Wheat database heaven?

The USDA is promising people like Luigi1 a get out of hell free card. Shiaoman Chao, a molecular geneticist, sequences and fingerprints thousands of wheat and barley samples sent to her by breeders around the country. The results can help breeders to decide whether a particular seedling is worth persevering with.

But those data on their own become much more valuable when they can be married to other kinds of information from other kinds of laboratory. Enter GrainGenes, “a treasure trove of genetic information about wheat, barley and other ‘small grains’ like rye, oats and triticale”.

Personally, I don’t have the knowledge to make use of GrainGenes, or any of the other massive portals dedicated to just a few crops each: maize, strawberry, potato and others. But there is help out there.

The bigger question is the extent to which all those portals can be brought together and interlinked with other kinds of data: where selections grow, their visible characteristics, their utility, etc. etc. I know there are people coming at this from the non-molecular side of things, but I do sometimes wonder whether they really have the chops (and the resources) to pull it off. If some of the gene-jockeys decided they wanted to do it, and could throw some of their brains, brawn and bucks at the problem, I reckon Luigi would have his lifeline sooner. And it might be more reliable.

  1. Remember when he was Lost in Genebank database hell? []

3 Replies to “Wheat database heaven?”

  1. Well, maybe. But why don’t the gene-jockeys acknowledge the fact that germplasm databases even exist, for all their horror? This is further proof that genebankers and breeders live in different worlds. Ok, I’m exaggerating. If you look here on GrainGenes, for example, you do find a reference back to GRIN, but it isn’t exactly front and center, is it? It’s as if the link between the genomic data database and the germplasm database was a bit of an afterthought.

  2. You’re right, of course. We both are. So what we need is a short but sweet high-powered meeting to bring the gene-jockeys and the gene-bankers face to face in meatspace with the people who curate the various human genome portals. That’s where the real muscle is, and they seem to have sorted out most of the entertainingly difficult problems about linking various types of data about various types of entity.

  3. We are happy to help if you have questions–thanks for the acknowledgment :)

    I was actually wondering about plant growth databases the just other day when I saw this article.

    In case it goes away, here is a clip:

    Monsanto Co., the Creve Coeur-based manufacturer of Roundup, is launching a new program to tell farmers where, when and how much they may spray glyphosate-based herbicides. The program is run through a new website, http://www.pre-serve.org. It aims to protect threatened and endangered plant species from aerial spraying or ground application of glyphosate, an ingredient in numerous pesticides.

    Being a database junkie I had to check it out. It isn’t something we would cover, but maybe it will be of value to someone.

    However, it had the look of a public relations effort more than anything else. But it is not my field (so to speak), and maybe it will be a good thing.

Leave a Reply

Your email address will not be published. Required fields are marked *