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

June 24, 2015

Depressing predictions about the future

Filed under: Uncategorized — James @ 8:15 am

Now for something not directly related to plant biology:

After 300 years of breathtaking innovation, people aren’t massively unemployed or indentured by machines. But to suggest how this could change, some economists have pointed to the defunct career of the second-most-important [Editors note: Animal] species in U.S. economic history: the horse.

For many centuries, people created technologies that made the horse more productive and more valuable—like plows for agriculture and swords for battle. One might have assumed that the continuing advance of complementary technologies would make the animal ever more essential to farming and fighting, historically perhaps the two most consequential human activities. Instead came inventions that made the horse obsolete—the tractor, the car, and the tank. After tractors rolled onto American farms in the early 20th century, the population of horses and mules began to decline steeply, falling nearly 50 percent by the 1930s and 90 percent by the 1950s.

Source: http://www.theatlantic.com/magazine/archive/2015/07/world-without-work/395294/

The whole article is quite long, but made for an interesting read. For further thoughts in this area, check out the Plant Money “Will Your Job Be Done By a Machine” calculator. Plant biologists apparently aren’t common enough to be listed, but the odds for the biology-related fields* are low enough I’m not ready to run for the hills just yet … despite the fact that robots like this one are now being field tested in labs back in California.

*Animal Scientists are at 6.1%, Microbiologists are at 1.2 % and Medical Scientists are at 0.5%, so

June 23, 2015

Updated albino corn

Filed under: Uncategorized — James @ 9:26 am

A few days later, that albino corn plant I was complaining about has matured a lot.


Albino corn 10 DAP

Albino corn 10 DAP

One of the grad students has decided to transplant it and see how long it will manage to survive in the complete absence of photosynthesis.

June 22, 2015

James and the Tiny Corn Part 2

Filed under: Uncategorized — James @ 10:57 am

We’re now at 61 days since planting for my first generation of mini-maize and the kernels are just about fully mature.

Mini-maize ear 61 days after planting.

Mini-maize ear 61 days after planting.

The seed set isn’t wonderful. Unfortunately the tassel is really delicate on this genotype so this generation we only got one batch of pollen per plant. Next generation we’ll try to handle the tassels even more delicately, which will let us harvest 2-3 days worth of pollen and should result in more of the ovules on the ear being fertilized and more seeds produced per plant. Still, considering we started with a grand total of ten kernels, (of which only two still remain) just this one ear feels like an abundant wealth of kernels!

Here’s the link if you missed mini-maize part 1: flowering.

June 17, 2015

Albino Corn

Filed under: Uncategorized — James @ 3:13 pm

What’s wrong with this picture? (The title should have given you a hint.)


Here, I’ll zoom in.


These five plants should all be nearly genetically identical (from a single inbred line).

Lots of different things can cause albino corn. From defects in chlorophyll (the pigment that plants plants green) biosynthesis to defects in how the chloroplasts themselves (the plant organelles where photosynthesis happens) divide. One of the frankly awesome things about working with corn is that these sorts of mutants actually survive long enough to study, even though most (all?) of them ultimately prove lethal. In arabidopsis, mutations of most of the same genes wouldn’t even survive through germination. Alice Barkan’s lab estimates there are ~600 maize genes whose mutation produce reductions in chlorophyll (generally resulting in either yellow or white plants). <– click that link if for no other reason than to see a frankly beautiful photo showing the variation in shades of maize seedlings from healthy green through sickly yellow to pure snow white.

All that said: when you start seeing albino plants pop out in a batch of what should be genetically identical plants (all from the same inbred line), it’s a pretty good sign that particular batch of seeds is hiding some unrecorded complexity rather recently within its family tree.


June 11, 2015

Answers to Name! That! Millet!

Filed under: Uncategorized — James @ 1:41 pm

Hidden below the “read more” tag.


Name! That! Millet!

Filed under: Uncategorized — James @ 1:40 pm

But there’s a catch. You have to do it from photos of plants that haven’t yet flowered. While wild grass species can look ridiculously different when they are growing vegetatively (ie before flowering), at least among the panicoid grasses, domesticated grain crops have all converged upon very similar plant architectures.  Your options are 1. Foxtail millet 2. Japanese millet.  3. Pearl millet. 4. Proso millet (also called broomcorn millet, or half the time just “millet”), and 5. Maize (just for kicks). Check below for the pictures. To see the answers, click the “next post.”


June 8, 2015

How not to grow corn

Filed under: Uncategorized — James @ 10:14 am

In the spirt of Thomas Edison’s 10,000 approaches to making a lightbulb that do not work, here is one method that does not produce happy corn: 22 C (72 degree fahrenheit, a comfortable room temperature), under 24 hour LED lighting*. However, as failures to produce happy plants go, this had a more attractive outcome than most:

B73 under cold and/or light and/or day length stress.

B73 under cold and/or light and/or day length stress.

*For those familiar with corn, it will seem perfectly obvious that it wouldn’t like these conditions. Corn is happiest with temperatures in the mid to high 80s, and really prefers short days.

June 4, 2015

The current state of grass genomics

Filed under: Uncategorized — James @ 7:50 am

Through several recent interactions I’ve been reminded just how much of the information I take for granted about the state of genomic resources for different grass species, the relationships between different grass species and even the correspondence between common and scientific names is the product of my own meandering career path to date and doesn’t, by any stretch of the imagination, represent common knowledge, even among plant biologists.

High and low quality genome assemblies are here defined as "assembled to the pseudomolecule level" or not, respectively.

High and low quality genome assemblies are here defined as assembles with pseudomolecules (essentially chromosomes) that contain most of the core grass gene complement, and assemblies either without pseudomolecules, or where a large fraction of genes aren’t placed on the pseudomolecules yet. “We” in the legend above refers to a project from JGI’s Community Science Program (CSP).

This is by no means a comprehensive treatment. There an estimated 11,000 grass species, the vast majority of which are known only from physical observation (not so much as a single fragment of their dna has ever been sequenced).

However, if you’re interested in a more comprehensive treatment than my off the top of my head approach, go here and download “NPH_3972_sm_FigS1-S2.pdf” to see a tree of more than 500 total grass species, representing pretty much every single major group within the grasses. It’s my go to reference whenever I’m trying to discover the relationships between grass species I’m not familiar with and as far as I know it’s still THE reference work to which all other grass phylogenetics papers are compared (but feel free to let me know in the comments if you know of a newer paper that includes even more species).

June 1, 2015

Stress in Academia

Filed under: Uncategorized — James @ 6:29 am

In a previous study, the impact of giving a presentation to a group of several hundred maize geneticists was reported by (James et al. 2015)

Here we report a longer term study on the effects of academic stress: a comparison of heart rate (beats per minute (BPM)) on an academically stressed day (ie the day prior to the deadline for submitting an major grant to the National Science Foundation) and a control day (the day immediately following submission of said grant). Heat rate was quantified using a Basis Peak watch.

Heart Rate Before and After Grant Submission

Timepoints where the Basis Peak watch concluded the subject was “asleep” were excluded. Potential confounding variable: My first graduate student arrived on campus the same day as the “day before grant due” dataset was collected.

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