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

Lightly modified from my pitch to the university’s news/public relations office.

My collaborator Katarzyna Glowacka’s lab studies a process called non-photochemical quenching, which essentially acts as a surge protector for photosynthesis. If the amount of light hitting a plant’s leaf suddenly increases, for example if a cloud moves off the sun or wind blows a leaf from shadow into direct sunlight, non-photochemical quenching helps damp down the sudden surge of light energy that could otherwise damage or destroy the cell. Work Prof. Glowacka did as a postdoc showed that using transgenic technology it is possible to improve how fast non-photochemical quenching turns off and on and doing this can increase both photosynthetic productivity and overall crop yield.

Today, a new study came out in New Phytologist that was the result of a 3.5 year collaboration between my lab and Prof. Glowacka’s. Over two field season’s members of the Glowacka lab used a new high throughput technique to measure non-photochemical quenching in more than 700 types of corn grown in replicated field trials. A former postdoc in my lab, now on the faculty at the University of Warsaw, Marcin Grzybowski, used the measurements from the Glowacka lab to identify genes in the corn genome that controlled naturally occurring variation in the speed of non-photochemical quenching. The Glowacka lab was then able to confirm that these genes really do help regulate the process by looking at mutations of the same genes in arabidopsis (a model plant that is faster to work with than corn). 

The big potential implications of this study are:

• Discovering new genes regulating non-photochemical quenching which no one knew were involved before. The most important/exciting of these is gene called PSI3.
• Showing that there is a lot of naturally occurring variation in non-photochemical quenching in corn already, so it wouldn’t require a 10-15 year and $100M+ effort to translate her postdoctoral research into higher yielding corn varieties for Nebraska farmers, it may be possible to achieve the same outcome with conventional marker assisted breeding in ½ the time and at less than 5% of the cost of commercializing a new transgenic. 

Seema Sahay, Marcin Grzybowski, James C. Schnable, Katarzyna Głowacka (2023) “Genetic control of photoprotection and photosystem II operating efficiency in plants.” New Phytologist doi: 10.1111/nph.18980

One of the great things about academia is that is gives smart and motivated people without the social skills to do well in corporate world a way to be engaged and contribute to society.

I don’t do well with bosses. The one exception I ever ran into was my grad school mentor who was wildly known as somebody who gave grad students an enormous amount of freedom and autonomy. To the point that about half the students who joined his lab struggled with feeling directionless and to graduate in even seven years. The other half of students to join his lab seem to have loved and and gone on to be extremely successful professors and leaders in industry. Every other person I’ve worked for I’ve butted heads with consistently. Getting older I’ve gotten better at “managing up” but I still don’t enjoy it.

One of the great things about being a professor — especially a tenured professor — is that we can spend a lot of time feeling like we don’t have a boss. My poor department head (whose priorities I don’t agree with but who is a perfectly decent human being) has something like 70 direct reports most of whom she cannot hire or fire. Academia is a good place for people who don’t do well taking orders … but launching your own company is even better.

Do you know how long it took me to get a raise for my amazing lab manager in my academic lab? Four months. At least ten meetings with three different people. Biweekly follow up e-mails. Multiple appeal forms and reworking of position descriptions while crossing my fingers and doing my best to combat the bitterness I see setting in to an enthusiastic and motivated scientist who can’t understand why it’s taking me so long to follow through on the raise we’d discussed months ago. Responsibility without authority sucks. A lot.

Do you know how long it took me to get a raise for an outstanding plant breeder in one of my companies? Three minutes. Me to co-founder: “We should really raise $X’s pay, he’s taken on so much extra work this year.” co-founder to me: “I agree. How about $Y,000?” “Sounds good. I’ll e-mail our HR contractor.”

The same relative ratio of work applies to buying a piece of equipment. Or renting new space as your team grows. Or paying an invoice. Or hiring a new person. In academia I typically have to fight through layers of people whose job it is to make sure I don’t do the wrong thing and get the university in trouble. At the startup we just decide, it happens, and if we make a mistake we deal with the consequences.

Of course the power to give your team raises doesn’t matter if we don’t have money to pay that new higher salary. Securing the money to be able to do stuff is a big thing both professors and founders put a lot of their time and effort into. But that’s a discussion for part two.

While yesterday was draining, it had some really high points and I want to get these written down to remember on harder days.

On my way up the stairs to my office, one of my newest colleagues stopped me to ask a few questions and ended the conversation to tell me how much she likes the mentoring style she’s seen me exhibit with my students and we sympathized with each other on how hard it can be to thread the needle between leaving students without enough support, or just doing everything for them so they don’t have a chance to solve problems or figure out how to answer questions on their own.

Then an hour later I got an email from a former sandwich student (got his PhD at a chinese university, but got a fellowship to come do two years of his thesis research in my lab). He is just starting up his own lab in Sichuan.

Congratulation in advance for your promotion and I believe you will be an extraordinary scientist in the short future (such as the guy building the atom bomb, hahaha). … I finally realized the hardships of building a laboratory as you told us before. We are now training some undergraduate students in our lab but the process is very hard and I have to do every experiment in person to make these students do not “blow up” the lab.

Sent me a couple of photos of his students and lab and the fieldwork they’re doing that I was showing off to everyone I met with the rest of the day.

So yes. This is what a good day looks like as an assistant professor.

I’ve now been a part of the publication of three genomes, all grasses. One as a grad student (Brachypodium distachyon). One as a postdoc (Dichanthelium oligosanthes). And now one as a PI (Panicum miliaceum). Each species had different motivations: Brachypodium was intended to be a genetic model selected because it belonged to the same part of the grass family as wheat, barley, rye, and oats, but had a genome that was 1-2 orders of magnitude smaller. Dichanthelium was a comparative grade genome picked because stood between two groups of C4 grasses with sequenced genomes (maize and sorghum on one side, foxtail millet and pearl millet on the other) yet still used C3 photosynthesis, the ancestral state. Panicum miliaceum (proso millet or broomcorn millet) was sequenced because it’s an actual crop people grow in some of the driest cultivated land in the world (like inner Mongolia and western Nebraska), and having a reference genome sequence really does help with things like genomic selection, marker assisted selection, and QTL mapping. And each was sequenced using completely different technologies: Sanger sequencing (Brachypodium), Illumina short reads and mate pairs “next gen sequencing” (Dichanthelium), and PacBio long-reads combined with HiC “third gen sequencing” (proso millet). PacBio assemblies are SO MUCH BETTER than what we could manage with Illumina + mate pairs (I realize this is not news to most of you, but it’s one thing to hear it, it’s another to see it for yourself).

If I’ve learned one thing from these three experiences it is that it makes sense to work together with a whole team of people to put together a genome. The Dichanthelium genome project I was mostly working with a single other postdoc who also thought the potential for comparative genomics/biology of the species was cool, and in retrospect we bit off way more than we could chew, and were lucky to make it across the finish line to a paper. For both proso millet and brachypodium, I had the joy of working with big teams of people including folks whose whole job was genome assembly and annotation, and they were really REALLY good at it.

So what can I tell you about proso millet? It produces grain more efficiently per unit of water transpired than any other grain crop studied. It can produce grain in fewer days than any other crop I’ve worked with (some varieties are ready for harvest 50-60 days after planting!) It’s an allotetraploid, although so far we’ve only found a diploid lineage related to one of its subgenomes, not the other. One early approach we tried (see Ott et al below) was to use a technology designed to separate and phase the haplotypes of a diploid human to separate and phase the two subgenomes of an inbred tetraploid individual of proso millet. I’ve actually met farmers in both China and the USA who grow the crop, which is a really nice feeling. With one of my private sector hats on, I’ll get to use this genome to try to make higher yielding varieties of proso millet for those exact farmers. With my main public sector hat on, I’m excited to have a model for NAD-ME C4 photosynthesis that is easier to germinate, grow, and propagate than Panicum hallii or Panicum virgatum. There is nothing like working with wild grasses to make you appreciate the work all of our ancestors did to select against seed dormancy and photoperiod sensitivity while they were domesticating crops from wild species over dozens and hundreds of generations.

Zou C, Miki D, Li D, Tang Q, Xiao L, Rajput S, Deng P, Peng L, Huang R, Zhang M, Sun Y, Hu J, Fu X, Schnable PS, Li F, Zhang H, Feng B, Zhu X, Liu R, Schnable JC, Zhu JK, Zhang H. (2019) “The genome of broomcorn millet.” Nature Communications doi: 10.1038/s41467-019-08409-5

Ott A, Schnable JC, Yeh CT, Wu L, Liu C, Hu HC, Dolgard CL, Sarkar S, Schnable PS. (2018) “Linked read technology for assembling large complex and polyploid genomes.” BMC Genomics doi: 10.1186/s12864-018-5040-z

Editor’s note: this is a repost of an article which originally ran on James and the Giant Corn March 26th, 2017. I’m choosing to post this new, slightly amended version a little more than a year later to mark the publication of the paper describing Genotype Corrector. All told it took approximately 18 months from initial submission to final publication. However, to be fair a lot of that time was spent waiting for a single round of peer review at a different journal from the one in which the paper finally appeared.  

When doing anything even vaguely related to quantitative genetics I would chose more missing data over more genotyping errors any day of the week. There are lots of approaches to making missing data less of a pain. The most straightforward of these is called imputation. Imputation essentially means using the genetic markers where you do have information to guess what the most likely genotypes would be at the markers where you don’t have any direct information on what the genotype is. This is possible because of a phenomenon known as linkage disequilibrium or “LD.” Both imputation and LD deserve their own entire write ups and they are on the list of potential topics for when I have another slow Sunday afternoon. For now the  only thing you have to know about them is that, when information on a specific genetic marker is missing, it is often possible to guess with fairly high accuracy what that missing information SHOULD be. But when the information on a specific genetic marker is WRONG… well it’s usually a bit more of a mess (but I think the software solutions for this are getting better! Details at the end of the post.)

Figure 1: Genotype calls along chromosome 1 for six recombinant inbred lines (RILs).

(more…)

I’m now worked at four different scientific institutions in some capacity or another, and I’m always surprised how empty buildings are when I come in on Saturdays or Sundays. To be clear, I’m certainly not at work every weekend day myself, and I don’t expect the students or collaborators to work weekends.* I’m just realizing that, after 13 years of thinking “wow, people at University X really have a more relaxed approach to research than most places” maybe my idea of how many hours it is normal for a researcher to log in a week might be a tiny bit skewed.**

Although, to be fair, 9:15 AM on Easter Sunday might be the MOST representative time point. 😉

*I always say that my mentoring style is to focus on productivity, not hours worked in lab. I’m still working out what that means in practice. For an entertaining — as long as the person writing the e-mail isn’t your boss — glimpse of what the opposite sounds like, be sure to read this classical e-mail from 2002. 

**Growing up, I thought every family had dinner around 8 pm once everyone got home from the office, and that once you got a real job, “weekend” actually meant “sunday morning.”

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. 😉

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.

Freeling referencing "Evolution, as viewed by one geneticist" https://t.co/iepY0a9olk#mgc2017

— Dr. Erin E. Sparks (@ErinSparksPhD) March 11, 2017

"There’s no law that says the truth has to be testable” “Maybe underground & underwater & no sex is the way to survive” Freeling #MGC2017

— Jeffrey Ross-Ibarra (@jrossibarra) March 11, 2017

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

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 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.