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

Finally, let me speak up for scientists. In my experience, the vast majority of scientists are honest, sometimes slightly nerdish people who are grateful to be able to work on something about which they have a passionate interest. Scientists can be arrogant: but overall they do not deceive themselves, or the public.

From an article written by Philip Strange. I’m not sure about slightly nerdy, but there is a lot of variation even among people studying science, and I’m probably at the nerdy end of the spectrum.

I just got out of a meeting about how we’re going to improve the annotations of the maize genome. It’s got me riled up.

But first, what is gene annotation (in twenty words or less): (more…)

One of the themes, looking over the abstracts and talks for this year’s maize meeting before I leave is that a year from now we can expect to have much more detailed information about where genes are expressed in corn, and at what levels. One of the great dividends of the dropping cost and increasing speed of short read sequencing.

At this meeting alone we’ll be hearing about the incredibly detailed leaf transcriptome[1] (which seperates out expression of four developmental zones of the leaf, plus uses laser capture to look at the expression of genes the bundle sheath and mesophyll cells within the maize leaf seperately). And at least two posters on the subject also caught my eye (although there may be a lot more that involve profiling expression using high throughput sequencing). Two groups based at Oregon State and Stanford are in the process of sequencing the transcriptomes of the male and female gametophytes* of maize[2], and a group based primarily at Cold Spring Harbor is in the proccess of sequencing the transcriptome of developing ears (the kind covered in corn kernels, not the kind you hear out of)[3]. Both of these transcriptomes actually represents a number of seperate data sets from different tissue types and/or developmental stages.

All these datasets makes me wish the Fort Lauderdale Accords** applied to expression data in addition to genome sequences themselves, but since it doesn’t, I’ll happily oooh and awww over other people’s cool data.

A special thanks to Andrea Eveland’s abstract for introducing me to units that can actually quantify the wa expression is measured in these studies RPKM (Reads Per Kilobase of exon per Million reads).

*Plants practice alteration of generations, switching between diploid (two copies of the genome, one from each parent) and haploid (only a single copies of their genome) multicellular forms of life. In flowering plants, the kind we spend most of our time with, the haploid generation is almost vestigial, but it still exists. Plant pollen contains an entire male haploid plant (the male gametophyte), which has been reduced to a mere three cells (two which are sperm cells). The female gametophytes of flowering plants are only a little larger, at seven cells. In other plants, the gametophyte can exist as a free living life form visible to the naked eye.

**The agreement that allows genome sequence data to be released to the whole community before the people who sequenced that genome have published their paper.

[1] Pinghua Li et al. “Characterization of the maize leaf transcriptome through ultra high-throughput sequencing” Talk #14 2010 Maize Meeting (Presented by Thomas Brutnell)

[2] Rex A. Cole et al. “Analysis of the Maize Gametophytic Transcriptomes” Poster #27 2010 Maize Meeting (Presented by Matt Evans)

[3] Andrea L. Eveland et al. “Transcriptome sequencing and expression profiling during maize inflorescence development.” Poster #113 2010 Maize Meeting

The maize meeting is a once a year chance for people nearly as into studying corn as I am to gather in one place, talk science, drink beer, and talk science.

I’ve got a few pre-scheduled updates (fewer than I was planning) based on interesting posters and talks I want to check out at the meeting, but aside from that you probably won’t be hearing much from me for the rest of the week.

Hopefully I’ll see at least a few of you there!

WordPress keeps stripping the GoogleMaps embedding code out of the post, but if you go back to the previous entry the map should be visible.

FREEDOM!!!!

Of course this is Berkeley, so mid-terms come twice a semester.

This is the other reason I’ve had so little time to post lately.

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.