26 October 2016


All right folks, it's time to learn about where food comes from!
Specifically today, it's peanuts.
Peanuts come from the ground!  And the sun!  Like all food, when you get down to it, including meat, since animals eat plants.  But really.
As you no doubt vaguely remember from school, a peanut is a legume.  A simpler word would be "bean."  Yes, peanuts are beans.  So are chickpeas and favas and snow peas; hummus is just bean dip with a better agent.  Peanuts are unique in the bean world, though, because they're more or less the only bean that grows underground.  (Okay, so, there are about 70 species in the peanut genus, some of which share the peanut's frankly bizarre growth habits, and one or two from related genera, but that's it.  There are over 19,000 species of beans.)
Say you want some peanuts and there are no stores anywhere around because of a recent zombie apocalypse (which has apparently since subsided, but that's another story).  But luckily you happen to have a raw peanut (why?  I don't know; again, there's clearly more to this story).  (Also, this doesn't work with a roasted peanut.  Cooked seeds mostly don't grow very well...although I once had an ash tree seed germinate after it went through the dryer in the pocket of my shorts so maybe this needs to be investigated more thoroughly.)
So anyway, you stick that raw peanut in the ground.  You should shell it first; wild peanut ancestors have much thinner shells that allow water in and the germinating seedling out, but we've bred peanuts for tougher shells so we can roast them and ship them and eat them at ballgames and litter the floors of "roadhouse" style restaurants with them.
If the ground is warm enough, the peanut will germinate and grow.  It's a pretty little plant.  After a few weeks, it will start flowering.  These pretty yellow flowers are a nice treat.  Notice how many there in just a small area!
They don't have much smell.  Anyway, an individual flower is only open for a day.  After pollination (it's self-fertile, so if the zombie apocalypse in this scenario also affected bees, you're still okay), the flower drops off, and the stem becomes what's called a 'peg,' a stiff downward pointing stem with a slightly hardened tip.  This tip penetrates the soil--hopefully you planted it is some nice sandy loam, and not clay--and once the plant perceives that it is below ground, the end of the peg starts to swell.  (Yes, plants perceive whether they are receiving light or not, but not in a way you'd recognize as 'seeing' and not in a conscious sense.  It's all electrobiochemistry and fairies.)
The peg, you see, had a secret--it was actually the peanut ovary.  You just wouldn't have noticed because it was tiny.
Once below ground, the ovary swells into a little peanut, and eventually into a big peanut.  The plant will continue to flower and produce new pegs and peanuts for quite a while, as long as it stays sunny and warm.  As autumn comes on it will stop flowering as much, and gradually start to die back; peanuts are annuals and don't live through the winter.  But if you wait for the plant to die, you're too late: most of the peanut shells will have succumbed to the constant assault of water and microbes that life in the soil entails, and you'll have mostly a bunch of rotten garbage.  So you want to harvest in mid-Autumn sometime, before any frost but after the bulk of the heat of summer is past.
And this is what you'll get: a bunch of peanuts in various stages of ripeness.
Generally if the peanut looks like a peanut, it's edible.  In this picture there are some little proto-peanuts, but mostly good mature peanuts.  You can see how they are attached to the pegs, and the pegs are attached to the stems of the plant.  So there you have it: peanuts grow below ground, like potatoes and rutabagas.  (Not that they are at all related to either of those things.)
You may wonder, why on Earth does the peanut do this to itself?  I mean, I have some perfectly nice runner beans out there growing on vines, flowering and producing pods right out in the sunshine, and even some nice bush butterpeas doing the same thing.  They seem to be just fine.
The truth is nobody knows why.  It's just what peanuts do.  For whatever reason the progenitor of the Arachis genus found it beneficial to grow this way; perhaps some predatory animal ate all the peanuts that weren't underground, gradually selecting for this growth habit.
What we do know is that the current version of the peanut, Arachis hypogaea, arose from wild progenitors in what is now northwestern Argentina, probably 8000-9000 years ago.  The wild relative can still be found in the Chaco area, but it's a very different plant.  Your domesticated peanut will have had a nice compact form, although low to the ground and gradually spreading--if you only planted the one, and it was a happy plant (like mine), maybe it would cover about a 3 foot diameter area.  In cultivation, they're planted in rows 30" apart, with individual plants about a foot apart in the rows.  This keeps them nice and compact and allows them to completely cover the soil and choke out weeds.  The wild relative is a vine that rambles along the ground and drops a peg into the soil every few inches; the nuts are much smaller, and almost exclusively come one to a pod (which are called unipeas.  Yes, they are; when there's only one seed in the peanut pod it's a unipea and nobody can tell me otherwise).  The shells are also thinner with heavier webbing.  But that's what a few thousand years of domestication will do for you.
Once harvest time comes around you basically have to go in there by hand and carefully, gently pull the plant out of the ground.  Mine came out in two parts.  I left about a dozen peanuts behind, but was able to sift through the soil to find them.  For many many years in the South kids could get a couple weeks work in the fall harvesting peanuts by hand, but the engineers have figured out a way to mechanize the process without leaving too many peanuts behind.  Since you only have the one plant--and in the post-zombie landscape you probably aren't going to find a working peanut harvester, much less someone competent to operate it--you'll dig yours up by hand, turn it upside down, and leave it in the sun for a day or two.  Then you can pop the little peanuts off and toss the plant in the compost heap for next year.
You'll want to roast them, of course, unless you'd rather boil them.
You'd rather boil them.
If you aren't familiar with boiled peanuts, what are you doing with your life?  Get down South and try some!  In any event you'll want to process them somehow before you eat them, although they are edible raw.  Be sure to set a few aside before you boil them, so you can plant them again next year.
(Note: in reality, if you started your peanut farm with a single peanut, you'd create what's called a genetic bottleneck: your entire farm would consist of plants that had only those gene versions--called alleles--that were present in your first nut.  This is a recipe for disaster, since you've only got two possible resistance genes for any given disease (and more likely you have none), and the whole population will be highly susceptible to any disease or insect that comes along.  This is called a 'monoculture', a huge field of genetically identical plants, and it's not a very smart way to ensure your survival as a species.  Of course after the zombie apocalypse humanity itself will have gone through a pretty severe genetic bottleneck.)
Incidentally, peanuts are a super crop to grow once in a while if you have a garden or just some unused land (note: lawns count as unused land.  You do nothing but spend money on it.  At least put some plants out there that will give you something back for your time and expense).  Why?  Well, like all beans (and certain other plants), peanuts are best friends with some little bacteria that normally live quiet, boring lives in the soil.  But when a peanut plant sends down roots, the roots exude a chemical that signals to the bored little microbes that it's time to party.  They associate with the root, and the peanut plant sends some tasty carbohydrates their way.  They feast on these, and in return, they take nitrogen in the soil and atmosphere and turn it from a boring, useless gas (which really doesn't do anything for your tires that regular air won't do, regardless of what the ads say) into ammonia.  Plants can't do that by themselves; neither can animals.  In order to get nitrogen into your body--and without nitrogen, you can't make any proteins, enzymes, even your DNA--it first has to be fixed into ammonia by these little microbes.  Much of the nitrogen they fix gets absorbed by the peanut plant (which is why you compost the plant rather than putting at the the curb in a garbage bag), although plenty of it stays behind in the soil when the microbes die, and is left there for other microbes and plants and soil-dwelling animals, which is how it gets into the food supply.  This picture is of a peanut root--all those little bumps are called nodules.  Each nodule grows from a single root hair, which is colonized by several microbes.  Each nodule is a protective home for a batch of microbes as they churn out ammonia.
So there you have it.  Peanuts!
Next time: pumpkins!

03 August 2016

Sorghum breeding

Strictly speaking I work in corn breeding.  But that's just what I do at work.  (I also have some at-home corn breeding experiments planned for next year.)  At home, I breed pumpkins and sorghum.

Here is some sorghum.
This is a mix of things.  The paper bags on two of the plants are there mainly to keep the birds from eating all the grain (although they're really pollination bags).  You may notice a single very tall plant in the back (it's hard to see because it's so narrow and the grain head hasn't emerged yet).  That is a breed of popping sorghum called Allu Jola, which I've never grown before.  But in front of that are six plants of the variety I call Smitty's Dwarf.  You may notice that the three on the left are not especially short.  They're a bit shorter than the grain sorghum I started with, but they're nothing special.  The three on the right are a bit shorter.  None of these are great, though.  (Still, I want the grain this year.  Last year the birds ate almost everything.)

Last year I planted about 40 plants of a standard white grain sorghum originally from Kansas.  The average plant was about five feet tall.  I want a dwarf plant.  (Why?  I don't know.  I just wanted a project.  I tell people my goal is to breed up a high-yielding dwarf that I could grow to sell to brewers for a gluten-free malt.  But that would probably require that I actually malt the grain, and I don't have the capacity to do that.  If you'd like to donate to a Kickstarter that would allow me to buy both a set of commercial ovens and 25 acres of farmland....)
After last season I selected the two shortest plants, and retained the grain from them.  I would have preferred four or eight plants, but have I mentioned the birds?  Grosbeaks LOVE sorghum.

 This sorghum is a good bit shorter than that in the first picture.  You can see one of the regular-height plants here on the far right, and the six shorter plants in the plot to the left.  You may also see the popcorn that's growing behind the six shorter plants.  I strongly suspect proximity to the much more vigorous popcorn might have something to do with how short these plants are relative to the ones in the first picture.  It's tough to say, and I'll include these plants among the total when I select the shortest ones for next year, but it's impossible to say whether this is the genetics or the environment at work.  (Notice also the big batch of river oats intruding from the left side of the picture; this sorghum is hemmed in on all sides.  Next year the sorghum is getting a big plot all to itself.)

So.  Sorghum is self-fertile, like most plants.  This means that I could plant a single sorghum plant and, assuming there was a bit of wind while it was shedding pollen, the pollen from that one plant would pollinate the ovaries on that plant and I'd get fertile seed.  The fertilization rate wouldn't be great, although I could slip a bag over it and capture the pollen and hope to get better fertilization.
When multiple plants are around, though, sorghum plants can cross-pollinate.  Pollen from one plant may get blown around and fertilize ovaries on another plant.  There's no way for the plant breeder to know when that happens (hence the paper bags).  Plants in the field like mine, left uncovered, are referred to as "open-pollinated."  I'm not deliberately trying to self- or cross-pollinate them.  In an open situation, the percentage of seeds that arise from pollen from a different plant is referred to as the "outcrossing rate."  In a large field of grain sorghum outcrossing rates may range from about 7% to 35%, although research has reported outcrossing in certain varieties and environments all the way from 0% to 100%.  The 100% rate seems impossible and I'm suspicious of the methods of the researchers who reported it.
Anyway, in my yard, since the sorghum isn't terribly close together, I expect a fairly low outcrossing rate.  And since I'm putting bags up before the last 1/3 of the seeds are pollinated, that's reducing my total outcrossing rate.  (If I'm being diligent, and I don't want to ensure selfed plants, I'll select seeds for next year exclusively from the top 2/3 of the seedheads, which pollinated before the bags went on.  Or, if I do want selfed plants, I'll select from the bottom 1/3.  I haven't decided which I'm going for yet.)
So, I'll select the shortest 10 or 20% of plants, and take 20 or so seeds from each one (this is easy, because sorghum makes hundred or thousands of seeds per plant).  I'll put the seeds in labelled packets and sow them in blocks next year.  Then I can both compare how the blocks perform against each other, and how the individual plants within each block perform.  I'll self-pollinate the ones I like best and continue.  Because of the way plant genomes work, it takes several generations of self-pollination to get a batch of plants that are truly genetically identical If I had acre upon acre (and days upon days, and funding from an interested party) I'd self ALL of them and plant a whole huge field with 150 or 200 plots and try to get several different lines out of it.  But this is a side project.

Now here's an interesting candidate plant.  You can't quite tell in this picture, but this plant is only a foot tall.  It's extraordinarily short, shorter than even dwarf rice and wheat are.  Possibly this is a mutant, or it has a disease (it is yellowing early), or a virus, or some other condition that's causing this.  If it's a mutant, hooray!  By self-pollinating it, and then selecting the dwarfiest of its progeny and selfing them, and so on for four or five generations, I should be able to isolate a population of foot-high sorghum.  Provided it also actually produces a decent yield (this plant has a surprisingly large grain head considering how small and yellow it is) and is reasonably disease tolerant, this would constitute the end goal of the Smitty's Dwarf project.  I might even apply for a patent on it.  But that would be several years down the road.

That stunted dwarf is only one of the interesting plants I got in this year's batch.
This picture has several interesting things going on.  (Okay, I know that when I say "interesting," what I mean is, "interesting to me."  But you're reading this.  Whoever you are.)

If you click on the picture to blow it up, you'll see a few markings.  The two plants with the brown bags are about 3 feet high or so, which is pretty dwarven as sorghums go.  And marked with a red A is the white tassel bag from the micro plant pictured above.  It is REALLY short.
Above you see C and D.  These refer to two of the key elements of sorghum plant height: C is the height between the "flag leaf" (the very top leaf, just below the grain head), and the second leaf.  In all these short plants, the main leaves are quite close together, and then there's some greater distance between the second leaf and the flag leaf.  In regular plants, those distances are all about the same.  This suggests that the distance between leaves (called the "internode length" because each leaf is a node) is not controlled by the same gene as the distance between the flag leaf and the second leaf.  Additionally, at D, you can see that in these two plants, there's a significant difference in length between the flag leaf and the start of the grain head (which is right at the bottom of the bags).  In a large-scale planting, you want the distance between flag leaf and grain to be as great as possible, and uniform across all the plants in the field.  Otherwise you're likely to end up with a lot of leaf and stem trash in your harvest.  So, as a breeder, I will be selecting for long D lengths and shorter C lengths.  Assuming I can find such a thing.
Then, over on the right, there's plant B.  Sorghum can look a lot like corn when it's allowed to grow tall, but it really acts more like wheat or barley.  These are traditional small grasses.  The seed germinates and produces leaves and a stem.  Then, once there are three or four leaves, the plant stops making new leaves and instead creates a new little stem off to one side, which will produce its own leaves and eventually its own grain head.  These little side stems are called "tillers" and almost all grasses make them, including corn and sorghum.  In corn, the tillers are a nuisance, often sterile or with one of those combined tassel/ear things I've posted pictures of.  Tillers tend to be a nuisance in sorghum, too, not because they don't produce viable seed--they do--but because they are generally shorter and much later maturing than the main stem, so the seeds aren't ready when harvest time comes along and even if they were, the combine won't cut them because they'll be so much shorter than the main grain head.
In wheat, barley, and rice, however, the plants add new tillers throughout the growing season, then, responding to a change in day length or temperature (or both), all the tillers will produce a grain spike at the same time.  So when you see a field of wheat, say, and you go out and look and count 30 or 40 separate spikes, those could be from as few as one or two plants.  This means you can get a field full of grain with fewer seeds.
Now, a single grain spike of wheat or two-row barley might have 24 or 30 seeds max.  A single spike of sorghum can have over 3,000 (although in a typical field it's likely to be substantially less).  But you need one seed for each spike.  What if we could get sorghum to grow like wheat--make a bunch of tillers at the beginning of the season, and send up all the grain heads at the same time?  Potentially, this could mean more grain comes out of the field with less seed being planted.  Since seed is a substantial cost to farmers, this would make sorghum much more economical to grow.
Well, that's what plant B in the picture above looks like.  It produced five tillers (for six total stems) before it started flowering, and it looks like all six grain heads will be flowering within about a week of each other.   (In the picture, I have spikes 1-5 labelled.  The sixth one is actually hiding directly behind number 1.)  I didn't expect to see anything like this and actually almost tore the plant out last month because it looked so...broken.  I'm glad I didn't.  Each of the six grain heads is smaller than the one head on most of the other plants, but taken as a group I suspect they might be much bigger.  Given that this plant is growing in the same soil and within two feet of several other plants that look normal, I really don't (want to) think this is an environmental effect (although, again, viruses can do very strange and unexpected things to plants).  So this is now sorghum project number two: a tillering sorghum (Smitty's Tillering Sorghum sounds pretty bad, so for now I'm calling it Hydra).  If this turns out to be a trait that can be passed down, and again the plant isn't for some other reason horrible, this could be a very interesting side project.  

02 January 2016

Cotton Blossoms

Cotton is nifty.  You may not know very much about it; I didn't, when I started working in crop science.  We have a lot of cotton plants growing in the Phytotron at NC State, and today at work I took some pictures of various stages of cotton flowers.
Cotton is a tropical perennial, and can live for several years and grow quite large.  Unusually for perennials it blooms in the first year on new growth, so we culture it as an annual.  Typically for a perennial, it is slow to germinate and seedlings are not vigorous.  It develops branches at each leaf node on the main stem, and a boll develops at the leaf nodes along the branches.  You get more cotton with more branches, but the more branched the plant is the harder it is to grow as a row crop, the more likely the leaves on the lower branches won't get much sunlight, and thus the less likely that the lowest branches won't ultimately develop bolls.  Most of cotton breeding has consisted of managing these variables: stronger seedlings, taller, straighter plants with upright branches that can capture enough sun to produce multiple bolls in a single growing season.  A researcher here at NC State is even trying to manipulate the shape of leaves at different levels of the plant to allow more light through the top of the canopy while capturing as much as possible at the bottom.
Here we see some little wee leaves and blossoms just getting their start in life on a new stem.  Your T-shirt and jeans start here.

Another day or two goes by and the flower bud becomes clearly visible.

On the left is another flower bud.  I could not find anything between the stage there on the left, and the fully open flower on the right.  Note the fully open flower is white with widely separated petals.  This will last for just a few hours.

This is just a few hours later.  Still white, but the petals are beginning to fold up.

A few hours later still.  The petals have all folded.  Note that the flower is open for just a few hours of a single day.  Still white, though.

Here just the barest hint of pink is beginning to show up at the edges of the petals.

Just a bit more pink.

Now we have quite a nice slightly pink flower.  This flower is done; it's been pollinated by now, if it's going to be, although pollination isn't necessary to get a boll.  

A bit more time passes, a bit more pink.

As you can see the petals are starting to wilt and sag.

Even as it wilts this a really pretty flower.  They have a nice aroma, too.

The last stage.

Suitable for dried arrangements.

The dried flower separates from the boll.

And the green boll begins to emerge.  The boll at this stage is referred to as a square.

Okay, this is pretty much the same stage as before, but it's a nice picture.

The square expands.

At this point I think the square looks like a lime.

The square opens...

And the boll emerges!

And, voila!  Cotton, ready to be picked.  Bolls in the field are likely to be much bigger and fluffier, but in the tightly controlled, windless atmosphere of a greenhouse chamber, this is what you get.

Here you can see flowers in many stages at once on a stand of plants in the greenhouse.

I took all these pictures today.  One plant will have flowers in all stages at once.  
Now of course the plant is producing flowers, squares, and open bolls all at the same time, being a perennial, and so if you simply ran a cultivator through the field you'd end up with a bale of cotton consisting mostly of leaves and dried flowers.  So once you have a good number of open bolls--and decades of breeding have produced , you have to spray a defoliant on the field to kill the plants and get the leaves to drop off.  It may be some weeks before you're ready to pull the cotton out of the field; those of you who've driven through the South around Thanksgiving time have seen the fields of cotton ready for harvest.  
I think the most interesting thing is the greenhouse chamber with all the flowering cotton plants has the most wonderful flowery scent.  Roses, which have no purpose other than to be pretty and smell nice, have been bred down to the point that none of the smell nice at all any more.  But here we have cotton, which nobody gives a rip about whether or not it smells pleasant and which has been bred for every reason but flower aroma, and they just smell fantastic.  We are a strange species, we humans.
Anyway, hope you've enjoyed this little photographic guide to the cotton lifecycle.  Now you how your T-shirt came to be.