RAD LongRead – a tool for local genome assembly

At the annual ‘world cup of genomics’ at the Plant and Animal Genome XVIII conference in San Diego, Floragenex debuted results from its RAD LongRead sequencing method. The results of a pilot study were displayed in a poster authored by Floragenex, VP of Research, Dr. Rick Nipper. A PDF copy of the poster is available here.

The RAD LongRead technology is an extension of the patented Restriction site Associated DNA  (RAD) sample preparation method, developed by Floragenex. The technique enables researchers who want SNP information in species lacking an assembled reference genome a path towards developing SNP based high-throughput assays. The 300-600 contigs that can be generated from the Illumina Genome Analyzer system using this sample preparation method and Floragenex bioinformatics tools, offer researchers wishing to use  any of the leading commercial genotyping platforms, enough flanking sequence to design effective assays.

Floragenex and its animal sciences/biomedical division, Biota Sciences, offers RAD LongRead sample preparation, sequencing, and analysis services to customers working in any organism.

Agricultural Biotech in 2010

You know that you’re in an interesting business when the NY Times is covering the technology you use and Forbes names the leader in your target market as their company of the year. No, this isn’t Web 3.0 and Twitter, but genetic sequencing and marker assisted breeding and Monsanto; the world’s superpower in the seed industry. This is an interesting start to the decade.

In this well written and researched article, the other side of agricultural biotechnology gets some very good press. The technology described is marker assisted breeding – using genetic information to accelerate the tried and true process of crossing and selection to develop new varieties of plants. In an interesting twist of perspectives, Forbes announced that Monsanto is the 2009 company of the year. The title ‘The Planet Versus Monsanto’ is appropriate.

The ‘other side’ of ag-biotech is part of what Floragenex supports. Finding the specific segments of DNA (genetic markers) that can be linked to a specific trait, is now much quicker and easier than ever before. This technology is hitting its stride and heading up the adoption curve, as the cost of getting and applying that information keeps dropping. Projects that took years just a few years ago are being completed in months.

The scale of what Monsanto has and will accomplish in terms of the world’s food supply is astounding.  When you think about the facts of our situation; population going up, arable land holding constant or decreasing, and climate changing, it’s hard to bet against a company that sees those macro economic factors as an opportunity.

While there are many that vilify the corporate giant from St. Louis, I’d also ask those same people to think about what they ate today. Given that Monsanto’s vegetable group is one of the largest vegetable seed producers in the world, the chances are pretty good that something they purchased in the last month, whether it’s fresh broccoli or ethanol in their Prius, can be traced back to Monsanto.

The seed industry is an evolving business that deserves more attention in this country. It’s an important piece of the economy that will get more coverage as we pay more attention to where our food comes from and who profits from our choices as consumers.