// Twitter Cards // Prexisting Head The Biologist Is In: 2019

Thursday, December 5, 2019

Tomatillo Breeding (1/n)

Tomatillos are a wonderful vegetable plant to grow. There are several distinct varieties available, but nowhere near the numbers we see for tomatoes, peppers, or other crops. What's the difference?

Tomatillos are almost exclusively out-breeders. You need two or more plants growing in an area to get good production of fruit. As a result, every plant is a new hybrid and a population will maintain a high degree of genetic diversity. This also makes it difficult for different varieties to be grown in the same area, as they will generally cross and meld into one diverse population.


A few years back I started an experiment with breeding tomatillos. I grew one plant of a variety with small purple fruit next to one plant of a variety with large green fruit. I had saved seeds from a CSA and the local grocer, so I don't have any specific variety names to give you. (If you want to replicate the experiment, the purple variety was similar to: https://www.edenbrothers.com/store/purple-tomatillo-seeds.html; the green to: https://www.edenbrothers.com/store/rio-grande-verde-tomatillo-seeds.html.)

Four tomatillo fruit, from left to right. 1) Medium purple. 2) Small purple. 3) Large green. 4) Medium purple.
#1. Medium purple fruit.
#2. Small purple fruit.
#3. Large green fruit, with purple dots.
#4. Medium purple fruit.
Because the plants are such extreme out-crossers, every seed that year was expected to be a hybrid between the two different varieties. The next year I grew four plants, from seeds I saved from the purple plant. Each plant grew distinct fruit. (1-4, left to right in photo at right.) This diversity tells us that both parental varieties were highly heterogeneous, so the specifics of each hybrid plant depended on exactly which allele they inherited from each parent. As none of my neighbors were growing tomatillos, we can be pretty sure each one was pollinated by the other three.


Two large green tomatillo fruit at right. Six small pale purple tomatillo fruit at left.
F2s from F1#3.

The next year I planted seeds I had saved from plant #3. I grew 11 plants, but only 5 produced any fruit. The plants looked like they'd been exposed to an herbicide from the commercial garden soil I had added to the garden at the start of the season (Herbicide carryover). All the fruit were green, with some later developing some purple pigment as they ripened off the plant.

Ten bowls filled with tomatillo fruit. Contents of each bowl are different sizes and/or shades of green and purple.
F2s from F1#4.
This year I planted seeds I had saved from plant #4. I grew 12 plants and all produced fruit. These showed a much wider range of pigment levels, including a pair of plants with visible purple pigment and large fruit.

One plant had a trait I didn't like at all. The fruit from spoiled very rapidly after picking. (Previous year's fruit stored for months.) That plant was one of two in an isolated garden, so I immediately culled all of the fruit from both plants. I didn't want to risk the genetics associated with spoilage turning up in the garden again next year.

Overhead view of orange plastic bowl filled with large tomatillos. The fruit are combinations of green and dark purple. One fruit at center is mostly green with three purple stripes starting at the bottom.
One plant had fruit I really liked. The fruit were large and developed purple pigment, the traits I have been trying to combine in one plant. I wasn't expecting the fruit to develop stripes as they were maturing, however. These fruit are not lasting as long as I'd like, but the other good traits means I'll be saving seeds from them anyhow.
Overhead view of green plastic bowl filled with medium tomatillos. The fruit are dark purple, with the most ripe looking black..
A couple other plants produced intensely dark purple fruit, appearing ink-black. This is the color I've been looking for, but the fruit aren't as large as I want. I'll save seeds from these as well.

Because the plants are out-crossers, I know they will have been pollinated by the others in the garden. Even though these two have trait combinations I really like, it will be unlikely to find offspring with the same traits because of all the other traits in the garden.

I've tried to diagram the overall history of the project so far. (I didn't have any photos of the original varieties, so they get cartoon representations.)

At top are a small dark purple and large green circle, representing the original varieties I crossed. From the dark circle, a black line goes down to a second row consisting of four tomatillo fruit pictures. (From left to right: medium purple, small purple, large green, & medium purple.) Black lines are drawn from beneath the right two fruit downwards to photos. Left line goes to a photo of 5 bowls of green fruit, with a photo of pale purple fruit to the left. The right line goes to a photo of 10 bowls of fruit with varying colors of purple and green.
Tomatillo project history so far.

About this point I started thinking about how I might get around the issues caused by the potential for genes from every plant in a garden to turn up in the next generation. I don't want to have to cull everything from a garden when something strongly negative turns up in the population. Right now I only have two isolated garden spaces, so that strategy can only go so far.

For my solution, come back in a week for part 2!


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Thursday, November 28, 2019

Fava Beans

Cluster of brown/purple flowers on a fava bean plant.
[Photo from link.]
I've eaten fava beans (Vicia faba) from time to time, but I've never grown them. I was recently perusing some postings from blogs I occasion and found an interesting post. The post contains a wonderful series of photos of fava bean flowers in the author's garden, ranging in shades of red/pink and brown/black. A forum discussion revealed that these variations were the result of crossing the varieties "Crimson Flowered" and "Red Epicure". After searching around a bit, I found that for the vast majority of fava bean varieties the flowers are only red/pink or brown/black.

The flowers are impressive enough in the garden already. Some improvement in flower size or color range would be awesome. My biology background leads me to think of at least two strategies.
  1. Hybridize F. faba with related species with different flower colors.
  2. Find rare varieties of F. faba with different colors.
1. Hybridization? I like this strategy generally, but the usefulness of the strategy depends on the plant being worked with. It turns out that there are no known species which can be used to produce hybrid seed with V. faba. There is some research looking into why crosses don't work. F. faba as seed parent crossed with V. galilaea and V. johannis both appear to result in fertilized eggs. F. faba as pollen parent crossed with V. bithynica also appears to result in fertilized eggs. The fertilized eggs don't seem to result in viable seeds, however. There is some later developmental failure which interferes with the cross. It might be possible to use embryo rescue to allow some of those crosses to grow up. This is well outside my skill set for now.

Variously colored fava means laid out in a grid, 11 beans wide and 6 beans tall.
[Photo from link.]
2. Finding old/rare varieties relies on such varieties still existing. The internet provides us with an amazing ability to find things, so long as someone, somewhere has put it online in some form. The image at right and others suggest there's a great deal of genetic diversity around, which might include interesting traits impacting flower color. The task of getting seeds to trial may be rather involved, but it is definitely a way forward.


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Thursday, November 21, 2019

The Color of Onions : The Whims of Genetics

I've previously posted about what might go into changing the color of onions (the-biologist-is-in.blogspot.com/2013/12/the-color-of-onions.html), but now I've gone and done an experiment. It was an accident, really, but many useful experiments start out as accidents.

We planted out a batch of "red" onion seedlings this last spring. We got them in a trade from someone who had started them. We got a pot of onion threads, and they got a couple squash babies in return. I'd never grown onions before, so I just put them (along with several types of decorative onions, hoping the deer would leave them all alone) into a raised bed that I had recently cleared. I watered the babies a few times when I noticed the soil was dry. I never fertilized or amended the soil. I basically ignored them. In retrospect, this is not the way to get those luxuriant onions you see in the store. Somehow, almost all the plants survived and produced bulbs. Inch-long bulbs, that is.

I pulled each onion as its leaves died down. They got cleaned, dried, and then left alone on the kitchen windowsill. After too many had accumulated, I moved them to a spare drying rack left over from an ongoing tomato-jerky experiment with a food dehydrator. A couple days later, I happened to notice that one of the bulbs was a much darker color than all the others. An early thought was that this was the color of some mold infesting the bulb, but on close examination there didn't seem to be anything wrong with it. It definitely was a darker shade.

I started looking at the color of the collected onions. One stood out as being more red than the others... actually red instead of that purplish color that "red" onions typically are. Another was a rich purple color.

12 vials in a row, filled with clear colored liquid going from red at left, to blue, green, and then yellow at the right.
www.braukaiser.com/wiki/index.php?title=An_Overview_of_pH
Since "red" onions are colored by anthocyanins that change their color depending on pH, we can estimate the pH of the cellular structures where the pigment is found. The red bulb approaches a pH of 2, while the purple bulb approaches a pH of 5. If we could drive the pH further to the right by the same interval, we'd get a pH=8 onion that looked blue.


I was planning to save the color outlier bulbs (red, purple, dark) to grow the following year for seed. Unfortunately, they didn't survive the winter. I was pretty sure they wouldn't survive outside, but I didn't think about how best to get them to survive inside.

I may re-do this initial experiment next year. Onions with unexpected colors would be fun.


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Thursday, November 14, 2019

Biology of Blue

Two plants on the forest floor, with broad oval leaves growing from the base and a thin stem topped with dark blue berries.
Blue-Bead Lily (Clintonia borealis)
Blue is very hard/expensive for biology to produce.

Blue light is higher energy than other visible frequencies, so chemistry to absorb everything else but pass/reflect blue light is ... tricky.


The lovely blue feathers of the Blue Jay (Cyanocitta cristata) and Eastern Bluebird (Sialia sialis) have no blue pigment in them. The vibrant blue so often seen in dragonflies is produced without any blue pigment. Even the blue color we see in the eyes of some people has no blue pigment. These and many more examples of blue in biology all are referred to as structural colors instead.

Structural colors are produced by the presence of microscopically fine structures that interfere with light. The blue of some human eyes is caused by very small particles of melanin (a brown pigment), for example.


Molecular structure diagram, illustrating the general structure of flavones, with three six-carbon rings.
Flavone structure.
Some blue berries, like those of Marbleberry (Pollia condensata) are blue due to a structural color. Others, like the Blue-Bead Lily (Clintonia borealis) I photographed in northern Minnesota (at top-left) have a blue flavinoid pigment. The flavinoid pigments are derived from or structurally similar to flavone (at right).

Some insects (like the Lycaenid butterflies) are blue due to flavoniods like kaempherol. Some of the more common flavinoid pigments are the anthocyanins responsible for the red/purple/blue colors seen in fruits and other plant tissues. Different compounds in the group have various modifications to the basic flavone structure. Those modifications impact the stability of the ionic form of the molecules at different pH levels, as well as the specific frequencies of light that are absorbed.

I don't have a solid grasp on the physics that leads to all the differences in color, but the following quote from this paper seems to be illustrative.

"Confining electrons to a smaller space makes the light absorbed bluer and if they move around in larger space the light absorbed is redder."

When the light absorbed is bluer, the light transmitted (and thus observed) is redder, and vice versa. Thus, when electrons are more de-localized, the molecule will have a more blue color. Conversely, when electrons are more restricted, the molecule will have a more red color.


In the structure of lycopene, responsible for the classical red color of tomatoes, electrons are restricted to travel within very localized regions of the molecule.

Molecular structure figure, single enlongated carbon chain with double and single bonds.
[From Madu & Bello, 2018.]

Compared that to the anthocyains, where the electrons are de-localized into aromatic carbon rings. Here the electrons are much more free to occupy larger spaces. The molecules often absorb more red and appear bluer.

Molecular structure figure, illustrating the basic structure of anthocyanins.
[Modified from Khoo et al, 2017.]

One of the anthocyanins that is more stable at higher pH is called delphinidin. It is responsible for the clear blue color found in delphiniums and can also be found in various purple plant materials. The exact shade it presents us with depends on the specific pH of the cell and the association of the delphinidin with various molecules or ions in ways far more complex than I've been able to become clear about with my readings so far.


So. Why does biology often go with structural colors, when there are commonly available molecules which produce the color? Two partial answers that come to mind are:
  1. It may be that the flavinoid blue pigments are more energetically expensive to produce than other pigment types.
  2. It may be that structural blues are very easy to come by on accident (like iridovirus infection of isopods).
Evolution is a tinkerer, not a planner. It can be very hard to ever answer questions of "why" in biology. It is far easier to answer questions about "how" or "what". In the end, biologists often have to say, "I really don't know. Do you have any ideas about how we might find out?"


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Thursday, November 7, 2019

Botanizing in Alaska: Alpine Blueberry

Small blueberry bush with unripe green berries.
The Alpine Blueberry (Vaccinium uliginosum) grows throughout Alaska. I took this photo during midsummer. The berries ripen during fall, so I didn't get any on the trip when I took the photo.

The ripe berries are well-regarded by humans and bears alike. Both can be found collecting them along roadsides in the fall. Ideally not in the same place at the same time, but you have to keep aware of your surroundings while berry picking in case you're lucky/unlucky.


On a more recent trip than when I took this photo, I was lucky enough to find plenty of ripe blueberries to pick as well as a black bear filling itself on blueberries. I was especially lucky in that the two of us were picking berries in different places.

Within each berry are several tiny seeds. The seeds need a period of cold moist stratification before they will germinate effectively. I'll be planting a batch of seeds in a pot outside to see if I can get any plants to grow next year.

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Thursday, October 31, 2019

Lavendar

Botanical drawing of lavender plant, showing details of flower structure.
[From link.]
Lavender is a wonderfully aromatic plant with gorgeous flowers. When I moved to Minnesota I learned that most lavenders don't survive our winters well. There are a few varieties listed as surviving here, but they require "some winter protection".

I want lavender to grow and thrive here without care. This led me to start thinking about how I would go about breeding cold-hardy lavenders.


The first step with any breeding project is to figure out a plan. It can be a simple or complex plan, but something. Anyhow. I wanted to gather seeds from the most cold-hardy varieties available. But since I had never actually grown lavender before, I was hesitant to start with buying several relatively expensive plants that I might just kill the first winter.

While investigating the available varieties I realized the most cold-hardy ones were all from the species Lavandula angustifolia and that seeds for L. angustifolia were readily (and cheaply) available in any spring-time seed packet kiosk.

So, I picked up a few packets.


View into small square pot with dark soil and tiny green seedlings.
Lavender seedlings in pot.
This spring I scattered the -tiny- seeds on to the soil in a larger pot, pressed them in, and waited for something to happen. The seeds may have been old, or lavender may not be quick to start from seeds.

Eventually I had some little green seedlings that I didn't recognize growing in the pot. One day I was examining the plants closely, trying to figure out if they were stray weeds or not. To my surprise, I could smell lavender. Even the tiny seedlings are exuberant with their scent production.

Once the seedling had gotten a bit larger, I separated them out and transplanted each one to its own pot. I kept the pots where I could keep an eye on them and keep them watered. A few of the plants began to put on new growth, but most seemed to suffer and remain stunted. (In retrospect, I and our rains may have been keeping them too wet. Oh well, that just counts as a first selection pass. I don't want plants that have to be given special conditions, anyhow.)


Now that winter is coming on, I've brought the three best grown plants inside to overwinter under lights. I left the others to their fate outside in a cold-frame.

Since lavender varieties are propagated by cuttings, I could refer to these three plants as three new varieties. However, only time will tell if they're worth propagating. And really, I don't expect them to have the cold-hardiness that I'm looking for. The odds of one of these three meeting that criterion are astoundingly low.

Lavender plant growing under lights.
Lavender #1.
Short lavender plant growing under lights.
Lavender #2.
Lavender plant growing under lights.
Lavender #3.

I do like the dwarfed growth habit of the second plant. A closer look shows that it does have shorter internode distances than the other plants. It isn't just behind in its growth, it is actually growing differently.

Close view of lavender plant stem leaf.
Lavender #1, stem.
Close view of lavender stem tip on short plant.
Lavender #2, stem.
Close view of lavender plant stem tip.
Lavender #3, stem.
I also like that it looks a bit more silvery than the other plants. A very close up view of some leaf tips shows that the second plant has much more prominent and branched trichomes. These photos were taken hand-held. I think I can probably do better and closer with some more technical preparation (tripod, lights, maybe focus stacking, etc.).

Extreme close up of lavender leaf tip, showing tiny branched trichomes on leaf surface.
Lavender #1, leaf tip.
Extreme close up of lavender leaf tip, showing tiny branched trichomes on leaf surface.
Lavender #2, leaf tip.
Extreme close up of lavender leaf tip, showing tiny branched trichomes on leaf surface.
Lavender #3, leaf tip.


What lessons have I learned and how do they impact my longer term goals?

Lavender varieties are propagated clonally, so there's no need for them to be homozygous for various alleles. As a result, lavender seeds would be expected to contain a surprising amount of genetic diversity compared to domesticated plants that are routinely grown from seed. The few plants I've grown have shown variations in ability to prosper in the temperature/water conditions I was growing them in, as well as having height and trichome differences.

I have no reason not to expect variations in cold hardiness will also be manifest when I grow out a larger population, though I don't expect one of these three to be a winner in that regard. I'm also looking forward to what other interesting traits may turn up.

The next steps are to acquire a larger number of seeds, grow more seedlings, then plant them out for winter. For initial hardiness trials, I can have many small plants in my back yard. If I find survivors, I'd want to collect seeds and begin the cycle again. Later I can plant seedlings or cuttings at a family property further north. Ideally, I would eventually find trial space in the far north of Minnesota, so the plants can be tested against the coldest that Minnesota winters can provide. That would be several years out, so I have some time yet to make arrangements if things develop such that they would be useful.


Why?

Funny you should ask. In the medium-term, I'm simply motivated by the desire to play around with the plant and produce something I can grow in my yard without having to spend too much effort at keeping it alive. In the long-term, I want to produce varieties that can be farmed for fragrance production in Minnesota. (All current lavender farms in USA are a few growing zones warmer than is available here.) This would open up a new crop for local agriculture and help to diversify what is grown in the state. I don't know if this will come to pass, but that's the thing about long-term goals.


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Thursday, October 24, 2019

Botanizing in Alaska: Black Spruce

Cluster of narrow black spruce trees growing alongside a road.
Black spruce (Picea mariana) are a common forest tree up in central Alaska, ranging north until the tundra. The trees in the image at left are in Fairbanks, Alaska.

 The trees grow slowly, eventually topping out at 20 meters in the southern parts of their range. The trees in Fairbanks are generally much shorter. The trees here are maybe 30 ft tall, growing less than a foot apart. They can get away with such crowding because those two trees are probably separate trunks growing from a unified root system. Large connecting roots grow horizontally just under the surface and graft together with their neighbors. The individual trunks share nutrients and carbohydrates and thus don't suffer from competitive shading as much as trees that don't cooperate in this manner.

 This style of growth also potentially helps them stay upright in the swampy soils they're usually found in. The horizontal grafted root structure spans wider than the cluster of trunks, allowing the cluster to stay upright even if the ground beneath part of the cluster can't support their weight. This style of growth would help them grow horizontally out onto a bog, with some trees suspended over the lake hidden below.

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