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

December 19, 2022

The Paspalum Genome

Filed under: agriculture,biology,genomics,Plants — James @ 4:41 pm

A paper eight years in the making and sixteen months in review. A real credit to Guangchao. I don’t think it ever would have come out without his dedication above and beyond what anyone could expect from a postdoc – James.

A team of researchers, led by Dr. Guangchao Sun and Prof. James Schnable of the University of Nebraska just published the genome of paspalum (Paspalum vaginatum) alongside evidence that paspalum may employ some tricks that could help its relative, corn, grow better with less fertilizer. 

Illustration of a paspalum vaginatum inflorescence.
A flowering paspalum plant growing in the University of Nebraska’s Beadle
Center greenhouses.


The Nebraska team, in collaboration with researchers from the Department of Energy’s Joint Genome Institute, the University of Georgia, and the HudsonAlpha Institute for Biotechnology, wanted to use the new genome sequenced this resilient grass to understand what makes the grass so much more stress tolerant that closely related crops, including corn and sorghum.

Using comparative transcriptomic and metabolomic analyses of paspalum, corn, and sorghum under optimal and stress conditions they identified a specific metabolic pathway — trehalose — that was being produced in paspalum, but not in corn and sorghum, in response to stress. 

The team used a strategy called chemical genetics to convince corn plants to also start producing and accumulating trehalose and showed that these corn plants grew faster and larger in conditions without enough fertilizer than corn plants without extra trehalose. Finally, the team used a combination of experiments to show that the reason these corn plants were able to grow more with less fertilizer was because of a process called autophagy, essentially a recycling program within plant cells that breaks down old, damaged, and unneeded proteins into spare parts that can be used to make new proteins. 

Guangchao Sun working with Aime Valentin Nishimwe measure nitrogen stressed plants in the Schnable lab at the University of Nebraska-Lincoln
Dr. Guangchao Sun working with Aime Valentin Nishimwe to collect data from
plants grown without enough nitrogen fertilizer.

“I’m so excited to see this story come out,” said Prof. Schnable, who is currently taking leave from the University of Nebraska while working at Google. “Paspalum is vegetatively propagated which means we cannot just save seeds, we always have to keep living plants for our research. There was a period where no one remembered to water the paspalum plant for a couple of months. But the plant was completely fine. In fact it usually grows so fast it’ll try to invade the pots of neighboring plants and the greenhouse manager has to yell at me or folks in my lab to come down and trim it. With this genome sequence and all the great work Guangchao Sun and the team have done, we finally are starting to understand just what makes this plant so
resilient.”

Sun, G., Wase, N., Shu, S. et al. Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass. Nature Communications 13, 773 (2022) doi: 10.1038/s41467-022-35507-8

January 1, 2022

James and the Tiny Corn Part 3: Even Tinier

Filed under: biology,Genetics,Plants — Tags: , , — James @ 4:42 pm

Back in 2015 we were one of the first groups to get to try out Fast Flowering Mini-Maize (FFMM) [1]. The plants were about two feet tall, flowered in five weeks, and were ready to harvest only 61 days after we planted them. But what if I told you that the same genotype could be even smaller?

This past summer a technician in the lab rediscovered our carefully guarded stash of FFMM seeds and we decided it was time to increase them. While we did most of the increase in the greenhouse, the idea came up at the same time we were finalizing the plans for our summer nursery* so we decided to plant the line in the field as well.

And this was the result:

Fast Flowering Mini Maize in the field in Lincoln Nebraska in the summer of 2021.
Fast Flowering Mini Maize in the field in Lincoln Nebraska in the summer of 2021. Planted May 13th. Photo July 1st. Non-fast flowering non-mini maize in the background was planted approximately one week earlier.
(more…)

March 30, 2017

Dichanthelium oligosanthes (One in a Thousand Series)

Filed under: biology,evolution,genomics,One in One Thousand — James @ 8:46 am

Inflorescence of Dichanthelium oligosanthes. Accession “Kellogg 1175”

Out of the ~12,000 known grass species, the genomes of less than one in one thousand have been sequenced. The “One in a Thousand” series focuses on these rare grass species.

Dichanthelium oligosanthes is a wild grass that grows in forest glades throughout the American midwest. It is a small plant. Doesn’t grow particularly fast. Its flowers aren’t particularly striking. And it has enough issues with seed dormancy that growing it in captivity is a major pain. Dichanthelium is a one in one-thousand grass with a sequenced reference genome.*

The reason folks are interested in Dichanthelium isn’t because of what it is, but who it’s related to. Dichanthelium occupies a spot on the grass family tree between a tribe** of grasses that includes foxtail millet and switchgrass, each one in a thousand species themselves, and another tribe of grasses that includes corn and sorghum, two more one in a thousand species. The relationship looks something like this:

Phylogenetic relationship of Dichanthelium oligosanthes to related grasses with sequenced genomes.

(more…)

April 23, 2012

In which I apologize to R

Filed under: biology — James @ 2:47 pm

R, you may be a confusing and hard to understand language where every package comes with its own set of quirks and foibles. You may make me feel less like a programmer and more like a not-very-well trained magician fumbling around for the right incantation to make magic happen.

But when you work, you do awesome things.

Sex specific splicing of a gene of unknown function of a gene syntenically conserved in all grass species.

With only four days work I was able to go from a giant pile of reads (from the still not properly appreciated Davidson 2011 The Plant Genome) to figures like the one above.

So what is the figure above showing you? One of a large number of genes which show a different pattern of splicing in male and female reproductive organs in maize.* The region “E8” is usually treated as exonic in female reproductive tissues but is spliced out like an intron in male reproductive tissues. What does it mean (if anything)? I have no idea yet! But it would have been a real pain to try to re-invent the wheel for identifying these deferentially spliced genes in python. In R, once I figured out the right incantation, it’s practically plug and play for any gene you could possibly be interested in. Including the software for the (actually quite useful) visualization shown above.

So thank you R. What you do — once I can figure out how to make you do it — you do incredibly well.

*Maize makes it easy for us by separating female and male flowers into two entirely different organs (the ear and tassel respectively).

Data from:

Davidson R. M., Hansey C. N., Gowda M., Childs K. L., Lin H., Vaillancourt B., Sekhon R. S., Leon N. de, Kaeppler S. M., Jiang N., Buell C. R., 2011  Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes. Plant Genome 4: 191–203. doi:10.3835/plantgenome2011.05.0015.

Analyzed using the R package DEXSeq:

Anders S, Reyes A, Huber W. 2012 Detecting differential usage of exons from RNA-Seq Data. Unpublished. (Link is to a PDF)

June 3, 2010

Transposon Mutagenesis

Filed under: biology,genomics — James @ 12:30 am

In yesterday’s Transposon Week post, I discussed how transposons can spread through a species by without providing any benefit to the animals, plants, fungus, or micro-organisms that host them.

Adding a little extra useless DNA doesn’t help an organism survive, but it also doesn’t cause serious harm. But in yesterday’s post I completely avoided one serious question:

When new copies of a transposon get inserted across the genome, what happens to the DNA they land in? For what matter, what kind of DNA do transposons land in in the first place?

The answer to the second question is that different kinds of transposons each have their favorite places to land in the genome. Some transposons like to land in centromeres. Some transposons like to land in other transposons. Some transposons like to land near genes.

Then there are transposons like Mutator. Mutator is a maize/corn transposon that really likes to insert itself into genes. Transposons that usually land in other parts of the genome are also sometimes found in genes.

When a transposon lands in a gene, whether because that’s where it likes to insert or simply by accident, the gene stops working. Depending on which gene has to misfortune to interrupted by a transposon, the effects can range from so-subtle-we-can’t-even-detect-them to so lethal the organism dies before we get a chance to study it. In between are a whole range of effects. From severe developmental mutants, to gorgeous and apparently random streaks of color in flowers, to the spotted corn kernels which were my first introduction to the world of transposons.* (**)

Transposons are always breaking genes. The deadliest mutations disappear from the population as quickly as their appear. More subtle mutations can linger on for generations given rise to all sorts of genetic disorders. And keep in mind many genes can be broken with no visible effect at all. Anything you eat from asparagus to zuccini has the potential to contain genes broken by transposons. And depending on the gene, you’d probably never even know it.

Sorry to put this post up so late (it’s technically already Thursday) and in such a poor shape. I had some craziness in lab today and was waiting (unfortunately without any luck) to hear back about some more interesting stories I could tell about the Mutator transposon.

*To be fair, the last two are actually caused by transposons jumping OUT of genes allowing them to resume their normal function. The original mutations caused by transposons inserting into genes were to break the biochemical pathways used by Dahlia’s to make red pigment in their petals and by corn to produce purple pigment (anthocyanin) in its kernels.

**I really wish there was a good source of freely usable pictures things like transposon sectors in flowers and corn kernels. I can usually find pictures of normal plants on Flickr with creative common licenses. But I really want to be able to show you guys the cool mutants that make genetics so exciting.

June 1, 2010

Transposons: The Difference Between Junk DNA and Selfish DNA

Filed under: biology,evolution,genomics — Tags: — James @ 3:47 pm

Tranposons are one of those really cool features of genomes that never really seem to make the jump into the public eye. Most people at least have some conception of what a gene is. It’s a piece of DNA that contains the instructions for making a protein plays some role in the cell. A lot of other people can recall hearing an off-hand statistic only some tiny fraction of the human genome is made up of genes, with the rest being “junk DNA”. The question of why most of our genomes have no apparent function is why there’s a slow trickle of scientific research that gets picked up in the popular press as “scientistists discover junk DNA not junk after all!”.

But the reason most of genetics-genomics people aren’t in a huge rush to discover the hidden function behind most of this “junk DNA” is because we KNOW what most of it does and where it comes from. It’s not junk, it’s selfish DNA. <– although there’s certainly lots of cool stuff remaining to be discovered in the much smaller fractions of genomes we can’t classify at all. (more…)

May 31, 2010

Welcome to transposon week here at James and the Giant Corn!

Filed under: biology,Genetics,genomics — Tags: , — James @ 2:23 pm

I’m just about wrapped up with the big project I’ve been working on recently. Hope to be able to say more about it in the not-too-distant future. Having to be secretive in science sucks.

But there’s a lot of be happy about! I’m done teaching for a long time. As much as I enjoyed working with the kids in my class, the other responsibilities of teaching (grading, sitting through lectures without the chance to break in for the discussions and arguments that make academia so fun, grading, designing assignments, grading) were really starting to wear me down.

And I’m only three weeks (June 22nd) from either passing my qualifying exam or becoming a beaten and broken shell of a man. For three hours four professors will question me on everything I’ve learned (or should have learned but didn’t) in my education up to this point, and everything I propose to spend the next few years of my life doing. This may not sound like a good thing, but it is. Because my qualifying exam has been hanging over my head all semester,

The lab has a new paper in press, having run the sequential gauntlets of Peer Review, Editorial Evaluation, and finally (and perhaps most dreaded) Your-Figures-Aren’t-High-Resolution-Enough e-mails from the journal’s publication department. But more on the details of that whenever the paper actually shows up.

But what was the point of this entry again? Oh yeah. Transposons. I have a soft spot from transposons (I’m guessing most people who work with maize genetics do). Today we may know that transposons are found in practically every genome under the sun, but they were discovered first in maize using old school genetics (breeding plants together and counting traits in the offspring), before DNA sequencing was a gleam in its inventor’s eye.

And on top of that, some delightfully high-copy number transposons are in the middle of proving a major scientific point for me, so I figured the least I could do was devote a week to them here on the site.

If you’re not a geneticist, should you still care about transposons? Absolutely! Transposons are one of the best arguments, not for why genetic engineering is safe, but for why, if anyone worried about hypothetical unintended consequences of genetic engineering should be worried about any food with DNA in it (and as far as I know, that’s all food.) To paraphrase a seinfield character: “No food for you!”

The week’s schedule: (more…)

April 9, 2010

The Peach Genome Is Out

Filed under: biology,genomics — Tags: , — James @ 3:28 pm

1.1 pound peach from the Berkeley Farmer's market.

Here. I had no idea anyone was even considering sequencing the peach genome until I heard a single off-hand comment at the maize meeting last month, and all of the sudden here it is. And in better shape in its first release than some genomes are even after they’re published.

This is a pre-publication release, so the Fort Lauderdale Convention is still in effect,* but the peach genome looks really great from the quick and dirty analysis I have already run. They’ve already got the genome assembled into pseudomolecules (chromosomes), unlike some genomes I could mention that have already been published, and marked the locations and structures of genes in the geneome (there was a weird period last summer when there were pre-release versions of the maize genome organized into chromosomes, and pre-release versions with the genes marked, but none that had both.)

*In short, you or I can download the peach genome, play around and study it to our hearts content, but we can’t publish anything on it until the people who actually sequenced the peach genome publish a paper describing their work.

March 19, 2010

Helitron Capture Creating New Genes?

Filed under: biology,Genetics — James @ 1:15 am

One of the things that has made annotating genes in the maize genome so difficult (there are currently two sets of gene models one with only 32,000 genes, which is low estimate, and the other with 100,000 is far too many) is the presence of large numbers of gene fragments that have been captured and duplicated by a class of transposon called helitrons (yes I know that sounds like a character from Transformers).

The helitron captured fragments are copied from real genes (often multiple pieces are captured from different genes) which is why many gene annotation programs (trained to recongize the difference between genes and non-coding DNA) will identify the fragments being genes themselves.

What if some of those fragments actually are genes? By combining pieces from completely different genes, helitrons could be a whole new source of crazy new genes that natural selection could act upon.

That is the question the authors of this poster are trying to get at, by identifying more helitron fragments and checking to see if those fragments were actually expressed in the genome.

Allison Barbaglia et al. “Accessing the transcriptional activity of Helitron-captured genes of maize” Poster #243 2010 Maize Meeting

March 18, 2010

Missing Genes on a Massive Scale

Filed under: biology,Genetics,genomics — James @ 1:15 am

Edit: stripped out all the numbers as they clearly applied to an earlier version of the data and I don’t know if the new ones are intended for public release yet.

Last november when the maize genome was published, one of the companion papers looked at genes where a different number of copies were found in different breds of maize (this is called Copy Number Variation) and genes found in B73 (the variety of maize that was sequenced) but completely missing from the genomes of other varietes. There’s a great post on that paper written up by Mary at OpenHelix.

A few months later, it sounds like this dataset has grown substantially. Over XXXX B73 genes (that’s X% of the filtered B73 gene set!) that appear to be lost (or have sequences so different they no longer register) in at least some varities of maize. And because the new dataset incorporates data from XX different maize breds and XX different teosinte* lines they’re able to identify some of the losses as older because they’re found in multiple comparisons, while some appear to be lost in only a single breed, and might represent more recent losses.

Sit back and think about that for a second. At least X% of the genes in corn sometimes go missing. This could have implications for everything from inbreeding depressions and hybrid vigor, to the kind of basic research I’m actually working on myself.

As you can imagine I’d love to get my hands on this dataset myself, but the next best thing will be to take furious notes when Nathan Springer talks about the project on Friday morning**, and being sure to swing by Steven Eichten’s poster soak in the awesomeness.

Ruth A. Swanson-Wagner et al. “Combined Analysis of genomic structural variation and gene expression variation between maize and teosinte populations” Talk #1 2010 Maize Meeting (Presented by Nathan Spinger)

Steven R. Eichten et al. “Extenisve Copy Number Variation Among Maize Lines” Poster #139 2010 Maize Meeting

*Teosinte is the wild species from which maize/corn was domesticated.

**And he’s talking at 8:30 AM on a day when I still plan on being heavily jet lagged.

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