Tuesday, March 29, 2016

Mutation Breeding

The natural genetic diversity found in a crop species was formed over long periods of time by the slow accumulation of mutations in different lineages. We can simulate this process, in shorter time-frames, by dramatically increasing the mutation rate. This can be done by exposing the limited germplasm we have to ionizing radiation (such as X-rays) or any of the many chemicals that damage or modify DNA, thus causing mutations.

"Taihei" (center) and mutants (ring).
Adapted from fig2 on p259 at [link]
and image at [link].
Once we have this newly-made genetic diversity, we can then select towards whatever our goals are.  (Well, we can if some of those mutants happen to be of the sort we find interesting.) Mutation breeding was used to generate the diversity of colors in chrysanthemum seen at right. Another such project is responsible for the intensely red grapefruit types we've gotten used to.

Really, mutation breeding has been used to improve crops in all sorts of ways.

X-rays and Gamma-rays are extremely energetic types of light. They're so energetic that they break DNA when they make a direct hit. When used for mutagenesis, they tear chromosomes apart. Cells can heal this damage, but errors (such as mutations and chromosomal rearrangements) are often introduced in the process. They're relatively easy to generate (even for a relative amateur), but they're difficult to handle. They'll pass through almost anything. It takes heavy lead shielding to keep them contained.

High-energy particle beams (think neutrons or electrons) wreak havoc to DNA like X-rays. With advances in technology, such particle beams may eventually be easier to come by. However, for now, they are limited to research institutions with much larger budgets than mine.

Lots of chemicals can damage DNA and hence cause mutations. Ethyl methanesulfonate (EMS) is commonly used because it is relatively easy to handle (including neutralization for disposal) and effective in generating mutations. The problem with mutagenic chemicals is... well, that they're mutagenic. Things being mutagenic in the lab often translates to them being carcinogenic (cancer causing) in real life. I don't feel like mutating today. Do you?

If I wanted to do some mutation breeding in my home lab/garden, I would want a way to make mutations that I could turn on and off. It is feasible to build a device to generate X-rays (with some intensive electrical engineering), but ideally I'd want something that would only impact what was in a very small space.

Ultraviolet (UV) light causes mutations. (That is essentially what a sun-burn is, after all.) UV-C in particular is referred to as germicidal-UV because it causes large numbers of DNA breaks, resulting in the destruction of chromosomes and death of cells. This germicidal-UV is used to sterilize surfaces/water/etc. in various situations in the lab, hospital, or restaurant. All it takes to generate UV-C is some slightly fancy fluorescent bulbs. Since these can be turned on and off with a switch and the fancy light they produce can easily be contained in a box, this seems like it might be a way to go.

What isn't clear is if UV-C light can be effectively used to induce mutations in seeds. UV-C is readily absorbed by organic materials, so large doses will be probably be needed to impact the embryo protected within any but the smallest of seeds. There seems to be very little research available on this topic, so I'll have to do some experimenting.


Tuesday, March 22, 2016

Making my own Carrots 4

I've been breeding my own carrots over the last few years. Because carrots have a biennial life-style (growing roots the first year and flowering the second), it takes an extended time to see any results of your work. My main goal has been to breed up a locally-adapted mix of carrots enriched with red and purple shades.

The basic outline for the project:
  • [2013] Grow mixed varieties of carrots, including as many intensely colored forms as can find. Select roots for diverse color and vigor.
  • [2014] Roots selected for survival in fridge. Grow final selections for flowering; allow open crossing; save seed.
  • [2015] Plant seed densely. Select for apparent F1 hybrids, vigorous roots with colors intermediate between parent types.
  • [2016] Roots selected for survival in fridge. Grow final selections for flowering; allow open crossing; save seed.
  • [2017] Grow (F2) carrots, eat carrots, enjoy life. Make selections.
  • [2018] Grow selections to flowering.
  • Cycle the steps for the last two years until project is 'complete'.

I planted "Atomic Red" carrots into the original mix, but at the end of the first growing season I had no roots with the pretty lycopene-red color of the variety. I also planted "Cosmic Purple" carrots, which have a thin layer of anthocyanin-purple skin over a more typical orange core (giving an overall purplish look), didn't do well in my garden and survived winter storage poorly. "Solar Yellow" and "Lunar White" carrots did very well in the garden and in storage. Orange "Bambino" carrots also did reasonably well.

My first parental generation of carrots was 3 "Solar Yellow", 3 "Lunar White", 4 "Cosmic Purple", 1 "Bambino", and 1 "Purple Haze" (I think. I picked it up from a farmer's market). Two or three of the "Cosmic Purple" plants decided not to bloom, so the final population was heavier on genetics for white and yellow than I had originally planned.

1. White and yellow mess.
I didn't take any useful photos of the next generation plants during the growing season. The planting grew stridently and produced some really large roots, along with many smaller ones. We didn't thin the planting sufficiently, but we got way more mass of carrots than we could eat. (Nearing the end of March now, I'm still giving carrots to friends.) This first generation from saved seed ended up being mostly various yellow and white shades, but there were enough colorful roots to keep the project moving forward.

2. Purple blush hybrids.
Several of the roots that survived storage into 2016 are obviously hybrids. Three large roots had "Cosmic Purple" as a parent, with "Solar Yellow" or "Lunar White" being the other parent. These roots (in image 2) are pale in color, with a blush of anthocyanin-purple covering the surface. I was struck by how pretty these roots were when I first pulled them out of the ground.

3. Orange/yellow hybrid.
One large root has a yellow core and an orange medulla (at left in image 3), a combination of colors not found in any of the parent varieties. I suspect this one had "Bambino" and "Solar Yellow" as parents. I only found one root with this color combination.

4. Small hybrids.
Among the smaller roots that appeared to be hybrids, there is a mix of traits. One root appears to have a purple medulla (like "Purple Haze"), but clear/white skin. (The second from the left in bottom of image 4.) One root has a purple skin (like "Cosmic Purple"), but has white flesh. (The left in top and bottom of image 4, compared to "Purple Haze" at the right end of the top.) A few others have the same purple skin, but have flesh showing a gradient between white and orange. Some of these roots are obviously alive and growing new greens, but for some of the most interesting ones it remains unclear if they will be able to contribute genetics to the next generation.

5. Preparing for growth.
I've put all the hybrids in water and under light. I hope that some of the more interesting hybrids wake up and show some new green growth.

The reason I'm so focused on the obvious hybrids is because by virtue of them being hybrids, they're heterozygous for genes involved in the formation of interesting colors. In the next generation of seeds produced from crossing these plants, there will be all sorts of interesting segregants. What this means to non-biologists is that the next generation of carrots will include both very light and very dark colored specimens.


Tuesday, March 15, 2016

From Weeds to Trees and Back Again (and Again)

In a post a few weeks ago, I discussed the evolution of trees and gave a few examples illustrating how simple it is (evolutionarily) to transition from a tree to a weed or back. "Evolutionary time" is generally interpreted to mean "a very long time" and probably "a long time ago". Most of the interesting evolutionary transitions people think about took place long in the past, so these interpretations aren't entirely without cause.

However, evolution definitely happens over very short time frames, we just have to pay attention for long enough to notice it. The image at right is a composite of a the flowers from a bunch of different individual specimens of the California Wild Radish. This population is derived from hybridization between feral Garden Radish (Raphanus sativus) and wild Jointed Charlock (Raphanus raphanistrum) in the central valley of California.

During the process of forming this hybrid population, the ancestral species were absorbed and eradicated. (Well...  garden radishes still exist just fine, but they're not actively reproducing in the wild of California any more.) The population is full of plants with all sorts of lovely shades of color (including nice combinations with both pink and yellow pigment) because the genetics of the population is still sorting itself out.

One specific plant caught my interest. Its flowers were pretty, but didn't stand out from the many others I'd already seen that day. What did stand out... was that this plant was a woody shrub which has been growing for several years. Both R. sativus and R. raphanistrum (the parent species) are annual weedy plants.

How long did it take for this [small] tree to have evolved from the weedy ancestors? The weedy parents merged together over just an estimated hundred years. So, it took something less than a hundred years for an albeit small tree to have evolved from its herbaceous weedy ancestors. I think that's a pretty quick transition.

Almost every reference I can find talking about the California Wild Radish only talk about herbaceous weedy forms. At best, there is the occasional reference to some plants being short-lived perennials. I haven't found any descriptions of woody perennial California Wild Radish plants growing as shrubs. The next time I visit this part of the country, I hope to spend some time looking for more specimens like this. If I'm lucky, I'll be able to collect some seeds and then grow out such a plant for a more detailed examination in the lab.


Tuesday, March 8, 2016

An Early Spring

I found a few daffodils coming up the other day. The plants are in an exposed location, so they've been experiencing the full brunt of our southern Minnesota winter. The first emergence of daffodils signals the official start of spring (at least from the perspective of daffodil biology).

This year I first noticed the sprouts on 29-Feb-2016. Daffodils emerge by the end of February in the UK, which has far milder winters than we are used to in southern Minnesota. I haven't been able to find records for local daffodil emergence, but given how warm it has been getting, I would be very surprised if this was within the range of normal emergence dates for around here.


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.