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Using Genomics to Breed for the Future: Illumina Workshop at PAG XXIII

Estelle Giraud, Ph.D.
| Jan 22, 2015

For those who may not know, our core mission at Illumina is to unlock the power of the genome to transform healthcare and beyond. The research conducted every day with high throughput genomics is changing the way we treat cancer, understand complex and genetic disease, and improving many aspects of human health. However, having just finished up at the 23rd annual Plant and Animal Genome conference, I am seeing another, even more fundamental step of this principled cause. Dr. Mike Thompson (Illumina’s Associate Director of Agrigenomics Market Development) clearly highlighted this in his opening address to the packed ballroom at the Illumina workshop. The people who attend PAG do much of the critical research on food and its security; without an abundant, secure, and sustainable source of food, there are few opportunities to improve human health. Nutritious and sustainable plants and animals are central to humanity's survival, and thus an area of great importance to the work we do at Illumina.

It’s always a thrill to hear  the winners of the Agricultural Greater Good Initiative announced during the workshop. This annual award provides free reagents to allow the development of sequencing and genotyping tools to support a project that  significantly impacts food security, and has direct benefits to developing countries. This year's winner is the African Orphan Crops Consortium (AOCC), which seeks to study the genetic diversity of 100 crop species, with an emphasis on those grown by African subsistence farmers. Dr. Allen Van Deynze of the University of California at Davis accepted the award on behalf of the organization, and I’m looking forward to hearing how they are changing the world next year at PAGXXIV.

The Illumina workshop highlighted the work of several researchers, and a central theme through many of the talks was that array technology is still a very relevant part of agrigenomics work. The complementary nature of sequencing and arrays means that researchers can truly follow a cycle of Discover/Develop/Deploy, with high throughput genotyping playing a central role in breeding and screening programs at a very cost efficient price. Highlights of the talk for me:

  • I have a healthy appreciation for what goes into a genome assembly – especially when that genome is 16 Gb, highly repetitive, and you know absolutely nothing about it. A presentation by Richard Finkers from the University of Wageningen in the Netherlands told this exact story on the onion assembly, aptly titled “Tears of Joy." What was striking was how far you can get these days, and fairly quickly. The researchers initially did one HiSeq 2500 run and were able to assemble 40% of the genome, significantly exceeding their expectations.
  • A presentation by André Eggen, our European Market Development Manager, showcased recent exciting discoveries in the 1000 Bull Genomes Project. A combination of sequencing and array screening work led to several functional discoveries that could be immediately integrated into breeding practices. Collaboration is a cornerstone of this community, and something we are very proud to be a part of at Illumina.

In the midst of many of our systems and solutions announcements to make genomics research more accessible and easier, there was one more during our PAG workshop. We now offer an Illumina Concierge Service that will allow us to design custom amplicon and capture sequencing library preps for any species! Look for more information coming soon on our website, to learn more about this exclusive service.

Thank you to the presenting scientists, attendees, and to the organizers of PAGXXIII for giving us the opportunity to present exciting results, new developments, and give back to the people doing foundational exploration and analysis in agricultural research. See you next year in San Diego!

* Updates 3/5/15 to correct Dr. Allen Van Deynze and Dr. Tim Close's affiliations.