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

March 17, 2010

Abnormal Chromosome 10

Filed under: biology,Genetics — James @ 1:14 am

There is a piece of DNA that is sometimes found on the end of the tenth maize chromosome. In plants that possess this extra chromosome segment, chromosome knobs* (including one that’s a part of the extra segment included in abnormal chromosome 10) start to act like centromeres**. But this story graduates from odd to downright weird when I tell you that possessing this extra centromere-like activity gives a chromosome an unfair advantage in being passed on to the next generation.

Plants, like animals, possess two complete genome copies, one from each parent. They’ll only pass on one copy (mixtures of pieces from each parent) to their offspring. Any given sequence has a 50% chance of being passed on which seems fair given the plant is passing on 50% of its total genetic material. But abnormal chromosome ten cheats (using those extra centromere-like sequences I mentioned earlier). It has up to an 83% chance of being passed on.

Since the breed of corn (B73) the maize genome was based on has the normal version of chromosome 10, we know very little about the extra DNA found in abnormal chromosome 10. The authors of this poster are going to correct that oversight, by sequencing the region, figuring out how (and how long ago) abnormal chromosome 10 came into being, and hopefully identifying the genes within the region that make chromosome-knobs act like centromeres.

*Knobs are dense segments of DNA that scientists have been able to spot visually within chromosomes since before we knew for sure that chromosomes carried genetic information.

**Centromeres are the part of the chromosomes that bind together during cell division (the center of the X in the traditional drawing of a chromosome). They’re also the place where the molecular machinery that pulls chromosomes apart at the end of the process of cell division.

Lisa Kanizay and Kelly R. Dawe “Uncovering the sequence and structure of maize abnormal chromosome 10” Poster #165 2010 Maize Meeting.

March 9, 2010

Wow!

Filed under: biology,Campus Life,Genetics,genomics — Tags: , , — James @ 2:56 pm

Who could have predicted maize geneticists would be so interested in maize genes? The entry I posted last night on Purple plant1 and Colored aleurone1 easily received more traffic in its first day on the site (it’s still got a long way to go before it catches long term readership attractors like water chestnuts and the NIPGR tomatoes), than any entry since the heady days of the maize genome release back in November.

The relationships of the four grass species with sequenced genomes. The branches are NOT to scale with how long ago the species split apart. Green stars represent whole genome duplications. The most important one to notice in the one in the ancestry of maize/corn. That duplication means that every region in sorghum, rice, or brachypodium is equivalent to two different places in the maize genome, one descended from each of the two copies of the genome that existed after the duplication.

And this morning the dataset I drew that example from, 464 classical maize genes mapped onto the maize genome assembly plus syntenic orthologs in up to four grass species: sorghum, rice, brachypodium, and the other region of the maize genome created by the maize whole genome duplication (technically syntenic homeologs since we started in maize to begin with, by the principle is the same), went out to the maize genetics community (thank you MaizeGDB!).

A postdoc in our lab tells me more people have visited CoGe today than any day on record (and we hit that mark before noon!).

Anyway, thank you guys, it’s great to feel appreciated!

March 8, 2010

Two classical maize genes, synteny, and the mystery of the missing gene

Filed under: biology,Genetics,genomics,Plants — Tags: , , , , , , — James @ 12:50 pm

Colored aleurone1 and Purple plant1 are both genes with long histories in maize research and are involved in the regulation of anthocyanin biosynthesis.The mutant version of purple plant1 does exactly what it sounds like. (In the proper genetic background) it has plants producing anthocyanin (a purple plant pigment) everywhere, resulting in purple plants. The mutant form of colored aleurone1 was identified from a mutant that changed the color of individual corn kernels. Guess which of these two classic maize mutants made it into the top 15 most published on genes in maize, and which fell barely short.

Ears segregating for the colored aleurone mutant phenotype. Image courtesy of MG Neuffer via MaizeGDB.

Purple plant1's phenotype is highly variable depending on the genetic background the mutant is in. Images courtesy of MG Neuffer via MaizeGDB.

The two genes are also duplicates (homeologs) resulting from the maize whole genome duplication. From the picture below you can also see both the two genes and the regions they are in match up to single regions in rice and sorghum, two grasses that haven’t gone though a whole genome duplication since the great radiation of grass species that took place an estimated 50 million years ago (well after dinosaurs stopped walking the earth). (more…)

March 3, 2010

Oliva Judson’s Salute to Grasses

Filed under: biology,evolution,Genetics,Plants — Tags: , , , , — James @ 2:33 pm

People who can actually get the general public interested in science are almost as rare as hen’s teeth.* One of those gifted scientist-communicators is Olivia Judson, an english evolutionary biologist who sometimes writes a column for the nytimes and published an interesting/hilarious pop-science book titled: Dr. Tatiana’s Sex Advice to All Creation: The Definitive Guide to the Evolutionary Biology of Sex.**

I mention all this to explain why I was so excited to learn that her post this week sings the praises of a group of species near and dear to my heart, the grasses. The whole post is definitely worth a read. Even if you don’t learn something you didn’t already know, read it as a source of inspiration for telling OTHER people how cool grasses are. And the closing is truly excellent:

We usually talk of our domestication of grasses, and the ways in which we have evolved them: we have made plants with bigger, more nutritious seeds that don’t fall to the ground, for example.But their effect on us has been far more profound. Our domestication of grasses, 10,000 years ago or so, allowed the building of the first cities, and marks the start of civilization as we know it. Grasses thus enabled the flowering of a new kind of evolution, a kind not seen before in the history of life: the evolution of human culture.

Some of the comments are heart warming to read as well, although a bunch of people have fallen prey to the maize/corn confusion. (Explained in detail here)

*Speaking of cool science that most of the general public doesn’t know about: We’ve known for more than four years that mutations of the gene talpid2 in chickens cause chicken embyros to develop teeth, something we thought birds had lost the ability to do 60-80 million years ago (around the same time grass was bursting onto the world stage.) Don’t worry too much about getting bitten by a sabertoothed turkey, the toothed embryos have other problems that mean they don’t survive.

**There’s also a three-part video series based on the book that I can best describe as … odd.

February 11, 2010

Why to Celebrate the Publication of the Brachypodium Genome

Filed under: biology,evolution,Genetics,research stories — Tags: , , , , — James @ 4:28 pm

Brachypodium distachyon (photo courtesy of Devin O'Conner)

Sorry this is late going up. -James

This morning Nature officially published the paper* describing the sequence of the Brachypodium distachyon genome. This publication brings the number of grass genomes available for comparative analysis to four. In celebration I’m going to list four reasons to be excited about the publication of this genome.

The location of Brachypodium within the grass family tree.

Brachy (as I will refer to the species from here on) is a member of the Pooideae a sub-family of grasses from which no sequenced grasses have come. For the work we do in my lab this is exciting because it adds more depth to our analysis of changes in the grass genomes. The more distantly related grasses we can compare at the whole genome level, the better we can infer what the ancestral species that gave rise to all the grasses might have been like at a genome level. The most we know, or can make educated guesses about that species, the better position we are in to say what changed along the evolutionary paths leading to grasses like maize, rice, and sorghum. The choice of the Pooideae wasn’t at random, or even because of the sub-family’s distant relationship to other sequenced grasses. (more…)

February 9, 2010

MaizeGDB and CoGe: A Beautiful Friendship

Filed under: biology,Computers and Coding,research stories — Tags: , , , , , — James @ 2:50 am

Editor’s note: I have a new shorter, better, tutorial, here.

One of the earliest fruits of my work to define relationships between syntenic genes* was a list of sorghum genes and corn genes in one or both of the two related regions of the corn genome (each region in sorghum corresponds to two in corn because the ancestors of corn completely doubled their genome in the time after the ancestors of corn and sorghum went their separate ways.)

But this is not the post where I explain my research projects. That post would be confusing and densely written at the best of times, which two AM in the morning certainly isn’t. Tonight my goal is simply to introduce the embedded video below, which explains how any researchers who want to can check out the relationships I’ve identified between genes in the two duplicate regions of maize, and the genes of the sorghum genome can do so using the MaizeGDB genome browser, and CoGe’s own GenomeViewer application. Video below. If you’re going to watch, I recommend selecting the highest resolution youtube offers you. (more…)

February 6, 2010

Scientists at India’s NIPGR Create a Longer-Lasting Tomato (Studying The Regulation of Fruit Ripening)

Filed under: agriculture,biology,Genetics,Plants — Tags: , , , , — James @ 6:24 pm

ResearchBlogging.org

Author’s note: This would seem to be the week for vegetables I hated as a kid. Yesterday was onion, today tomato, if there’s a story about brinjal/eggplant in the next few days we’ll have hit all the big ones. 😉

Ripening tomatoes. Photo: Photos_by_Lina, fickr (click to see photo in its original context)

I was recently pointed to an early publication paper that went up on the Proceedings of the National Academy of Sciences website on Monday, where a research group at India’s National Institute of Plant Genome Research describes two genes from tomato that, when knocked down by RNAi*, result in tomatoes that can remain ripe but not spoiled for up to three times as long as tomatoes where these two genes function normally.

Their approach targets specific genes involved in breaking down certain proteins found in the cell walls of tomatoes (in fact in the cell walls of all plants). Breaking down the cell wall is a key part of ripening in fruits (which the tomato is, botanically if not culinarily). Which makes sense if you’ll think about it for a moment. One of the traits we associate with ripening is getting softer, from bananas to peaches if it’s still crunchy when you bite into it, it wasn’t ripe. What makes plants stiff and crunchy? The strength of their cell walls. Since, unlike vegetables, fruits WANT to be eaten**, as they ripen they begin to break down their cell walls to make themselves more appealing to passing animals. Unfortunately, ripening and spoiling are, in a lot of ways, the same process. If fruits aren’t eaten when they become ripe, they continue to get softer, transitioning from delicious looking -> unappetizing -> inedible -> a puddle of mush on your kitchen counter.

Preventing ripening entirely is relatively easy, and there are plenty of known mutants in tomatoes and other species that never ripen (these naturally mutant tomatoes stay green and hard no matter how long you wait). But getting part of the way to ripeness but stopping before crossing the line into spoiled is a much less tractable problem. (more…)

February 5, 2010

Some Evidence Suggests Trees Are Growing Faster

Filed under: biology — Tags: , — James @ 11:06 am

A Tree photo: me

In a Proceedings of the National Academy of Sciences paper from this week that has been picked up across the popular press, researchers in Maryland report that the trees they’re studying are growing measurably faster than they “should” be.

From US News and World Report:

During the past 22 years CO2 levels at SERC have risen 12%, the mean temperature has increased by nearly three-tenths of a degree and the growing season has lengthened by 7.8 days. The trees now have more CO2 and an extra week to put on weight. Parker and McMahon suggest that a combination of these three factors has caused the forest’s accelerated biomass gain.

These aren’t small changes either. The authors are quoted as saying the forests they’re taking measurements on are growing two to four times faster than they normally would. Very cool stuff. What I’d read previously suggested the increased temperatures brought about by an increase in CO2 in the atmosphere would more than cancel out the benefits to plants of having more CO2 available. Of course most of the work I read about has to do with food crops, not trees*, and trying to predict how plants will react to changes in the atmosphere and climate can get a bit circular since how plants react will also influence the state of the climate and atmosphere in decades to come.

The research article itself is open access, meaning anyone can read it for free (without having to be associated with a major research university that holds an institutional subscription, which is how I normally get access). Click here and then click the Full Text (PDF) link on the right to grab the whole paper.

h/t to Greensparrow Gardens

*Not that trees can’t produce food.

February 3, 2010

We got to genetics in class today and the story of the shrunken 2 gene

Filed under: biology,Plants,Politics,teaching — Tags: , , , , — James @ 1:17 am

Arabidopsis that carries broken copies of both the AP1 (apetala1) and CAL (cauliflower) genes. The flower bearing stems have been replaced by these cauliflower-head-like growths. Image from "Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development" by Frank Wellmer et al (in PLOS Genetics a creative commons licensed journal). Article here: http://dx.doi.org/doi:10.1371/journal.pgen.0020117

Just in time for me to put together my worksheet for Thursday! I’ve managed to work in the CAL gene, which I talked about last week in my discussion of Cruciferous vegetables:

Cauliflower plants (and broccoflower plants) have broken copies of the CAL gene, which (when it isn’t broken) is helps the plant decide to switch from producing stems that were bear flowers to the flowers themselves. Without a functional version of CAL, cauliflowers just keep making denser and denser stems, producing the distinctive heads of cauliflower. If you have journal access, you can read more about the CAL gene at this science paper: http://dx.doi.org/10.1126/science.7824951

I also threw in a question that uses the shrunken2 gene (one of the two most common genes that convert normal starchy corn into sweet corn). From the question in question:

Note the shriveling of the yellow kernels that carry two broken copies of the shrunken2 gene, the purple kernels carry either one broken and one working copy of shrunken2, or two working copies. The change in color is controlled by another gene nearby on the same chromosome, shrunken2 itself has no effect on the color of corn kernels. Photo credit goes to MG Neuffer and MaizeGDB.

Corn kernels without a working copy of the shrunken2 gene can’t convert very much of the sugar provided by photosynthesis in the leaves of the corn plant into starch. Instead, sugar itself accumulates in the kernel making the corn taste quite sweet.

When sugary corn kernels are dried, they shrivel up, while starchy ones remain relatively round and smooth. This has to do with the fact that sugars are water soluble while starch is not. So, as I understand it, corn kernels with more sugar are also a greater percentage water than corn kernels that are made mostly of starch.

The mutant form of shrunken2 was identified by John Laughnan, a maize geneticist at the University of Illinois Urbana-Champaign. The story of the discovery as told in Maize Genetics and Breeding in the 20th Century by Peter Peterson and Angelo Bianchi: (more…)

January 27, 2010

First Day Teaching (epilogue)

Filed under: biology,teaching — Tags: — James @ 2:37 pm

Belated I know. The first section I ever taught could have gone better. Twenty-nine people showed up for a section with an enrolment cap of 25 in a classroom with only 17 desks and no eraser for the chalk board. So that was fun. Still, I made it through a review the parts of a plant (roots, shoots, and leaves), the parts of a flower (sepals, petals, stamens and carpels), and a diagram of why a plant needs both mitochondria and chloroplasts (chloroplasts harvest and store light energy, mitochondria turn stored energy into the form used by the cell, ATP). And the second section I taught, later that same afternoon, went a lot better (In addition to being more sure of the material, I had time to steal back enough desks to bring the room to its rated capacity of 25, hunt down an elusive chalk board eraser, and draw the first set of figures on the board before the students showed up.)

A recreated example (should be familiar to anyone who, like me, took the first two weeks of intro botany):

The basic diagram of four parts of a (eudicot) flower. From the outside in. A: Sepals, small, generally boring green bits that look a fair bit like tiny petals. B. Petals. C. Anthers. The male part of the flower, responsible for producing pollen. D. Carpal(s) The female part of the flower. Pollen lands on the top surface, then grows a tube down into the flower to fertilize the eggs and central cells.

I’ve seen variants of this figure in 3 courses I took as an undergraduate, and now I’m using it myself. I’d be interested to hear if anyone has seen (or can think up) variants that might be easier for people with no background studying plants to grasp. (more…)

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