The Biologist Is In: domestication

Showing posts with label domestication. Show all posts

Monday, October 29, 2018

Domestication of Yeasts

Saccharomyces cerevisiae is known as the Baker's Yeast. It has helped us make bread, beer, and wine since before recorded history. These days we also use it to make fuel, pharmaceuticals, and for basic biology research. With the innumerable industrial, food, and research purposes we use it for, it is a thoroughly domesticated organism.

With the various mammals we've domesticated, researchers have identified a "domestication syndrome"; a set of features common across domesticated animals. They have shorter faces, milder temperaments, reduced weaponry (teeth, horns, claws), and color changes. In short, they've become cuter. To some degree these are traits that could have been actively selected for, but it turns out that if we only select on temperament, all of the other traits come along for free because all those traits are mediated by the action of neural crest cells throughout the body.

Now, yeast don't have neural crest cells, but they're still domesticated. It didn't evolve to have a more amenable temperament, but it did evolve to grow rapidly in the amenable conditions we provide for them. There's a different sort of "domestication syndrome" that it would have developed along the way. Any trait or ability it needed to live as a wild yeast, but did not need to live under our care, would be lost. This would happen because any lineage that dispensed with those traits would be able to grow faster without the energy drain they represent.

So. What traits would yeast lose under domestication? It's not entirely clear. We can't just look at the cells and see a difference. Nor do we exactly have the wild progenitor yeast around to make comparisons with.

Here we're going to take a bit of diversion.

My first major project in grad school was to figure out how to use flow cytometry to determine the genome size of a different yeast called Candida albicans. In the past, This analysis had proven difficult to do with this yeast for others. This difficulty had been generally blamed on the organism's ability to grow either as independent yeast cells or as elongated hyphal cells that get all tangled up in each other.

Figure showing genome content size of a population of yeast cells. One large peak near the left edge, with a smaller peak at twice the distance along the x-axis. Smaller peaks at 3x and 4x locations.

I started with protocols developed for S. cerevisiae. At three months in, I was testing yet another protocol variation and the data that came out of the experiment looked like the figure at right. Previous data had much broader, indistinct peaks. (I'm sure I have some of those early figures around somewhere, but I'm not going to spend a bunch of time digging for them.) I was amazed and quickly set up a repeat of the exact same experiment. It failed miserably.

I had made a mistake somewhere in the protocol which made things work. Because it was a mistake, it wasn't written down in my lab notes. You can only write down what you know you're doing.

It took me another frustrating month to figure out what it was I had done wrong. I had used way too much EDTA in the buffers for processing the cells. With this improved protocol, I could get good flow cytometry data from even the most difficult hyphal-growing strains of C. albicans. This disproved the previous theory as to why this species was difficult to work with while doing this assay.

Subsequently, the protocol proved effective with every random yeast species I was able to acquire for testing. I never tested them with the original S. cerevisiae protocol for comparison. In retrospect, I consider this to be an oversight.

The flow cytometry protocol has since then been used in numerous papers from several separate labs. The flow cytometry protocol and analysis tools I developed become the second chapter in my thesis. The idea of wrapping up the material into a paper did come up after I graduated, but I really didn't have the time/energy to dedicate to the process. Researchers should probably cite that chapter, but I know that thesis chapters tend to only get cited rarely. If you are interested in all the details, you are welcome to have a read.

I pretty quickly developed a working theory about what was going on. EDTA binds to divalent cations (Ca²⁺ and Mg²⁺) in solution, locking them up so other enzymes don't have access to them. Many enzymes require certain levels of these ions to function normally. For whatever reason, the endogenous nucleases of C. albicans were much less sensitive to low levels of divalent cations than those found in S. cerevisiae. Now, I couldn't think of any way to test this theory. I wasn't in a biochemistry or structural biology lab, so the techniques that would have been useful were well outside our wheelhouse.

This uncertainty has stuck with me for the roughly seven years since then. Just a couple days ago, I developed an idea that in some sense explains the results. Domestication.

S. cerevisiae is a thoroughly domesticated species. It hasn't had to fight for what it needs, so it could very well have evolved enzymes that are used to easier environments with more consistent levels of necessary ions. I strongly suspect the flow cytometry protocol for S. cerevisiae only works because of the domestication syndrome of traits found in S. cerevisiae.

I'm not sure how one would test this theory, but it sure seems to make sense of the observations so far.

References:

Domestication Syndrome: http://www.genetics.org/content/197/3/795
Fox domestication: https://blogs.scientificamerican.com/guest-blog/mans-new-best-friend-a-forgotten-russian-experiment-in-fox-domestication/
PhD thesis of Darren Abbey: https://conservancy.umn.edu/handle/11299/185630
Papers with C. albicans flow cytometry analysis:

Monday, September 10, 2018

Botanizing in Hawaii: Solanum linnaeanum

Closeup of flower, leaves, and stem of plant. Flower is pink with four fused petals, forming a square, and has yellow anhers gathered in the center. The leaves are heavily lobed, with long sharp spines protruding from the underside. The stem too is covered in dramatic spines.

Hawaii has a long history of biological invasions. Plants and animals from all over the world have arrived and thrived there under the tropical sun. This can make it somewhat difficult to identify a random plant, because it could literally come from almost anywhere on the planet.

On one of my hikes, I found several plants I immediately recognized a member of the family Solanacea. This is the same family that includes tomatoes, peppers, and eggplants. I was pretty sure it was even a member of the genus Solanum, one of the several species sometimes referred to as "spiny eggplants".

Closeup of a few leaves and two small round fruit. One fruit is entirely brown. The other fruit is pale green with darker green stripes. The leaves are heavily lobed and covered in spines.

I collected a few fruit, intending to secure some seeds for planting back home in Minnesota. A couple days later, while sorting through my collection at a motel, I finally identified the plant as Solanum linnaeanum. Among its various common names are: "Poison Apple", "Devil's Apple", and "Apple of Sodom". They're native to parts of southern Africa, but have naturalized in Hawaii and various other places around the world.

The plant and its fruit are chock-full of toxins. Enough so that very few animals are willing to eat it. At about this point I decided not to take seeds home for garden trials. I do have a few seeds in my collection that come from highly toxic, or otherwise dangerous, plants. I wasn't entirely certain how much difficulty I would have with trying to leave Hawaii with collected seeds. If some official asked me what they were and why I had them, they might not appreciate my responses. So, to limit that risk, I dumped the S. linnaeanum seeds in the garbage.

(Several days later when I left the state, I learned I would have had no trouble at all. Dried seeds in vials didn't concern the USDA officials at the airport at all. Bringing seeds into Hawaii gets their attention, not taking seeds away from Hawaii. Next time I'll be a bit more bold.)

Interestingly, it appears this species can cross with domesticated eggplant (S. melongena). Doganlar et al. studied an F2 population derived from a cross of the two species in order to map the genomic positions of genes for traits important in domestication. Unfortunately, their paper doesn't have any photos of what the F2 plants looked like. Even with the risk of dragging the toxic traits from S. linnaeanum into the progeny, this would be a fun cross to recreate and explore. The wild species probably has numerous disease/insect resistance traits that would be useful in a garden eggplant, so there is probably value to the experiment beyond simple personal amusement. There's a few online vendors offering seed for this species, so I won't have to make another trip to Hawai'i to start on this project.

References:

Monday, July 30, 2018

Growing Bur Oak Trees 2

Large acorn cap resting beside a quarter coin for scale. Acorn cap is about three times as wide as the coin. Top half of image shows cap on its side, bottom half shows cap resting upright.

Burr Oak acorn cap.

One of my long-running interests has been domestication of oak trees for food. Now, you can already prepare and eat acorns and there is a long history of native peoples around the world doing so, but rarely does it seem like the oaks have been transformed by the process. What would be ideal is an oak tree that produced very large acorns which were very low in the tannins that make most acorns inedible without intense processing.

Several years back I found a Burr Oak (Quercus macrocarpa) tree with huge acorns littering the ground beneath it. When I broke one open and tasted it... It was straight up sweet. I probably could have taken home a bag full and made a meal from them. Instead, I collected several that looked in the best condition and took them home (to Minnesota) to grow.

http://the-biologist-is-in.blogspot.com/2016/04/growing-bur-oak-trees-quercus-macrocarpa.html

It's now been a couple years and the young trees have not only survived our winters, but they've been thriving. This wasn't a forgone conclusion. The seeds came from trees growing about two thousand miles south of where I planted them. This goes against the general guideline of planting tree seeds collected from somewhere near where you plant to grow them.

Each tree is distinct, with leave size and shape variations. They're all different heights too. I suspect these early differences in growth rate will continue.

Composite of eight images, showing top views (at top) and side views (at bottom) of four young oak trees.

Burr Oak seedlings, each photographed from above and the side.

The trees have only been outside for a couple winters, so it isn't guaranteed that they will survive long-term. Either later this summer or early next year I'll be transplanting the seedlings to cleared spaces in our woods where they can spend the rest of their lives. The local squirrels will be pleasantly surprised in about eight years when the seedlings should start making their first acorns.

References:

Sunday, January 8, 2017

Black Nightshade 2

The potential toxicity of Solanum nigrum fruit has been much debated. I had previously written about this species and some thoughts about why people might think it was poisonous. I generally consider it's ripe fruit to be edible and I routinely eat small numbers of them with no negative effects. However, there are still reliable reports of toxic reactions to the fruit (Joseph Lofthouse's reporting) that should be cause for concern to those unfamiliar with the plant.

I think the species had great potential as a future domesticated plant for the vegetable garden. The plants don't seem to have any real disease issues, especially when compared to the related tomatoes. Improvements in fruit size, sweetness, or total production would be worthwhile traits to develop. To that end, I've been on the lookout for wild plants with improved traits to help start a breeding program.

Last summer (2016) I grew several plants from saved seed. In our fenced in garden area, several additional wild weedy plants grew. I was pleased to find one of the wild plants had large berries, on average maybe twice the volume of the berries I'd planted. Rabbits were getting into the garden, so I kept a close watch on the plant while waiting for the fruit to mature.

Small round black berries at bottom, larger round black berries at top.

Top: Extra-large and extra-toxic.
Bottom: Typical and edible.

Once most of the berries had ripened, I collected a sample from the different plants. I took the berries inside to photograph and save seeds. The smaller berries tasted just as I had expected. The larger berries... I immediately spit them out. The larger fruit had a significantly higher level of solanine than I had ever experienced in this species. I knew exactly what this agent tasted like from tasting the closely related S. dulcamara, which is consistently toxic to humans.

This plant exemplifies some of issues leading to the ongoing debate about this species. I'll eat berries from most plants of this species, but there is no way I would ever eat a handful of berries (or even a single berry) from this plant. I know how to recognize the plant's poison, but you may not.

It took me several years of sampling fruit from every plant I found of this species before I found one that was poisonous. You might find a poisonous one on your first try. Your risk of tasting a couple berries will be minimal, but you should always take great care when eating a plant that you're not very familiar with.

Even though the larger berries were toxic, I'm still going to plant the seeds I collected from them. I'm hoping some of the plants in the next generation will have the larger fruit and yet not be toxic. Even if the two traits are closely linked, eventually I should be able to find a plant that separates them. Wish me luck.

References:

Wednesday, January 4, 2017

Early Chile Domestication

I first discussed Capsicum annuum var. glabriusculum in an earlier post. I've collected wild seeds for this species from a few different sources throughout the desert southwest.

Two photos of small pepper plants with tiny leaves and tiny green or red pods.

The two views at right are the same plant, grown from seed collected in Phoenix-Az. The comparison of above and side views shows how well the down-hanging fruit of this plant are hidden from above, where birds would be more likely to see them while flying overhead. Since birds are the primary distributors of wild chile seeds, this trait would not encourage dispersal of the seeds and so the trait would not spread.

Early human farmers would have found this trait useful, as it would help reduce crop loss to birds. The majority of non-ornamental chile varieties grown today share this trait.

The lack of any other traits associated with domestication make me think this plant either represents the impact of selection pressure by early farmers, or a much more recent introgression event where all the other modern traits were heavily selected against. The seeds were wild-collected in Arizona (where humans have been living and using chiles for thousands of years) and modern chiles are commonly grown in the area, so either scenario is likely.

An approach which might help clarify the plant's ancestry is to compare its genome to more domesticated types. If it has this trait due to a modern introgression, there will be regions of its genome that match the relatively low diversity found in domesticated chiles. If it has had this trait for far longer, it's genome will be covered in variations not found in domesticated chiles.

Processing out some genomic DNA (gDNA) is a pretty easy thing. The difficulty will come in getting the material sequenced. I do have reasonably simple access to a nanopore DNA sequencer, but the data that comes from that technology has been problematic for some whole genome analyses in my experience (and in the experience of others). Ideally I'd have the gDNA sequenced using Illumina technology. This technology also introduces errors into the resulting data, but at lower levels and in ways that I have already written software to compensate for.

As I continue to build out my lab, this is probably one of the projects I'll be investigating further. Clarifying the ancestry questions for this chile would be personally rewarding, but also might fill in a tiny little detail about how people of the desert southwest lived. This might be very interesting to a large number of people.

I expect the other seed lines I have for C. annuum var. glabriusculum will grow to have upright fruit, but otherwise match the characteristics of these plants. I like the small size and pungency of the fruit, so I'll probably keep growing them even if I can't think of a breeding project to use them in.

References:

gDNA prep:

www.thermofisher.com/us/en/home/life-science/dna-rna-purification-analysis/dna-extraction/genomic-dna-extraction/plant-dna-extraction.html

Nanopore sequencing:

Tuesday, June 14, 2016

How to Make a Better Strawberry

Drawing of wild strawberry plant, with smaller drawings illustrating details of flower and other part structure.

Over the last few years I've collected numerous isolates of the Woodland Strawberry (F. vesca) from around Minnesota and Wisconsin. Most of the isolates went into a strawberry tower I had picked up at a garage sale, with each isolate being given a separate pocket of soil. An isolate I found in the far back of our property was planted in a pot all on its own away from the others. I put all the containers near my garden and then proceeded to mostly ignore them for the rest of the year. I wasn't going to baby them along, so only the real survivors would prosper.

It was soon obvious that one of the isolates in the strawberry tower was dramatically better at spreading. It took over the tower and then spread to every nearby bit of exposed soil. This plant originally came from a patch of sandy soil above a large boulder adjacent to a lake in northern Minnesota, fully exposed to the sun. This plant was obviously a determined survivor.

The isolate from our property grew well. It produced large leaves and occasional robust runners which it dropped over the edge of its pot. I didn't think much of it at the time.

At the onset of winter, I continued my strategy of not caring for the plants. The planters containing the strawberries were left out to experience the full brunt of (the admittedly mild) winter. I treated some nice Garden Strawberry (F. x ananassa) plants I had received midsummer much better. Their pots were covered in leaves and then placed up against the basement wall under a porch packed with other items being stored for the winter. I had previously had difficulty overwintering strawberries, so I took efforts to protect them.

Once the earliest hints of spring arrived, the Woodland Strawberry plants started to wake up. The aggressive spreading isolate was found to be just as aggressive about surviving. (The other F. vesca isolates in the tower were not so much.) Every pot that it had spread into last year was soon full of new growth. This plant's thin runners didn't seem to let it spread into the tall grass around the pots last year, however, as there are no lawn strawberries where those pots were kept. Right now the plants are putting out flowers in impressive numbers. I expect any berries will be much larger than the tiny examples the plant produced last year, as the whole of the plant is much larger and happier looking this year.

Out in the yard where I kept the isolate from the back of the property, I found some robust strawberry plants growing. Some of this plant's runners had settled into the tall grass around its pot and found their way to the soil where they were able to survive the winter. The parent plants in the pot itself, however, did not survive.

The Garden Strawberries that I took efforts to protect... completely died out. One bit of vital green did make it to spring, but it soon turned brown and joined its conspecifics in the afterlife. Fortunately, I can easily get more plants from garden centers and other sources.

It would be really nice to have a plant that combined the extreme hardiness of the Woodland Strawberry and the larger berries of the Garden Strawberry, so I started thinking about hybridizing them.

All known strawberries (genus Fragaria) have a basic chromosome number of seven. Wild species range from diploid (2n) to decaploid (10n) with every even number of chromosome sets represented. There are also the occasional naturally formed sterile hybrids with an odd number of chromosome sets.

The two species of strawberry in my collection have a different number of copies of each chromosome.

F. vesca (Woodland Strawberry; 2n)
F. x ananassa (Garden Strawberry; 8n)

If the two species are crossed, sterile pentaploid plants result. To get around this, researchers have used colchicine to double the chromosomes in F. vesca. Crossing a tetraploid F. vesca with an octaploid F. x ananassa should result in a fertile hexaploid plant. The resulting plants ended up being decaploid instead, perhaps by the involvement of unreduced gametes from the octaploid parent with normal diploid gametes from the tetraploid parent (8n + 2n -> 10n). With this model, the hybrid plants would be 20% F. vesca and 80% F. x ananassa. Back-crossing this hybrid to either parent would result in changes in chromosome number with sterility being the result for most cases (x 2n F. vesca -> 6n; x 4n F. vesca -> 7n; F. x ananassa -> 9n), so this plant is essentially a dead-end with respect to further breeding for improvements.

Chromosome doubling in F. vesca can theoretically be done twice to produce octaploid plants (2n -> 4n -> 8n) that could then cross with F. x ananassa to produce an octaploid hybrid. The hybrid would be 50% F. vesca and 50% F. x ananassa. It would also be able to be back-crossed to either parent without producing progeny with sterility issues due to odd numbers of chromosomes. This would make the hybrid far more useful for further breeding projects, such as combining the extreme hardiness of F. vesca with the tasty and large berries of F. x ananassa.

Earlier I mentioned using colchicine to double the chromosomes of F. vesca. Colchicine is a toxic alkaloid originally processed from Autumn Crocus (Colchicum spp.). The compound interferes with the polymerization of tubulin into microtubules, thus preventing the migration of chromosomes to spindle-pole bodies during cell replication. The effect of this is that newly doubled chromosomes during cell replication aren't split into two new cells, thus a single cell remains with twice as many copies of each chromosome as it started with.

Plants with increased ploidy often have phenotypic changes, such as thicker stems/leaves and larger fruit. Even when the overall plant remains much the same, an increase in ploidy can be observed by noting an increase in the size of pollen grains. If there is no apparent change, even in the pollen, then one would have to count the actual chromosomes to be sure the chromosome doubling protocol has worked.

So, when will I set about doing this? I've got so many projects lined up, that I don't know when or if I will actually do this. I really like the idea, and the protocols aren't all that difficult (or dangerous), but my resources are limited, so we I'll have to stick with, "We shall see." for now.

Anyone else interested in taking a go at it in the meantime? If you do, please let me know of your progress.

References:

the-biologist-is-in.blogspot.com/2015/06/strawberries-galore.html
Strawberries

en.wikipedia.org/wiki/Fragaria

Woodland strawberry:

Garden strawberry: en.wikipedia.org/wiki/Fragaria_vesca

Fragaria x vescana

Decaploid strawberries

journal.ashspublications.org/content/117/5/856.full.pdf

Colchicine treatment

Colchicum

en.wikipedia.org/wiki/Colchicum

Chromosome spread protocol

www.wfu.me/andersonlab/wp-content/uploads/2011/10/Alternative-Fixatives-2009.pdf

en.wikipedia.org/wiki/Spindle_pole_body

Tuesday, April 26, 2016

Growing Bur Oak Trees (Quercus macrocarpa)

Oak trees (Quercus spp.) have a long history of being used as a food source. Acorns are produced in large amounts by older trees, usually in alternating years. This fruiting strategy, called "masting", helps to prevent the population of seed predators from overwhelming the tree and killing every acorn every year.

1. Bur Oak (Q. macrocarpa)
acorn cap.

I've made an occasional habit of tasting acorns over the years. They routinely have the strongly bitter taste of tannic acid, but occasionally I find one that doesn't taste so bad. When I was in Texas for my oldest brother's funeral (November 2014), I found a nice Bur Oak (Q. macrocarpa) tree on a walk. The tree had a few acorns (in huge caps) on its branches, but the ground beneath was littered with them in various conditions. I broke open one intact looking acorn with my shoe. I noted the nut-meat looked in moist and in good shape, so I picked up one of the pieces and tasted it. The juice tasted distinctly sweet, with no bitter aftertaste.

I was astounded by this and collected a large handful of the best looking acorns I could find. I then continued with my walk. Back at my parents' house, I put the acorns in a resealable plastic bag and put them with my things. When I returned home to Minnesota, I added some moisture to the bag and put it into a basement micro-fridge I've dedicated for botanical specimen storage.

2. Bur Oak acorn; partially
dissected and sprouting.
(USA quarter for scale.)

A year and some four months later (March 2016), I decided to try growing the acorns. Winter here was wrapping up and I was already growing a Chestnut (Castanea spp.) tree in my basement. I took the acorns out of the fridge to examine them. I had previously extracted one nut-meat from its shell and found it had begun to mold. I discarded this one and opened up a few others. Each acorn with an intact shell survived storage without molding.

3. Germinating acorn.

I left the acorns (shelled, partially shelled, and intact) in a dark, but room-temperature spot and waited. By late in March, I noticed a small swelling forming on one acorn (images 2 & 3). At first I wasn't sure if I was actually seeing a change in the acorn, but once I was sure that I was, I removed the remaining membrane layer from around the germinating acorn embryo to get a better view of it.

4. Germinating naked acorns.

I had fully extracted two of the acorn nut-meats during my examination for mold. Once I noted the one acorn germinating, I took a look at these two. Both were obviously germinating too. One (image 4, left) had split in two, revealing the anatomy of the embryonic oak tree and its two cotyledons. To stabilize the baby tree, and partly mimic the acorn shell I had removed, I secured the cotyledons together with some small cable-ties. I secured the other naked acorn in the same way.

5. Stem growth.

Three of the germinating acorns are planted into air-pruning planters (just like the Chestnut trees). The acorns produced a stout taproot which extended to the bottom of the planter well before the stem had grown an inch or unfolded its first leaf. After stalling for a while at less than an inch tall, the stem started elongating rapidly.

6. Air-pruning in process.

The taproots were too thick to pass through the screen material, so the either terminated on impact or grew sideways for a bit before catching on the screen and terminating (or as in image 6, growing through the screen anyway). Many side roots then grew, soon after poking through the bottom of the planter.

As long as the large and tasty nut remains attached to the seedling, it will be a strong incentive to squirrel predation. I suspect I'll have to keep the baby trees in protective custody until at least summer of 2017. One tree will probably go into the back corner of my yard. (There are some very large Buckthorn specimens there to clear out first.) The others will probably go to my wife's family farm, joining a pair of the chestnut trees to form the start of a nut orchard.

7. Bur Oak range, source, and me.

This species of Oak is native to a large swath of the central part of this country (figure 7). The specimens at the extreme southern part of the range tend to produce larger acorns than those at more northern locations. It seems that this gradient is in part due to the history of glaciation on this continent and the improved ability of individuals with smaller acorns to travel north into areas where it was previously extirpated, though the details have not been fully worked out.

If these very southern trees manage to survive the cooler climate here in Minnesota, they should start producing their first acorns in somewhere from 10 to 35 years (depending on who you talk to). Hopefully I'll still be around (at somewhere between 48 and the ripe old age of 73) to collect some acorns and make a few meals of them. For the purposes of the ongoing domestication of the tree as a food source, I hope I'll also be able to convince the young'uns around at that time to plant some acorns from the best of my trees so as to grow their own.

References:

History of:

www.iloveacorns.com/history.html

Eating:

Masting: en.wikipedia.org/wiki/Mast_%28botany%29
Tannic acid: en.wikipedia.org/wiki/Tannic_acid
Q. macrocarpa:

Cotyledon: en.wikipedia.org/wiki/Cotyledon
Acorn size gradient: www.nrcresearchpress.com/doi/abs/10.1139/B09-008

Tuesday, April 12, 2016

Growing Chestnut Trees (Castanea spp.)

A couple of years ago, a member of a forum I frequent offered to send some Chestnut (Castanea spp.) tree seeds to interested parties. He has been breeding Chestnut trees over the last decade and was interested in sharing the results of his work. I expressed interest and soon after a small box arrived, packed with seeds from a few different sources. The box was far larger and held far more seeds than I expected the individual was going to send me.

The seeds were collected from a range of different Chestnut trees:

Chinese seedling (C. mollissima)
Miller's Hope (C. mollissima)
Szego (seedling of Linden; mostly C. mollissima/C. crenata)
Gillet (seedling from Colossal; C. sativa/C. crenata)
Kaibutsu (seedling from Colossal; C. sativa/C. crenata)
Silverleaf (C. sativa/C. crenata)
Double Sweet
Patterson

Most of them have a mixed ancestry, but all have been selected for high production of large edible nuts. From a long-term view, growing these varieties is entirely about the ongoing domestication of chestnuts as a food source, i.e., improving food security through increasing the diversity of our food plants.

American chestnut range vs. me.

Growing these chestnuts has nothing to do with resurrecting the American chestnut (C. dentata), which is something I consider a very important goal. The American chestnut, in the pre-blight era, dominated the Eastern Woodlands and provided food for a thriving ecosystem (and economy) that has been only a shadow of its former self. Go over to www.acf.org to read more about what they're doing to restore this tree to the dominant role it used to have. Because I live well outside the native range for the American chestnut, I'm not worried about interfering with the their restoration by growing closely related trees that can cross successfully with the American chestnut.

From a short-term view, I'm interested in growing chestnuts simply because I want to grow a new food source. I like having a hand in producing the food I eat and I'm interested in the process of domesticating plants to be better foodstuffs for the future. There really is nothing like planting a tree, that will probably outlive me, for having a future perspective.

When I received the package of chestnut seeds, I had just moved into a new house and didn't have the resources on hand to build the rodent-proof growing area I would need to keep baby Chestnut trees alive. They rely on the nutrients found in the seed for the first year, which is a long time to be exposed to hungry squirrels that like to pull up newly-sprouted nut trees to get at the buried nut. (I learned this when one pulled up a baby Black Walnut tree I was tending, ate the previously-buried nut, then left the uprooted seedling beside its pot.) I had read that Chestnut tree seeds could stay viable for a few years if kept chilled, so I planted a handful of the seeds and kept the others in the fridge. My idea was that by next spring I'd be able to build them some proper protection.

1. Radicle extending.

One of the first batch of seeds germinated and started growing. After it was a few inches tall, the growth point died. A few new branches formed below that point, but their growth points soon died. This pattern repeated a few times before the whole plant died. It had never produced a single leaf, but had branched several times while trying to.

2. Hypocotyl beginning to extend.

I spent some time thinking about what went wrong with that seedling. On the idea that it was getting too much water and developed a fungal infection of some sort, I decided to build a potting system that would allow the seedlings to drain much better. I built a set of primitive air-pruning pots and a raised wire-mesh platform so they could drain. In addition to the better drainage, these pots should help encourage the development of a healthier root system (so the seedling will better survive transplant later in the season).

3. New leaves.

Of this second batch of seeds, only one (a seed from the variety "Kaibutsu") has woken up so far. It is growing happily and is just opening its second set of leaves. The remainder of the seeds seem to have either succumbed to a mold, or are still waiting to wake up. There are reports of chestnut seeds derived from hybrid origin (as most of these are) having reduced germination, but I would need to test a similar batch of seeds as a control. Without that control, I'm left with hoping more decide to germinate, that the elongated winter they experienced didn't kill off the remaining seeds.

4. LED lighting.

When this seedling started waking up, I put it near the front door where I could keep a close watch on it to make sure it didn't dry out. After it grew a couple inches, the drive to find light became the stronger factor guiding its growth and it began tilting towards the nearby window. To help keep the seedling from becoming permanently crooked, I built a rack that holds an LED floodlight directly over it. The base of the structure is a platform extending forward underneath the tray holding the plants, so it has very little risk of falling over. This setup should keep the seedling growing straight until it is time for it to go outside.

5. New lighting and further growth.

After a few more leaves had grown, it became apparent the lighting setup I built was too bright for the seedling. Leaves closer to the light were looking sunburned, while those further away were colored lightly brownish from photo-protective pigments. I think the new fixture produces more light overall, but it is spread over a larger area and so the peak intensity is lower. (This new fixture can also provide light for other plants, like those carrots.)

6. Roots.

The home-made air-pruning pot seems to be doing its job. There are little roots poking out all over the bottom of the container. The roots start out whitish, but then turn a dark brown as the tip dies and dries out. At some point soon, I'll have to transplant the seedling to a larger air-pruning pot. This will allow it to become larger/stronger as well as giving us the time to figure out where it should go into the ground and how to protect it from deer and other hazards. I might be able to make such a planter the same way I made this one, but I suspect I'll have to go with a bit more robust commercial offering.

References:

Chestnuts:

Chestnut varieties:

Chestnut species:

American chestnut

Chinese chestnut: https://en.wikipedia.org/wiki/Castanea_mollissima
European chestnut: https://en.wikipedia.org/wiki/Castanea_sativa
Japanese chestnut: https://en.wikipedia.org/wiki/Castanea_crenata

Air-pruning:

depts.washington.edu/propplnt/Chapters/air-pruning.htm

www.instructables.com/id/Air-prune-tree-seedlings/

Tuesday, March 1, 2016

Vavilovian Mimicry

Vavilovian mimicry is a form of mimicry where an agricultural weed begins to take on characteristics of a domesticated agricultural crop due to the selective forces present in the agricultural system.

The first example is involving wheat. Well, really, it involves both wheat and barley. During the early phases of domestication of these grains, they weren't distinguished as separate plants. Initially, the large seeded grasses were collected from the wild and planted closer to home. The now-farmers would then collect the large seeds from the grasses they grew, eat most and protect some, and then plant what was left the following year. You could say that wheat and barley are Vavilovian mimics of each other, because we really don't know which was the first grass to enter domestication.

At some point while the wheat/barley agricultural system was developing, other weedy grasses invaded the prime growing habitat found in the fields. Two of these weeds evolved to become what we call "rye" and "oats". They developed larger, non-shattering seed heads and an annual life-cycle. This allowed their seeds to be collected, saved, and planted as contaminants to the main crop. Both rye and oats are more tolerant of cold conditions and poor soils. Because they had become mimics (and contaminants) of the major crop, when farmers tried to establish the crop system in marginal conditions, these mimics can come to predominate as the major crop.

Wheat/Barley -> Wheat (Triticum spp.)
Wheat/Barley -> Barley (Hordeum vulgare)
Wheat/Barley -> Rye (Secale cereale)
Wheat/Barley -> Oats (Avena sterilis)

Another often-cited case of Vavilovian mimicry is found in the agriculture of lentils (Lens culinaris). A common weed in lentil fields is the Common Vetch (Vicia sativa). The Common Vetch seeds are bitter, so farmers are able to sell their crop for less if there is too much vetch contamination. As farmers have increased the selection pressure on the vetch by mechanical (and computer-vision) assisted seed sorting, strains of the vetch have evolved so that their seeds mimic the lentils in color and size, as well as the characteristic flattened lens-shape.

A. Lens culinaris. B. Vicia sativa, wild and mimic.
(from: www4.ncsu.edu/~fgould/pdfs/Gould1991.pdf)

Lentil (Lens culinaris) -> Common-Vetch (Vicia sativa)
Lentil (Lens culinaris) -> Black-Pod-Vetch (Vicia sativa subsp. nigra)

If farmers could impart some selective force on the mimic vetches such that they would lose their bitter flavor, they would have effectively created a new crop. This new crop might grow better in some conditions where lentils don't thrive, thus spreading the useful area of agriculture.

The selection force involved in the development of Vavilovian mimicry can be mechanical (as in Flax weeds) or manual (as in Rice weeds). What is key is that the selection force separating weeds from the crop has to progressively get more and more stringent over time. This allows the weed population to always have some individuals that will escape the selection force applied to them.

Flax -> False-Flax (Camelina sativa linicola)
Flax -> Flax-Dodder (Cuscuta epilinum)
Rice (Oryza sativa) -> Early-Baryard-Grass (Echinochloa oryzoides)

An interesting case that I think is related to Vavilovian mimicry is the complex of Andean tuber crops. I don't know which crop was first domesticated in this region, but since before modern history, five species of tuberous crops have been traditionally grown together in fields. Growing several different crops together in this agricultural system mean that there will always be production, even if any given plant doesn't produce in some year (due to weather, disease, or other factors).

Potato (Solanum tuberosum) -> Maca (Lepidium meyenii)
Potato (Solanum tuberosum) -> Oca (Oxalis tuberosa)
Potato (Solanum tuberosum) -> Mashua (Tropanolum tuberosum)
Potato (Solanum tuberosum) -> Ullucus (Ullucus tuberosus)

Though I doubt any of these species entered the agricultural system as weeds, I expect that each species will undoubtedly have evolved towards a set of traits similar to those of the most common plant grown in the fields. Any individual plants that didn't prosper in the agricultural system would have contributed less to the next generation and the species would shift to a form that did prosper. This shifting of the traits of one species to align with another, due to the selection forces favoring the majority plant species, is a characteristic common between Vavilovian mimicry and whatever this case should be referred to as.

References:

en.wikipedia.org/wiki/Vavilovian_mimicry
www.liquisearch.com/vavilovian_mimicry/examples
en.wikipedia.org/wiki/Wheat
en.wikipedia.org/wiki/Barley
en.wikipedia.org/wiki/Flax
en.wikipedia.org/wiki/Camelina_sativa
en.wikipedia.org/wiki/Cuscuta_epilinum
en.wikipedia.org/wiki/Rye
en.wikipedia.org/wiki/Rice
en.wikipedia.org/wiki/Avena_sterilis
en.wikipedia.org/wiki/Echinochloa_oryzoides
http://www.bioone.org/doi/pdf/10.1614/WS-D-13-00122.1
Erskine, W. et al. 1994. Mimicry of lentil and the domestication of common vetch and grass pea. Economic Botany. 48(3):326-332 [link]
Barrett, S. 1983. Crop mimicry in weeds. Economic Botany. 37(3):255-282
Gould, F. 1991. The Evolutionary Potential of Crop Pests. American Scientist. 79:496-507 [link]
hort.purdue.edu/newcrop/proceedings1990/V1-428.html

Tuesday, April 21, 2015

Transgenic Sweet-Potatoes

One of the first tools available to biologists seeking to make transgenic plants was a natural bacteria called Agrobacterium. The bacteria infects plants and induces the production of auxins and cytokinins, plant hormones that together trigger the growth of a disordered plant tissue called a gall. The gall provides nutrients that the bacteria then uses for its own growth. The bacteria pulls off this trick by inserting genetic information into plant cells. It can do this because it carries a plasmid that can function both in its own cells and in the cells of a plant. When the bacteria infects the plant, the plasmid is transferred into the plant's cells. Once there, the plasmid integrates into the genome of the plant and activates. The bacteria are natural genetic engineers.

Genetic remnants can be left behind whenever the bacteria does this trick and nowadays we can do genome sequencing to find such remnants. Kyndt et al found remnants of this process in sweet-potatoes (Ipomea batatas). In particular, they found such a fragment inserted into an intron of an F-box gene in the sweet-potato genome. Interestingly, this interruption is found in all domesticated sweet-potatoes they examined and not in wild related species.

The insertion contains multiple complete genes and results in the interruption of the F-box gene. F-box genes are generally involved in protein degradation and in plants they're involved in the regulation of development during growth. It isn't clear that the insertion they found results in a change in the development of the plant associated with domestication, however. They are still working on this.

Oh yes, did I mention they found this fragment in all samples they examined of domesticated sweet-potatoes? This means that every single sweet-potato is a transgenic organism, a GMO. We didn't make it a GMO, but there is no way around it, every sweet-potato is a GMO.

Every sweet-potato is a GMO.

Are you against GMOs? Then don't eat any more sweet-potatoes. Are you actually against the business practices of Monsanto surrounding their GMO and herbicide products? Then rail against those business practices instead of the red herring that GMOs are in the overall story.

References:

Agrobacterium: en.wikipedia.org/wiki/Agrobacterium
Kyndt et al, 2015: m.pnas.org/content/early/2015/04/14/1419685112.full.pdf
F-box genes: en.wikipedia.org/wiki/F-box_protein
Red herring: en.wikipedia.org/wiki/Red_herring

Monday, March 9, 2015

Convergence on the Seaside

Cakile maritima flowers.

I found this plant growing on the beach on a trip to southern California two years ago. The four-petaled flower and shape of the seed pods told me it was in the family Brassicacea, like the wild radishes which are common in the region. The thick and succulent leaves, however, indicated this plant was unlike any plant in the family I had seen before. I collected a few seed pods, hoping to later identify the plant.

After periodic internet searches over the last two years, whenever I found myself thinking about the plant, I finally found an image of a flower with the right shape and color that also grows in beach habitats above the high-water line. I've identified the plant as Cakile maritima (European Sea-Rocket). It and the related C. edentula (American Sea-Rocket) and C. lanceolata (Coastal Sea-Rocket) have small seed pods which contain one or two seeds and are dispersed by floating in water. The pods and leaves differ in shape between the species, but they are otherwise very similar.

C. maritima seed pods.

The species in this genus are generally described as edible, with leaves tasting spicy like horseradish. The plant I found had leaves which tasted mostly sweet. This may be just because I chose young leaves to taste, or I might have lucked onto a plant that was mild instead of hot. Hopefully the seeds I've stored will germinate so I can find out. Either way, I see it as an interesting plant to develop for the salad garden.

Sea-Rocket is commonly described as edible, but it doesn't seem it was ever a major crop. I've found one reference to it being grown in a garden in 1596-1599, but it isn't clear if was grown for vegetable or botanical use.

Another interesting beach-side plant in the Brassicaceae is Crambe maritima (Sea-Kale). Both plants have succulent leaves and dry fruit that effectively float and disperse their seeds. I find interesting that the two species evolved convergently from related ancestors to similar forms in the shared environment of European coastlines.

Sea-Kale appears to have been commercially harvested in Roman times and was cultivated in Europe from around the 1600s, but went out of fashion around the time of WWII.

References:

Cakile maritima (Sea-Rocket)

en.wikipedia.org/wiki/Cakile_maritima

Biology of: onlinelibrary.wiley.com/doi/10.1111/j.1365-2745.2006.01131.x/full
1596-1599 garden: books.google.com/books?id=nmwZAAAAYAAJ&pg=PA28#v=onepage

Crambe maritima (Sea-Kale)

Thursday, February 12, 2015

The Case of the Marvelous Meiosis

1. Meiosis in male (A) and female (B).

The typical story of meiosis is described in detail in many a biology textbook. It all starts with a diploid somatic cell. The chromosomes duplicate and homologs align along the cell's mid-line. The aligned chromosome doublets crossover and then the doublets are divided into two new cells (Meiosis I). The chromosome doublets align along the mid-lines and the new cells divide again (Meiosis II) to produce the final gametes. This model well matches the process of spermatogenesis (Fig 1A), which was used as a model to study and understand the process. Oogenesis follows basically the same process, except that each division is asymmetric. The result is one large gamete (Fig 1B) and two or three non-viable cell fragments with the extra chromosomes.

2. Meiosis in male (A) and female (B) Caninae group roses.

Roses in the group Caninae (Dog Roses) do a peculiar version of the process. The basic example is tetraploid, but produces haploid male (Fig 2A) and triploid female (Fig 2B) gametes. During meiosis I, two homologs for each chromosome align to form a bivalent and the rest remain as monovalents. The monovalents are lost during spermatogenesis, but retained during oogenesis. This system is referred to as "permanent odd polyploidy". It even works with extra uneven chromosome copies. The extras form monovalents and are discarded or retained just like the red and blue chromosomes in Figure 2. This system allows fertility to be maintained even with odd chromosome counts that would normally make a plant sterile.

I came across this peculiar variant of meiosis while researching what complications might develop in a cross between Rosa pomifera (4n, group Caninae) and R. rugosa (2n). Both parent species have relatively large fruit. My initial plan was to hybridize the two species, generating at least one F1 plant, then allow them to self and screen many F2 progeny plants for increased fruit size.

That the two roses are not very closely related and both species have numerous smaller-fruited relatives suggests their large fruit was evolved separately. This is useful for a breeding project as it means that different mutations accumulated as each plant developed large fruit. Those separate mutations can possibly be recombined via hybridization to generate a progeny plant with even larger fruit.

I expect the project of domesticating roses as [more of] a fruit will take decades. It should be an amusing hobby and I expect to have enough time left to see some nice results.

References:

Meiosis: en.wikipedia.org/wiki/Meiosis
Rose groups: en.wikipedia.org/wiki/List_of_Rosa_species
Dog rose meiosis:

Thursday, January 8, 2015

Weedy plant domestication

Most of our garden vegetables and crop plants started out as weedy plants. Part of the evolutionary syndrome of being a 'weedy' species is being r-selected ("r" for reproduction), meaning the species invests in producing as many offspring as possible instead of defending any one life that much. The opposite reproductive strategy is referred to as K-selected ("K" for… well, I have no idea), meaning a species invests a great deal in each offspring to help ensure they have a high chance of survival.

In the context of plants, this means that weedy plants tend to not be spiny, tough, or poisonous... In short, weedy plants tend to be more edible for a non-specialist vegetarian like us humans.

Since I was a child, I've liked the idea of domesticating weedy plants. I have several projects in mind, but have only taken the earliest steps of gathering seeds for some plants I find interesting (Arctium lappa, Carduus nutans, Lepdium virginicum, Leucanthemum vulgar, Malvaviscus drummondii, Oenothera biennis, Thlaspi arvense).

The internet is a wonderful thing in that it lets one find others who have similar interests, no matter how esoteric.

The left half of the image is a botanical plate for Plantago major. It is a common yard side weed native to Europe and Asia. It is easily confused with the related native species Plantago rugelii, which is equally weedy and much more common.

The right half of the image is the result of a project by a plant breeder over at Arrowhead Alpines. The variety is named "Purple Perversion". If you order the plant, it will probably spread its genes widely - contaminating the Plantago population already growing in your yard with genetics for interesting colors and textures. (Some other varieties can be found at Plant World Seeds.)

Plantago species have edible leaves that are rich in B vitamins, which gives them a savory taste reminiscent of mushrooms. Some further selection, perhaps with mutation breeding, could transition this plant from a yard weed to a prime garden vegetable. As a domestication project, this plant is already partly done, so I could imagine making significant progress with it.

References:

Plantago major: www.minnesotawildflowers.info/flower/common-plantain
Plantago rugelii: www.minnesotawildflowers.info/flower/rugels-plantain
Purple Perversion: www.arrowheadalpines.com/shop/index.php?main_page=product_info&cPath=65_112&products_id=6909
Other varieties: www.plant-world-seeds.com/store/flower_seed_categories/PLANTAGO_SEEDS
r and K selection: www.bio.miami.edu/tom/courses/bil160/bil160goods/16_rKselection.html

Saturday, December 27, 2014

Mystery Plant ID Found!

1. omnilexica.com/?q=silphium

A little over a year ago, I was involved in a wedding party and we were walking through a park to a site for some of the arranged photographs. Along the walk, we crossed a stream and there I came across an interesting plant.

The plant was done flowering, but the seed heads retained a nice green color and had the lovely geometry seen in image #1. I picked a sample of the plant, using the pocket-knife I almost always carry (largely for such purposes as this).

Neither myself, my mother, nor my aunt were able to identify the plant. Now this was getting interesting, as my mother and aunt have a long history of gardening and interest in wildflowers. My aunt noted the material had the scent of sunflowers, but this only helped identify it to the family level, which the structure itself had already provided. I tucked the sample into my pocket, hoping to keep it intact until I could identify it at some later time. On returning home, I consulted the field guides I owned. I had no luck, since they all seem to focus on the most charismatic aspect of the wildflowers… usually, the flowers themselves.

As the plant material dried, I realized that I had collected very mature looking seeds of this unknown plant. I cleaned the seeds and stored them in a vial, hoping to identify them when I later had the chance to grow plants from them. Part of the motivation was also because I thought that the green seed heads would make a nice display in a vase, so I could use the plant as part of my home flower cutting garden.

2. diggingdog.com/pages2/plantpages.php/P-1403

…a year passes…

I am in the final stages of completing my PhD thesis and found my mind wandering. I was reading about the efforts to breed perennial versions of annual crops and to domesticate new perennial crops from wild plants. While looking through a document on the efforts to generate perennial seed crops, I saw a dried plant specimen of Silphium integrifolium (Deam's Rosinweed) and it struck a memory. A quick web-search later and I found an image of exactly what I discovered on the creekside. However, there are several potential species in the genus Silphium that live in the area and have the memorable seed heads, so it will still take growing the seeds I saved to identify the plant down to the species level.

The plant was being studied for its domestication potential as a new seed crop. I still think it would be a worthwhile project to domesticate it as green material for florist use. Domestication of a single plant species can easily go in multiple directions at once, as the plethora of cabbage/broccoli/etc. plants indicate.

Now that I know what the plant looks like and that it will produce some really nice flowers (image #2), I can better plan for where the plant will go in my garden next year.

References: