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

November 24, 2009

Corn vs Maize

Filed under: Genetics,research stories,Site Business — Tags: , , — James @ 10:46 am

I use the words basically interchangeably on this site. I know it’s confusing and I at least attempt to pick one and use it all the way through a post (often without success, which I’ll catch, and wince at, days later). The problem is that naturally I use one word or the other depending on context.

The plant in question is studied internationally and while in America “corn” means those cool looking plants that you see me standing in front of one third of the time when you visit this blog, in british english the same word means any grain. I’ve never heard it explicitly said, but I assume the reason the geneticists who study the plant originally called it maize was to avoid confusion from those mixed definitions. It’s also possible “corn” was still considered a slang term back then, and not the sort of name a well educated scientist should be using regardless.

As a result of growing up in the midwest surrounded by corn and getting interested in comparative genomics by way of maize genetics, terms like “corn geneticist” and “corn genome” don’t sound right to my ear and ones like “maize plant” or “maize is selling for $5 a bushel” sound even worse. On the other hand, the sentence “Sequencing the maize genome is going to provide even more powerful tools to corn breeders” sounds fine, but I realize it can be confusing to people whose life experiences are different from my own.*

*An even weirder one: Back when I was still doing science that required writing with pen and paper instead of doing everything on the computer, without thinking about it I’d either cross my sevens or not depending on whether I was writing a number in a scientific context.

A crossed 7. Theoretically this is easier to distinguish from a 1, especially on tassel bags and row stakes that are going to be outside, exposed to the elements for months.

A crossed 7.

Theoretically a crossed 7 is easier to distinguish from a 1, especially on tassel bags and row stakes that are going to be outside, exposed to the elements for months. (And where a mistake has the potential to ruin a year or years of work. It’s not like maize geneticists can run down to Walmart and buy more seeds carrying the genotypes they’ve spent years putting together.)

November 20, 2009

About the Maize Genome Paper

Filed under: biology,Genetics,research stories — Tags: , , , — James @ 11:23 am

Looking at the maize genome paper in isolation it’d be easy to wonder what all the fuss was about. The paper itself is only four pages long with (plus a page of citations), with two figures, and as awesome as figure 1 is (and it really is very, VERY awesome), it doesn’t seem like an lot for a project that represents the work of more than 150 authors over four years. But the real fruits of the maize genome project are the sequences that can be found on either maizesequence.org or maizegdb.org and additional exciting research it is already enabling. And as the result of a quirk the way genome sequence is released to the research community, we can already get a sense of some of that other research. (more…)

The Family Tree Of Corn

Branches not to scale. Tree designed in Mesquite.

Branches lengths not remotely to scale. Tree designed in Mesquite.

This family tree shows the relationship of a few of the species in the grass family tree that I think people might be most familiar with. Genomes that were published before today are marked in green (there were only two, sorghum and rice), the maize genome which was just published today is marked in yellow, and brachypodium (which you shouldn’t feel at ALL bad if you haven’t heard of) is marked in grey as its genome project is in the final stages (a draft assembly was released to the public last winter) so it’ll probably be the next grass genome to be published. After that I’m less sure, I know there’s a foxtail millet genome project, but I don’t have any idea how far along the process of genome sequencing, assembly and annotation the genome project is.
What’s important to know about the relationship of the sequenced grasses? (more…)

November 19, 2009

Why should you be excited about the corn genome?

Filed under: food,Plants,research stories — Tags: , , — James @ 5:36 pm

Virginia Walbot has ten reasons in the latest issue of PLOS genetics. PLOS journals are all open access so anyone can read it without a subscription.

The two reasons I think will be the most interesting to non-biologists are #1 and #10:

Corn was domesticated a short 10,000 years ago and domestication is normally a huge genetic bottleneck that results in the loss of much of the gene diversity found in the wild ancestor. (Modern tomatoes are more diverse than heirlooms because breeders are intentionally working to bring some of that diversity back over.) Yet two lines of corn, which certainly shared many common ancestors in the last 10,000 years, contain more genetic differences than humans and chimpanzees which have been evolving separately for 3.5 MILLION years. That’s 10,000 years vs 3,500,000 years!

Number ten drives home how essential corn is to the world today with statistics like American farmers growing so much corn last year than it works out to a metric ton for every man, woman, and child in this country. Or that corn and cornfeed animals feed a billion people around the globe (those aren’t rice numbers, but hopefully it drives home why corn has definitely earned it’s place as one of the big three grains that support civilization around the world).

h/t to the beekeeper (who I haven’t see around the blog in months) for pointing me at this PLOS genetics coverage of the maize genome papers coming out both there and in Science.

November 7, 2009

Figure from my Research Proposal

Filed under: biology,research stories — Tags: , , , , , — James @ 7:17 pm

“My budget…triples the number of National Science Foundation graduate research fellowships.  This program was created as part of the space race five decades ago. In the decades since, it’s remained largely the same size –- even as the numbers of students who seek these fellowships has skyrocketed.  We ought to be supporting these young people who are pursuing scientific careers, not putting obstacles in their path.” – President Obama

I’m still feeling brain dead after the final push for submitting.

Speaking of NSF, here’s the one figure I managed to shoehorn into my research proposal.

Blast hits between an orthologous quartet of gene spaces, one in rice, one in sorghum and the two copies created by the maize tetraploidy.

Blast hits between an orthologous quartet of gene spaces, one in rice, one in sorghum and the two copies created by the maize tetraploidy. As usual click the picture to see it fullsized

If you’d like you can even click here to be able to play around with the figure yourself using the CoGe interface. Now I’ve got to try to explain what this figure is about. (more…)

November 6, 2009

It is Done

Filed under: biology,research stories — Tags: , , — James @ 4:21 pm

NSF fellowship application complete and submitted with just under an hour and a half to spare before the deadline. More inside. (more…)

November 4, 2009

How to Maintain Anonymity when Rejecting a Paper

Filed under: Link Posts,research stories — James @ 12:42 pm

Was just forwarded a hilarious post over at scienceblogs. Apparently researchers who are asked to review scientific papers* have to worry about a fair bit about being identified even though comments are supposed to be anonymous…especially if the researcher in question is giving the paper negative reviews.

Many specific fields of research aren’t that big, so an author receiving a paper back with negative reviews can often make educated guesses about who rejected the research he’d spent grant money like it grew on trees, and poured out grad students’ sanity like water to accomplish.

This post proposes a set of tactics for disguising your identity, though not with a straight face. Tactics include: Pretend to be British, pretend to German, pretend to be an American pretending to be German (if you are german), and my personal favorite, pick someone you don’t like and pretend to be them:

Pick one of the people from you own list of 5-6 enemies and pretend to be that person. Heavily cite their work. Reference their obscure conference presentations. Arrogantly suggest that person’s methods in favor of the methods used in the paper, especially where they are clearly inapplicable.

*Since the people who work as editors at the various journals can’t be the top experts in every fascet of the scientific work they cover (and even if they could be, leaving the decision on what science was worthy of publication in the hands of so few might make bias a little too tempting.) The solution is to have the scientific merit of scientific publications submitted for publication evaluated by a group of anonymous researchers, working in the same field. This, usually, makes sure the people reviewing the paper are up-to-date on the science and techniques involved, and since different papers are reviewed by different scientists, there’s less danger of personal opinions biasing the direction of published research. This method of evaluating the validity and relevance of scientific publications isn’t perfect, but it’s the best system we’ve come up with so far for advancing the understanding of the scientific community.

October 13, 2009

Potato Genome!

Filed under: biology,Plants,research stories — Tags: , , , , , — James @ 7:26 pm
Photo from graibeard

Sort of anyway. What was released was a pre-publication scaffold of the genome. A final, published, version might include more primary sequence data, will have fewer gaps, and most importantly of all, people will be able publish their own work which draws on the potato genome.

Overall I have mixed feelings on the current practice of releasing genome sequences prior to publication. As someone who does comparative genomics, having access to more genomes is great, but the agreements they’re released under severely limit how they can be used in publications prior to the publication of the genome paper itself (which can be a LONG time).

Within the grasses four genomes are available (Maize(corn), Sorghum, Rice and Brachypodium) however only two of them, Rice and Sorghum, are published. Any paper making use of whole genome analysis of all four cannot be published before the Maize and Brachy papers come out (hopefully before the end of this year!).

That said having even a rough draft of the potato genome is cool. Potato is a great plant for a lot of reasons. Potatoes are the fourth staple crop (behind only rice, maize and wheat) that provided enough food for people to build civilizations and probably the most important non-grass crop in the world. Currently there are no GMO-potatoes on the market, as I mentioned here. Domesticated potatoes are tetraploid and rarely breed true (their offspring aren’t much like the parents).* And I still owe it a post of its own.

Another reason to be interested in potatoes are is the family tree of the species. Potato can claim tomatoes, eggplant, and deadly nightshade as close relatives.** That whole group of species belongs to a different branch of the family tree of plants (the Asterids) from the early non-grass genomes (Arabidopsis, Papaya, and Grape) which were all in a group called the Rosids. These two groups are responsible for a lot of the diversity of species within the Eudicots*** so it’s good we are starting to starting to see Asterid genomes.

*Potatoes grown from seed not sharing many characteristics with their parents is why most cultivation of potatoes is done by planting pieces of potatoes instead of seed. The plant that sprouts out of a potato is genetically identical to the plant that grew the potato. It’s a clone. Apples actually face a similar issue with apple seeds not being much like their parents. That’s why breeds of apples are propagated by grafting. A breeder cuts off a piece of a branch from one tree and carefully connects it to the stem of an unrelated apple tree. If the graft is done properly the branch will grow, flower, and produce fruit just as it would normally. So all apples of the same variety (say Gala, Macintosh, or my new favorite Cripps Pink) are clones of each other.

**The obvious family resemblance to deadly nightshade was one of the reasons Europeans originally believed tomatoes and potatoes to be toxic when they were introduced from the Americas.

***For a sense of how Eudicots fit into the family tree of all plants, check out Phylogeny of Pineapple, a further explanation of awesomeness

March 13, 2009

Maize Meeting 2009 part 1

Filed under: Plants,research stories — James @ 1:10 pm

In a lot of ways its like a reunion. Of the five people I did science for as an undergrad (this is what happens when you work in a new lab every summer) four of them are here. No to mention the grad students and post docs I’ve worked with, or took classes with, or who TAed classes I took. One of the reasons I like working in maize so much is the how connected the community is.

The rest of this entry will be a random collection of cool things I took note of on my iPhone:

*Arabidopsis genome cost 70 million dollars and took approx. 500 people seven years to complete. Today re-sequencing that genome costs 7000 dollars and takes two postdocs a week. (Note that this is re-sequencing a known genome. Having to assemble a new genome from scratch costs more because you need longer reads and takes a LOT longer.)

*The talk on developing exemplars of transposons was very cool. All sorts of complicated statistics related to defining families by relatedness, and then using that to pick the “most normal” copy for that family in the genome

*A guy presented a tool that, given a single gene, will find all the related genes in a genome. Define their gene structure, and then build a phyogenetic tree of the genes. Basically everything I had to do to make the tree in this entry, only instead of taking one grad student 2-8 hours, it takes a computer program 1-3 minutes.

*Talked to a woman who has a poster here looking at FT-like genes in maize. (That giant phylogenetic tree I made was looking at FT genes in grass species.) Great to meet a total stranger with a common research interest. 

More to come later. I’m considering posting my raw notes as a text file at the end of the meeting. Between the random things I think are worth copying down and the iPhone exaserbated spelling errors, I at least, find them hillarious. I’ve beat a strategic retreat from the poster session for little while to post this update and should probably return now.

January 18, 2009


Filed under: Photo Posts,Plants,research stories — James @ 9:57 pm

Jamesandthegiantcorn turned one year old on thursday (and a good friend of mine turned 23 that same day). As it happens this will also be my 100th entry, I’ve averaged about two updates a week over the past year, which is pretty good given my previous experience with blogging. Without further ado, my 100th entry:

Brachypodium? What is it? Well it’s a grass species that looks like this:

 Brachypodium distachyon

I first mentioned it almost a year ago in an entry I posted during my interview weekend at berkeley:

Most “I’m definitely a potential grad student” moment: 


“Um…wait…I can’t remember his name but he works on a species called bracopodia brachypodium.” <– I’m better at remembing the names of new species of grass than of the people I meet who study them.

Obviously while I remembered the name, I did not learn the spelling. But since then I’ve learned a lot more about the species and why people study it. Brachypodium is a tiny temperate grass that is (like so many other species) an “emerging model organism.” That means people think studying brachypodium can teach us more about other species*, and are having brachypodium’s genome sequenced. Part of developing a useful genome is annotating genes, which is something I’ve been working on during my rotation.

*I would say the reasons its considered a good model are first that brachypodium is what arabidopsis (the first plant ever to have it’s genome sequence) would be if arabidopsis were a grass: a small plant with a small genome and a generation time of only six weeks (compared to 3-5 months for corn, or 15-20 years for humans). 2. It’s much more closely related to wheat than any other sequenced plant, and wheat could use better molecular resources.

Of the big five crops, rice, maize and sorghum as all getting their genomes sequenced. The two that aren’t are potato and wheat. Potato is tetraploid (where humans have two versions of every chromosome potatoes have four versions), and wheat is hexaploid (six versions of every chromosome!). Until sequencing and assembly technologies improve, the closest we can come to sequencing these vital crops is a related species with a more tractable genome (tomato for potato and brachypodium for wheat).

PS The new comment posted will be the fiftieth non-spam comment on this blog. A lot of milestones this week.

« Newer PostsOlder Posts »

Powered by WordPress