin Petrone
Participants in the International Sheep Genome Consortium intend to use Illumina’s
OvineSNP50 BeadChip in a series of genome-wide association studies set to commence
later this year.
The studies will be part of an ongoing effort to develop testing panels to increase
productivity in the global livestock industry, and could be a boon to Illumina, which
predicts the agricultural biotechnology market will become a “great opportunity” for the
company’s business (see BAN 1/20/2009).
Illumina launched the OvineSNP50 earlier this month. The 12-sample BeadChip includes
more than 50,000 SNPs for interrogating genetic variation in multiple sheep breeds. It
was developed with the help of ISGC, a 7-year-old international group of institutes and
companies from more than a dozen countries (see BAN 1/20/2009).
According to an ISGC statement, the group this year plans to sequence the genomes of as
many as six sheep, produce a reference sequence of the sheep genome, and undertake a
preliminary study of copy-number variations in the animals.
But some ISGC participants told BioArray News this week that before they move their
projects to either higher- or lower-throughput technologies, they would first like to
conduct association studies on sheep populations to narrow in on regions of interest that
could play a role in future breed or animal selection.
“We will use the OvineSNP50 BeadChip as a research tool to deliver information about
genomic variation in sheep to the livestock industry through whole-genome association
studies,” Brian Dalrymple, a senior principal research scientist in Australia’s
Commonwealth Scientific and Industrial Research Organisation, which is coordinating
the ISCG, told BioArray News this week.
Dalrymple said that CSIRO’s livestock industries group, based in Brisbane, will use the
Ovine SNP50 to generate information of variation in sheep that will become available via
an industry-wide database.
“At this stage we do not have firm plans for another SNP chip, and researchers will need
a year or so to use and analyze data from this one,” said Dalrymple. “We also plan to take
six breeds of sheep to much higher coverage using paired-end short-read technology,
[which] will enable us to discover many more SNPs and also identify major CNVs in
these animals.

“We also plan to aim to move from draft to a reference genome sequence for sheep
heading for as high-quality, close to complete sequence as possible,” he added.
Dalrymple added that, as more information becomes available, ISGC participants will be
able to access it to create “smaller, more focused-trait selection arrays” to aid in their
studies.
New Zealand
Meantime, in New Zealand, the nation’s AgResearch institute hopes to genotype several
thousand sheep by summer using the OvineSNP50, according to John McEwan, a senior
scientist at the publicly funded research organization.
“The primary reason that the Illumina SNP chip was developed is for whole-genome
selection in sheep,” McEwan told BioArray News this week. “It can also be used for
understanding mutation, breed diversity, [and] helping create linkage maps of the
genome, but the primary reason and the vast amount of money was invested [to make this
chip] because the sheep industry in New Zealand wants to do whole-genome selection
just like the dairy industry does.”
McEwan said that AgResearch has already genotyped 3,000 sheep and hopes to type up
to 2,500 additional animals by July. “Our hope is that we will have analyzed those results
and have some commercial tests available in a year’s time” for animal selection, he said.
Any potential tests that come out of AgResearch’s association study will be SNP-based
and will probably make use of the Illumina BeadChip or Sequenom MassArray
platforms, both of which AgResearch has at its campus in Dunedin. McEwan said that in
the past AgResearch has developed microsatellite and SNP-based tests for bovine
selection.
According to McEwan, there is “significant” demand for new genetic tests for animal
selection in New Zealand, adding that up to 10 percent of export GDP in the country is
related to the sheep industry.
“If you put a ring around sheep and dairy products, you are talking about a very
substantial part of New Zealand’s income,” McEwan said. “For those reasons, this is
quite an important industry to New Zealand. An increase in productivity could make a
substantial contribution to GDP.”
McEwan said that current selection technologies rely on older techniques like Western
blot to identify phenotype and mutation information. With the new Illumina chip,
AgResearch hopes to identify markers for traits that have been historically hard to select
but that are very important, such as “longevity of the ewe, feed intake of the ewe,
reproductive ability, how well it milks, disease traits,” and others.

While AgResearch may make headway in its goal to develop testing panels this year,
McEwan said that its results will most likely not be applicable in other countries. He said
that limits in current technology suggests that genome-wide selection in animals is
probably only going to be applicable within a breed, or a breed and some closely related
cross breeds of sheep.
Since most countries around the world produce different sheep breeds, researchers in
those countries will have to perform their own association studies to produce similar
tests. “It may well be that within five years time, the technology will advance to a stage
where a particular group can do research that’s broadly applicable around the world,”
said McEwan, “but today, that is not the case.”
France
While AgResearch prepares to genotype 2,500 more animals before summer, plans are
being laid to genotype several thousand animals in France. André Eggen, a scientist in the
Animal Genetics Department of the French National Institute for Agricultural Research,
told BioArray News this week that the Ovine SNP50 will be run on between 3,500 and
4,000 animals this year.
“This will be done for several purposes, especially to know a little more about milk
production in sheep and to know about parasite and disease resistance in sheep,” Eggen
said. “There is also an interest in specific protocols about temperament and understanding
more about sheep seasonal breeding cycles.”
In the study, INRA will work with Labogena, a Parisian commercial genotyping lab, and
will use a mix of INRA reference populations together with samples collected from
French sheep breeders. Eggen said that Labogena is already serving the French cattle
industry by genotyping around 10,000 animals per year for selection, but that it will take
time to develop similar panels for use in sheep due to data analysis challenges.
“You have to apply the right statistical model to the data as well account for the pedigree
of the sheep, so it will take several months alone to do the analysis,” Eggen said. In terms
of the panels, Eggen said that current technology, including Illumina’s OvineSNP50, will
not permit affordable, high-volume genotyping of markers in sheep, but that several
platforms in development look promising.
“You want to have a system that allows you to genotype a few hundred markers at a very
cheap price because sheep are not of as high an economic value in France as, say, cattle,”
he said. “This genotyping technology is not out yet, but it is coming and we hope it will
become available later this year.”
He declined to discuss which platforms he intends to use, but said that he knew of tools in
development at both Illumina and Life Technologies that could serve such purposes.

Eggen added that due to INRA’s previous experience with Labogena in serving the cattle
industry, it would likely follow a similar model when it came time to implement animal
selection testing for sheep breeders.
“The industry sends blood samples from young calves to Labogena [which] performs the
genotyping, and INRA compiles a genomic index assessing the genomic value of an
animal,” Eggen explained. “The industry can then select the young calves they want to
raise and produce semen from. That is a way in which we have implemented such a
program within the industry.”
Israel
ISGC participants from countries with smaller industries also have plans to conduct
similar studies, albeit on a lesser scale. According to Elisha Gootwine, a scientist in the
Agricultural Research Organization, the research arm of the Israel Ministry of
Agriculture, plans are being made at the ARO’s Institute for Animal Science in Bet
Dagan to genotype several breeds of Israeli sheep.
He said that ARO is now collecting samples from three different breeds and hopes to
outsource the genotyping to CSIRO’s facilities in Brisbane. ARO and CSIRO will work
together to analyze the resulting data.
“We hope to get information regarding breed diversity and how breeds differ from other
breeds in the world,” Gootwine told BioArray News this week. “By comparing the
markers on the genome, we can see how breeds are similar and in what regions they are
similar to other breeds. By collecting samples, we can also collect data on how animals
differ in certain productive traits.”
Gootwine noted that agriculture accounts for about 2.5 percent of Israeli GDP, part of
which is derived from exporting sheep milk and meat. “We have both dairy production
and lamb production in Israel,” he said. “It is not a big business, but some people live on
sheep production, and that is why we are working on it.”