James and the Giant Corn Rotating Header Image

Albino Corn

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.


Answers to Name! That! Millet!

Hidden below the “read more” tag.


Name! That! Millet!

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.”


How not to grow corn

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.

The current state of grass genomics

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).

Stress in Academia

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.

Chocolate and Vaccines

A colleague of mine from grad school has some thoughts on the recent “chocolate causes weight-loss” bruhahaha. If I had to try to distill his piece down to a single sentence it would be:

Teaching people to ask critical questions about things reported as scientific discoveries in the popular press is good, but it is way too easy of falling into the trap of doing so in a way that undermines people’s confidence in science itself.

Three line sentence, arg. Must simplify more.

Making people feel stupid by abusing their trust isn’t a good way to encourage them to believe you in the future.

Maybe it’d be best just to go read the original post.

Species capitalization

How would you format the phrase “maize, sorghum, setaria, rice, and arabidopsis”?

If you don’t understand why this is a question that comes up in publishing scientific papers you can stop reading now, never come back, and go on to live a happy and fulfilling life without every revisiting this issue.


Step 1: Grow Plants

Comparative genomics (what I mostly did in grad school) just required a whole bunch of well assembled genome sequences from different species. Comparative gene regulatory studies (one of the things I do now) requires actual living plants. Ideally you can just repurpose datasets which others have already generated and published online, but eventually you hit a wall where the only way to move forward to grow some plants of your own. And not just one or two plants, but trays and trays of them.

Why do we need so many plants to address even simple research questions? Because even with completely identical genomes, grown in carefully controlled environments, different individual plants will grow slightly differently,* and those growth differences will translate into variation the levels at which different genes are expressed. So to make sure we’re actually identify the differences in gene expression that result from [a mutation of a particular transcription factor/differences in growing conditions/different tissues/different species] we need to look at data across lots of individual plants so we can tell which differences have absolutely nothing to do with the thing we are actually trying to study.

All of which is made an awful lot harder when the majority of your seeds are killed by fungus before they even break the surface of the soil!

Each of those little pots should have a happy little corn, sorghum, or setaria plant growing in it. Normally I'd consider >90% good germination and <70% poor germination. This I would call "abysmal."

Each of those little pots should have a happy little corn, sorghum, or setaria plant growing in it. Normally I’d consider >90% good germination and <70% poor germination. This I would call “abysmal.” The corn, (top right) on the other hand seems to be fine.

*Micro-environmental variation, differences in seed size and quality, variation in soil mix, spooky epigenetic “stuff.” Take your pick. I’m inclined to blame it mostly on the first two.

James and the Tiny Corn

Mini maize, 33 days after planting.

Mini maize, 33 days after planting.

Today is the day proposals are due for NSF Plant Genome. Well organized scientists submitted their proposals back on Friday, before memorial day weekend. Scientists like me worked through the weekend and pulled a couple of late nights, to finish up the proposal on the day of submission.

But this isn’t a story about grant writing. This is a story of feeling tired and burned out, waiting for people who are proofing said grant before we hit the final “submit button” and wandering down to my greenhouse to check on my plants. And there I discovered our mini-maize plants*, already silking and with the very first anthers starting to emerge in the tassel! These plants were planted on April 24th and as I write this, it is the 27th. That is a time to flowering even the very fastest millet species we work with (japanese and proso) would be hard pressed to match!

Now I could decide to be upset that we didn’t catch it in time to put a shootbag over the emerging silks, but instead this tiny little plant just makes me very happy. For anyone else growing this variety, be aware that the ears really sneak up on you (in this plant the ear shoot never made it past the leaf ligule, it looks like just a bunch of silks). Honestly I’m not sure HOW we’re going to shootbag these plants in the future. We may just have to grow them in greenhouses without any other corn (which is actually reasonably feasible here, there is a lot of dedicated space for sorghum).

*The mini-maize pictured here comes from seed provided by Morgan McCaw, a member of Jim Birchler’s group at Mizzou. For a detailed descriptions of its genetic history see his abstract “Fast-Flowering Mini-Maize: Seed to Seed in 60 Days Update” from the 2015 Maize Genetics conference.

Editor’s note: if you’re curious, here’s an update from a month later at the end of the mini-maize lifecycle.

Now, here have some more mini-maize photos: