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

It’s even smaller than mini-maize!

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.

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.

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.

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 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

Part #1 of a likely infinite part series.

Today’s innovation was figuring out how to manually set the exposure/AEB setting on the camera so images didn’t look frightening washed out when photographed against a traditional black background.

So here’s today’s procrastination figure:

Post-anthesis Setaria italica (foxtail millet)

Of course we really should compare to the wild progenitor, Seteria viridis (Green foxtail). Unfortunately, our Setaria viridis isn’t flowering the greenhouse yet. Fortunately, my tomatillo batch at home is prone to weeds. Unfortunately, I’m not enough of a botanist to code this plant out beyond the genus level. The image below is either Setaria viridis (the direct progenitor of Setaria italica), or (according to the list of grasses native to Nebraska) it could be Setaria faberi, Setaria pumila or Setaria verticillata. I’m reasonably confident it isn’t S. faberi or S. verticillata but S. pumila (Yellow foxtail) is a real possibility. Actually, the more I read about it the more I think this is Setaria pumila given the largish spikelets and tan color of the bristles.

Either Setaria viridis (green foxtail) or Setaria pumila (yellow foxtail). But probably yellow foxtail…

Study of the S. viridis clade also needs to include S. pumila (Poir.) Roem. & Schult., a common weed that often grows in mixed populations with S. viridis and its relatives. Although it appears to be of African origin (Rominger, 2003) and is not closely related to S. viridis in phylogenies (Doust et al., 2007; Kellogg et al., 2009), the ecological preferences of S. pumila are similar to S. faberi and S. viridis (hereafter collectively the “S. viridis clade”).*

So just a tiny bit of DNA sequencing would answer my question once and for all….

In the meantime, I’ll just have to wait for our validated S. viridis plants to flower. Currently twenty one days after planting.

Foxtail millet (Setaria italica genotype Yugu1) on the left hand side and green foxtail (Setaria viridis genotype A10) on the right hand side. Both plants are 21 days old. Note that Yugu1 is significantly taller but unbranched, but the A10 accession of green foxtail has already started producing tillers.

*Daniel J. Layton and Elizabeth A. Kellogg “Morphological, phylogenetic, and ecological diversity of the new model species Setaria viridis (Poaceae: Paniceae) and its close relatives” Am. J. Bot. March 2014 101:539–557 doi: 10.3732/ajb.1300428

Remember how similar grass species look prior to flowering? Flowering is a whole different story. Here’s a couple of nice pictures we took in lab this week now that we’re no longer constrained by the use of cell phone cameras. (Click to zoom in to a ridiculously high resolution.)

Dichanthelium oligosanthes is a wild species. We’re collaborating with the Studer lab at UIUC in some comparative biology on the species. So few seeds per inflorescence! (At least we’re lucky enough that each plant produces a lot of these infloresences, or building up a significant reserve of seeds would really be impossible.)

Japanese millet inflorescence. Lots of big seeds forming here. If you click and zoom in to the maximum resolution, you’ll be able to see the anthers hanging out of many of the individual spikelets.

If I am lucky our Paspalum vaginatum will flower sometime in September. Until them I’ll continue to use this blurry iPhone photo.

Paspalum vaginatum flowers. September 2013

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

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

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.

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.

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.

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.

Hidden below the “read more” tag.

(more…)