James and the Giant Corn Rotating Header Image

McClintock Prize

Last night my major professor received the McClintock Prize in Maize Genetics.

His acceptance talk was really exciting and full of his newest ideas about the big problems of biology and evolution. However, looking back at his history, one of the amazing things about his career is that he’s reinvented himself entirely, switching from a research program focused on transposons and developmental biology to an entirely different career focused on taking the rigorous hypothesis development and hypothesis testing to the world of comparative plant genomics (and he started when there was exactly one sequenced plant genome, so being able to do comparative work at the time was quite something).

In many ways it makes me nostalgic for my time in the lab. In grad school you are essentially paid to think, while it often feels like as a faculty member you are paid mostly to attend meetings, fill out forms, and spend four hours a day answering e-mails. ūüėČ

But this post isn’t about me. Congratulations Mike! Really is one of the fathers of modern maize genetics.

A partial sample of the 76 people who either received their PhDs or Postdoc’d in the Freeling Lab at UC Berkeley

Complete list of lab alumni here.

I really like tasselseed

Corn is a weird plant in a lot of ways, but one we don’t think about very much (because it is so obvious) is that a corn plant has entirely separate male and female reproductive structures: tassels and ears respectively.* This isn’t unheard of in the plant kingdom, but in the particular group of grasses corn belongs to (the Andropogoneae) it’s quite remarkable. Tripsacums, the closest relatives of corn outside of corn’s own genus (Zea), have separate male and female flowers, but those flowers still share a common reproductive structure with the male flowers at the tip and the female flowers at the base. I’d like to have a photo of my own to show you, but I won’t until the Tripsacum plants growing in our greenhouse flower this summer, so in the meantime, go look at this great photo someone else took.

But I bring this up to point out that the segregation of male and female flowers into entirely different parts of the corn plant is still a relatively recent, and fragile, evolutionary development, and it doesn’t take a lot to disrupt it. There’s a series of tasselseed mutants.** Stresses can do it. Various infections can do it. And sometimes corn plants, particularly tillers, just decide to be confusing.

A maize (corn) tiller exhibiting the tasselseed phenotype which is often found in these secondary stalks

*And no, don’t call sorghum ¬†heads (or panicles, it depends on how formal you feel like being) tassels.

**Why aren’t there just as many anther ear mutants? It could have to do with the way corn flowers are wired. If female floral organs start developing, they actually cause the male floral organs to die prematurely. But anther ear phenotypes still happen.***

***QTL Controlling Masculinization of Ear Tips in a Maize (Zea mays L.) Intraspecific Cross

James B. Holland, Nathan D. Coles

My lab’s social media policy and the maize news letter


This will be on each poster from my group at the maize meeting


The maize genetics cooperation newsletter (MNL) dates all the way back to 1929. It was (and is) a way for members of the maize community to share interesting findings and preliminary data with their colleagues. Some of those results would ultimately turn into peer reviewed papers (a process that could take months or years) and others were just little weird pieces of data or observations which would otherwise have been lost as negative or ambiguous results. Here’s a good example of what a MNL note might look like.

That the maize genetics community has made the decision to be trusting and open with our hard earned data and analysis for almost 90 years, with nothing preventing others from taking advantage of this openness other than community norms, is a great example of the better angels of our collective nature. It’s a standard I drive myself to live up to.*

*Keeping in mind I probably don’t even qualify as a geneticist, let alone a maize geneticist.** But I am descended from maize geneticists, both genetically and academically.

**One of these days I really hope to clone my very own mutant.

My research focus in a single figure


My favorite figure.

The photo really says it all. In the first second your eye is immediately drawn to just how similar the two plants look. In the second, you start to wonder about the differences between the two (the sorghum plant is way more waxy, the corn plant has a purple auricle from anthocyanins).

I want to understand the conserved genomic features that maize corn and sorghum so similar, and the subtle genetic changes that make them so different.

Some thoughts on open science and the power of defaults

Tomorrow I’m driving out to St. Louis for four back-to-back related meetings. Genomes to Fields, Corn Breeding, MaizeGDB, and Maize Genetics Conference.

For the 3rd year in a row the Maize Genetics Conference is going to operate under an “opt in” social media policy. Unless people explicitly opt in, attendees are forbidden from discussing talks or posters on social media (presumably this include blogs). Seven years ago, at my second maize genetics conference ever, I would have been in violation of this policy (if it had existed at the time) because I wrote these two posts. I know one of the authors well and he’s never expressed any concern over that post, and, while I’ve only met the second author in passing, I’m guessing she wasn’t bothered by my post since she cited it in her masters defense announcement.

In principle opt-in and opt-out should give identical results, but we know from a number of natural experiments that this is not the case, and that changing between these two can be used as a small nudge to produce socially desirable outcomes. (more…)

A worrying trend


There are undergrad EVERYWHERE!

Which I suppose is not an unexpected development on the first day of classes for the fall semester. But it holds a special something this year. This semester for the first time as an actual assistant professor… I have to teach. First lecture tomorrow. Wish me luck, because I’m going to need as much of it as I can get.

My previous teaching experience was heavily weighted towards being a TA in multiple “science for non-majors” courses, which could have been a lot of fun. Unfortunately, each course had a reputation as an easy-A which attracted students who had absolutely no interest in the material.

Tomorrow should go a lot better than that. Much smaller class, specifically for the major, teaching material I developed myself. … fingers crossed….

Mini-Foxtail Millet

It’s even smaller than mini-maize!

Developed by Xianmin Diao at CAAS and growing just outside of Beijing, China

Developed by Xianmin Diao at CAAS and growing just outside of Beijing, China


And here are the wonderful group on researchers who work on Setaria italica (foxtail millet) at the Chinese Academy of Agricultural Sciences.


Just got back from a two week visit to China that let me catch up with a lot of old friends and collaborators as well as hopefully making a few important new connections.

Five cities (Shanghai, Tai’an, Wuhan, Chengdu, and CAAS) and seven presentations in fourteen days. And classes start on Monday.

The race between foxtail millet and green foxtail continues

At 32 days after planting, the wild species (Setaria viridis, A10.1, green foxtail) takes a commanding lead in life cycle over the domesticated crop (Setaria italica, foxtail millet).


Domesticated foxtail millet on the left, wild green foxtail on the right. Both 32 days after planting.

Domesticated foxtail millet on the left, wild green foxtail on the right. Both 32 days after planting.

But don’t despair, you fans of working with domesticated species: Foxtail millet still have a good chance of taking the lead in the generations per year game. After they are harvested seeds from that green foxtail plant won’t be ready to germinate for months, while the foxtail millet seeds can be planted as soon as they are mature enough to harvest.

Narrowing in on Setaria viridis

So I’m now confident the Setaria photo in the last post was yellow foxtail (Setaria¬†pumila). One of the key diagnostic criteria is the larger spikelets of yellow foxtail relative to green foxtail (Setaria viridis), which sounds fine on paper, but you need a reference point to compare against. Now I have one. This is either Setaria viridis or Setaria faberi* but either way you can see the much smaller spikelets than yellow foxtail.

Setaria viridis or Setaria faberi. Setaria faberi is an allotetraploid formed by a cross between Setaria viridis and a closely related species.

Setaria viridis or Setaria faberi. Setaria faberi is an allotetraploid formed by a cross between Setaria viridis and a closely related species.

Setaria pumila (yellow foxtail).

Setaria pumila (yellow foxtail). Click to zoom.

*From the description of Setaria faberi “Characteristic foxtail-like seedhead that droops when mature and leaves with many hairs on the upper leaf surface, which helps to distinguish this weed from both Green Foxtail (Setaria viridis) and Yellow Foxtail (Setaria glauca**). Giant foxtail may be identified by the presence of many short hairs on the upper surface of the leaf blades, unlike the other foxtails.”

Source: Division of Plant Biology, University of Missouri: http://weedid.missouri.edu/weedinfo.cfm?weed_id=256