James and the Giant Corn Genetics: Studying the Source Code of Nature

January 17, 2010

Jazzman Rice

Filed under: Uncategorized — James @ 1:16 am

Jazzman is a new breed of rice developed quite recently by researchers at Louisana State University. As the name implies, this was a conscious attempt to replicate some of the flavor, texture and aroma of Jasmine rice in a breed of rice adapted to American growing conditions. In comparing the two varieties the AP says:

The new variety yields up to three times as much grain per acre as the fragrant, nutty Thai strain, which grows too tall and flowers too late for U.S. farms.

So this is a cute little story about plant breeders developing crop varieties that are well adapted to local conditions and fulfill some desired food niche. Well except for the little problem that right now the demand for Jasmine rice in the US is fulfilled by imports from Thailand. The Director-Genernal of Thailand’s Rice Department was quoted back in September as saying he isn’t worried that competition from Jazzman rice on quality although given the higher yields, it might be a threat to lower grade rice exported by Thailand. But here’s the kicker:

Mr Prasert said he would also consult with Thai agricultural officials overseas on the possibility of examining whether Jazzman rice had been genetically modified.

He said GM crops normally provide better yields than natural crops.

The article quotes numbers on yield (in hybrid of metric and southeast asian specific units) that work out to just more than the 3 fold increase in yield I just quoted from the associated press. I don’t know that any of the advocates of genetic engineering have ever claimed current traits, or anything in the pipeline, could triple yields*. I’ve seen people categorically opposed to genetic engineering say a lot of things in my time, but this is the first time I’ve run into people exaggurating the benefits of the technology.

*Outside of situations, like bt crop is introduced into an area that hadn’t previously used ANY method to control insect pests previously, which don’t apply to rice grown in the US.

January 16, 2010

School Lunches

Filed under: food,Politics — Tags: , , , — James @ 5:44 am

In yet another article on the evils of corn syrup, I came across a weird quote:

Because SFUSD has focused on reducing fat and empty calories in cafeteria items, the meals are now very close to the USDA minimums, and are based on a meal which includes either 1-percent white milk or skim chocolate milk. “Replacing skim chocolate milk with skim white milk would cause the calorie count of the meal to drop below the USDA-mandated minimum,” says Woldow [A member of the San Francisco School District Student Nutrition Committee]

I feel weird thinking about this. Cutting sugar (regardless of whether it originates in sugarcase, or corn, or sweet sorghum, or the sugar beet) from school lunches is a laudable goal. But free and reduced price school lunches are also the closest thing some kids will have to a real meal all day. So San Francisco School District, in the push to make school lunches more healthy, if nothing else could you please increase the portions for healthy things as you cut out the foods you don’t approve of?

Cutting calories from a program that has a real impact on childhood hunger and malnutrition in our country isn’t something you should be proud of.

And just to be clear all that happened in the article linked above was to substitute sugar (produced from sugar beets, or sugar cane) for corn syrup on a calorie for calorie basis.

January 15, 2010

It’s Been Two Years!

Filed under: Site Business — James @ 9:44 am

…since my first entry. I wish I could call it a lengthy piece of insightful writing, but sadly, it is not.

With two years of data I can say that there’s a hint of an annual pattern to my writting with greatest number of entries being written in the final months of the calandar year and the least during the summer months. But two 1-year datasets isn’t nearly enough to prove a trend, simply suggest one.

It’s been a lot of fun to become more engaged in the online community the past couple of years,particularly the last six months or so as this site slowly transitioned from a cool new computational toy to mess around with, to a way of communicating with friends and family, to (what I now like to imagine is) a place that’s telling interesting stories about plant genetics to people, some of whom I’ve never met, who might not have come across it otherwise.

When considering what ancient quotes to dig up from the archieves for this entry, there really wasn’t much contest. From Another Day of 10,000 Interviews (talking about part of my visit to Berkeley to interview for the graduate program I later joined):

This time I have seven[interviews]. Three with faculty, and four with the labs of absent professors. And I can honestly say that I walked out of each interview very excited about the science in that lab. … the grad students here at Berkelely seem happy.

And from Wrap up in Berkeley (the same visit):

I still can’t get used to palm trees. I’ve seen them in movies, but then again, I’ve seen velociraptors in movies too, and in my mind they both have about equal business showing up in the real world where people go about their daily business.

January 14, 2010

The Newly Published Soybean Genome and Fractionation

Here’s the key statistic: The maize genome paper estimated that roughly a quarter of maize genes are currently retained as duplicate pairs from maize’s whole genome duplication, while the soybean paper estimates just over half of soybean genes are similarly retained after soybean’s (apparently slightly older) duplication. <– had it buried at the end of this, but figured it’d be more fun to start out with something cool.

But first of all, let’s do this the right way this time. Here’s the paper in Nature describing the soybean genome. Here’s one of the places you can download the entire sequence from. Hopefully that establishes, beyond a reasonable doubt, that the soybean genome has, in fact, been published. (more…)

January 13, 2010

Even Faster Sequencing

Filed under: Fun With Numbers — Tags: , , , — James @ 12:01 pm

Just five years ago in 2005, the state of the art technology for sequencing genomes was Sanger sequencing, the same basic technology that had been used by biologists for decades, although the sequencers of 2005 were the result of decades of refinement of the basic technique. Five years later in 2010, the newest state of the art sequencer is the HiSeq 2000 from Illumina (at least until the Pacific Biosystems sequencers become available later this year… ::drool::). What difference does 5 years make? It would take more than thirty-thousand of the latest and greatest sanger sequencers from 2005 (right before the first next generation sequencer, a 454 machine built by Roche, was released) to produce as much DNA sequence data as a single one of the new HiSeq 2000s produces.* (more…)

No strawberry genome ::sniff::

Filed under: Site Business — James @ 12:26 am

From the article on the genome at scienceblog.com:

Contrary to the information posted in the article on January 11, 2010, the strawberry genome sequence has not been completed or released.

The news release above was a premature and highly inaccurate dissemination from the USDA. The strawberry genome has not been published, it has not been released, and analysis is not complete.

The genome of diploid strawberry (Fragaria vesca) will be sequenced and released in 2010. The effort was led by an international consortium representing over 40 institutions and the efforts of countless researchers. Details can be found at strawberry.vbi.vt.edu.

A formal presentation of the current state of the draft sequence was presented by Dr. Vladimir Shulaev at the Plant Animal Genome Conference in San Diego on December 9th, 2010 (editor’s note: as pointed out in the comments this was almost certainly intended to read January 9th, 2010). This presentation was potentially misinterpreted as a formal announcement, and a conversation with a scientist on the project laced the above article with inaccurate interpretations.

The draft sequence will be published shortly after complete analysis and peer review. The above article is not accurate in many facets and should not in any way be considered representative of the scientific efforts of the Strawberry Genome Sequencing Consortium.

The work was also supported by many organizations in addition to Roche, with substantial financial and other commitments from sources including (but absolutely not limited to) Virginia Tech, IASMA Research Center (Italy) University of Florida, Driscoll’s Strawberry Associates, Plant and Food Research (New Zealand) and the USDA.

A formal retraction of the initial press release is being pursued.

Kevin M. Folta
University of Florida, on behalf of Dr. Vladimir Shulaev and the Strawberry Genome Sequencing Consortium

From the outside it is hard to know exactly what happened but clearly SOMEONE jumped the gun and the internet echo chamber, of which I’m apparently now a component, swung into motion.

My apologies go out to everyone involved in the strawberry genome sequencing project, and anyone who was reading about the woodland strawberry genome here who got as excited as I did about the possibilities.

I’d still be fascinated to load a pre-release version of the strawberry genome into CoGe when/if it becomes available. And speaking as someone who has done gene annotation work previously on an newly sequenced genome CoGe is a GREAT tool to have  when one is sanity checking gene models and contig assembly.

January 12, 2010

Strawberry Genome Sequenced (Correction included)

Filed under: biology,Genetics,Plants — Tags: , — James @ 3:10 pm

After already needing to correct this post, I must now invalidate the whole thing. Seems I’ve been taken in by a premature press release that was turned into reliable sounding articles on news sites and was then picked up by blogs like mine that took the those sites to be credible sources. It’s a big mess. ::sigh::

Among the many things I’m currently missing at the Plant and Animal Genome conference, in addition to an update on the banana genome I’ve just learned (thanks to Mary over at OpenHelix) that the sequencing of the woodland strawberry genome has been completed!

I don’t know yet if the sequence has been released to the public yet. Either way I can’t find the sequence so I can’t yet comment on the quality of the sequence, or any ancient duplications in the lineage (though we already know it must share the ancient hexaploidy of the rosids, possible all eudicots).

Wild diploid strawberry (left) and domesticated octoploid strawberry (right)

What we do know is that modern domesticated strawberries are octoploid, the result of two recent whole genome duplications, but the woodland strawberry doesn’t have any duplications modern enough to be obvious from cytogenetics, visually looking at chromosomes.

Sequencing a genome is a complicated process but it started out with the work of Janet Slovin, a USDA scientist who created the inbred line* used in sequencing and seems to be the front woman from the project (Janet was kind enough to comment and point out the original article was misleading on this point, check out the link she included as well!), she’s quoted in the linked article.
And if you know how I can get my hands on the sequence please PLEASE, drop me a line at jcs98 (at) jamesandthegiantcorn (dot) com.

Ideas on why plant genomes rule?

Filed under: Site Business — James @ 1:11 pm

I’m considering starting a series on several ways that plant genomes can take more punishment than mammalian genomes and survive. Right now I can think of:

-Methylation knockouts

-Telomerase knockouts (for a few generations) and tissue culture for decades

-Whole genome duplications/and aneuploidy

Can you think of any other examples of things plant genomes can survive better than animal genomes? (Or counter examples of things that are horrible for plants but that animal genomes can shrug off without ill effects?).

I’m not asking anyone to do my research for me, I’ll track down the papers for myself. But in finding research results, like many things, knowning they’re there to be found is half the battle.

January 9, 2010

Pumpernickel and Rye and Vavilovian Mimicry

Filed under: Crop Profiles,food,Plants — Tags: , , , — James @ 3:24 pm

Delicious pumpernickel bagel.

Its tasty but what is it? First, a disclaimer. I’m going to be discussing traditional pumpernickel bread. The kind pictured to the right is almost certainly modern pumpernickel which gets its color from dark substances like molasses or cocoa powder, and often is made with wheat flower rather than the traditional rye. But that’s a boring story. This one is more exciting!


January 8, 2010

Shortest Book Review Yet!

Filed under: Book Reviews — James @ 5:34 pm

After posts yesterday and the day before.

If you’re interested in plant genetics or agriculture or biodiversity, read about Nikolai Vavilov. But I wouldn’t recommend reading “Where Our Food Comes From” (though I’m personally glad to have read it since I probably otherwise never would have heard of the guy). On second thought, you might like it. I kept getting angry with the author even as I was fascinated by the subject.

Case in point:

The corporate and academic plant breeders who are the most common recipients of seeds from those repositories typically do work that is a poor substitute for that done on-farm by vernacular plant breeders, traditional farmers.

’nuff said.

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