// Twitter Cards // Prexisting Head The Biologist Is In: February 2014

Wednesday, February 26, 2014

The Trouble with Seeds (1/3)

For someone interested in breeding plants, that some plants often don't produce seeds can be a major barrier. A breeder would be limited to looking for selectable mutations, rather than using the more general mixing and segregation of genetics to increase crop diversity.

Many of our common vegetables, fruits, and landscape plants are traditionally propagated by clonal divisions. In some cases (apples, pears, etc.) the complex genetic diversity of the crop means that every seedling would produce a distinct plant. The market demands for consistent production then encourage growers to clone the plants. In other cases, the clonal tradition is enforced by the plants themselves due to their inability to produce seeds. (I'll later discuss a third category of plants which have such long life-cycles that breeding projects become difficult to undertake.)

Researchers have figured out tricks to get seed and allow breeding to be done with plants that might otherwise prefer not to.

The Trouble with Seeds (1/3): Garlic, Horseradish, Potato Onion, Walking Onion, and Banana.
The Trouble with Seeds (2/3): Pineapple, Lily of the Valley, Potato, and Sweet Potato.
The Trouble with Seeds (3/3): Babington's Leek, Crosnes, and Bur Oak.

Most of this post is an accumulation of information from other sources (in colored quotes below) about how to get seeds from these crops. I've also included my thoughts and experiences where I felt something needed to be clarified or extended.

How to get garlic (Allium sativum) to set seed; notes on growing.

[1] "Most of our seed production is done with severed scapes kept in water rather than by leaving the whole plant in the ground."

"Garlic cultivars having flowers with purple anthers are much more likely to be male fertile and to produce seed than those with yellow anthers."

"Garlic umbels have both bulbils for asexual reproduction and flowers for sexual reproduction. Bulbils and flowers compete for the plant's resources. With certain exceptions, if the plant is left to its own the bulbils win and the flowers wither and die before they can produce seed. The bulbils must be removed from the umbel in order to tilt the balance toward seed production."

"Interestingly, in subsequent generations of seed-produced plants the bulbils are often far fewer and may not require removal for successful seed production."

"When the scape becomes nearly straight, the spathe (bract or leaf covering the umbel) should be slit open to examine the umbel's development. As soon as the bulbils have developed they should be removed. Bulbil removal is rather tedious and time consuming, but not particularly difficult after a bit of practice."

"Bulbil removal is a combination of plucking them out with tweezers and rocking them out to dislodge them."

"Because bulbils as well as flowers are usually still developing at the time bulbil removal begins, it is usually necessary to return a week or so after the initial procedure to remove any bulbils that subsequently developed."

"Initial seed yields are typically quite low, but subsequent generations of seed-produced plants yield significantly more seeds, sometimes more than 600 per umbel. Early efforts may be difficult, but later efforts can be exceptionally rewarding."

"Seed from garlic plants that have previously been propagated only by asexual means (cloves, bulbils) have a low germination rate ranging from 10% to an optimistic 35% at best."

"However, studies have shown that subsequent generations of seed-produced plants typically have a much higher germination rate, sometimes as high as 100%."

"First generation seedlings often exhibit a high frequency of unfavorable characteristics, such as stunted growth, deformed leaves, limited root development, and chlorophyll deficiencies. Subsequent generations of seed-produced garlic exhibit increasing vigor and a lower frequency of genetically deficient plants."

"Garlic seed has a period of dormancy and should not be planted immediately after harvest."

"Garlic seeds should be given a bleach soak prior to planting to help protect them from contamination, followed by a cold treatment to shorten dormancy. Soak the garlic seeds in a 1% solution of household bleach (1 teaspoon bleach in 2 cups water) for 20 minutes, rinse the seeds, distribute the seeds on moist paper towels, place the seeds in a plastic sack, and store in a refrigerator for approximately four weeks."

"Like the seed, newly harvested garlic bulbs, including rounds, have a natural period of dormancy. Various things affect dormancy but temperature is a major factor. Warm temperatures lengthen dormancy and cold temperatures shorten dormancy. We do not have a definitive recommendation, but as a starting point we suggest waiting at least a month after harvesting the rounds before replanting them in the fall. We have not found this to be an issue for us, but if necessary temporary storage in the refrigerator could be employed to help break dormancy sooner."

"Once the rounds are planted in the fall the seed-produced garlic is on a normal cycle and can be grown out just as one would with the rest of the garlic crop. Large rounds from vigorous seedlings should yield fully-developed plants and divided bulbs at harvest the following year. You can use these fully-developed plants to produce second generation seeds, though doing so severely diminishes the bulb and thus inhibits or sacrifices replication of what is essentially a new cultivar. You can also opt not to produce second generation seed from these plants and instead harvest the bulbs and cloves at maximum size for planting in the fall. This delays the next generation of seed-produced garlic until the following year, when you can use some plants for producing seed, and some for continued replication of the new cultivar via cloves. There isn’t a right or wrong way in this regard, and you may want to try some both ways. If you have a particularly promising cultivar, however, you may want to asexually replicate and preserve it before using some of its plants for a second generation of seed production."

Garlic can be grown from grocer-bought bulbs, though it can be difficult to break their hormone-induced dormancy. If you want to grow your own garlic, look for bulbs grown by local organic farmers. They are less likely to have been prepared for long-storage and more likely to grow when given sunlight and moisture.

I haven't successfully grown garlic (my last attempt was overgrown by zucchini), but I really like the idea of growing them from seed and exploring the genetic diversity hidden within them.

How to get horseradish (Armoracia rusticana) to set seed.

[1] "Horseradish may be an interspecific hybrid and is generally reported to be sterile. However, viable seed has been produced (14.1-7)"

[2] "I found an article about getting seed from horseradish, but misplaced it. The trick was to girdle the step just above the storage portion of the root, then replant. By cutting off the flow of carbohydrates to the roots, more carbs are reserved to nourish the developing seeds. Similar tricks have been used to get self-seeds from self-incompatible Easter Lilies, Narcissus and Amaryllis (Hippeastrum)."

Although there is limited information available about seeds of this plant, I expect the first generations of seeds would (like garlic) have very low viability. Across successive generations of reproduction by seed, viability should increase as chromosomal abnormalities are filtered out by selection. After several generations, it might be possible to develop a reliably seed-propagated horseradish line.

I'm mostly interested in the potential to improve horseradish as a perennial crop for additional uses from its root. The leaves [3,4] and flowers [5] are edible, having a bitter-pungency when steamed. Shorter or softer leaves might be useful. Larger flower heads, like broccoli, would be interesting. There are lots of potential ways to take this plant that have not been explored.

There is likely to be a lot of interesting genetic diversity hidden in horseradish, as recessive mutations have been accumulating for as long as we have been propagating it clonally. The first few generations of plants produced from seed will likely have some fun surprises.

How to get potato onions (Allium cepa var. aggregatum) to set seed; notes on growing.

[1] "One fall, I left a few Potato Onions in the ground to see if they would survive the winter. They survived just fine. However, these over-wintered Potato Onions all produced flowers the following summer. I had never seen any of my Potato Onions flower before. The over-wintering had triggered their flowering response."

"I planted one row of seeds, and as a control, I planted another row of Potato Onion bulbs. The Potato Onion seeds sprouted and grew, but were not like the control row which had been planted with the original clones."

"I found that these larger onions from seed did exhibit the trait of a long storage life. They easily stored the whole winter and well into the following summer."

"The following spring, I again planted two rows of Potato Onions: one row was from the same bulbs I had grown out for a decade, and the experimental row was planted with some of the very best large bulbs which came from the seeds. Again, the original bulbs were completely uniform. But, the experimental row showed a multiplicity of different traits. Some bulbs grew enormous top growth. Others went immediately to seed. Some developed a nest of small bulbs, others a nest of large bulbs. Some nests had many bulbs, other nests had only three or four bulbs."

During the winter of 2012/2013 I purchased some red onions. One was left alone all winter and when I was planting my garden in the spring, I decided to plant it. Typical onions are considered biennial plants, where the plant spends the first year storing energy in the onion and then uses that energy to flower in the second year. I was looking forward to seeing the flowers and to collecting seeds that I could later grow.

The onion grew nice bluish-green foliage and made a nice presence in my garden…  but it never flowered. When the garden season ended, I found the single onion had divided into three. The three onions were smaller than I could get at the local grocer, but they were larger than any others I had grown in Minnesota.

I set aside the new onions for storage during the winter of 2013/2014. Again, they held up to storage very well. Now that spring is beginning to beckon in the near future, the onions have started to grow small roots. I'll probably grow them in a planter this year, so I can more easily keep an eye on them and note the details of their growth.

This onion seems to be behaving like a potato onion (they multiply and store very well), even though nobody seems to claim they have dark-red potato onions, so I've decided to continue growing them and increase their numbers. Maybe I've accidentally found an onion that has the characteristics needed to be a nice dark-red potato onion.

I'm still hoping to get some seed from this onion. I might have to try leaving a few out in the cold next winter, or store them in a temperature-controlled fridge, to trick them into going to flower. Ideally, I would have several different types of onions in bloom at once so I could get some hybridization going on to work towards an onion well-suited to my garden conditions.

How to get walking onions (Allium cepa x fistulosum) to set seed.

[1] "In A. x proliferum, the parental chromosomes derived from A. fistulosum and A. cepa were unequivocally identified by GISH, proving the hybrid status of the crop."

The walking onion was formerly considered to be A. cepa var. proliferum, but is now known to be an interspecific hybrid between A. cepa (common onion) and A. fistulosum (Welsh onion).

[2] "Walking onions do not form true seed, even though they will get a few blossoms. They grow 'top sets' instead, a cluster of bulbils at the top of the stalk where the seeds would normally be."

This plant is propagated by planting the bulbils produced on the flower stalk. It gets the name "walking onion" because the plant will normally arch over the flower stalk and place the new formed bulbils onto the ground some few feet away, walking across a garden over several years.

Nobody seems to be talking about saving true seed for walking onions. It does produce flowers, but they are starved of nutrients by the adjacent bulbils and wither. There is the potential to generate viable seed by removing the bulbils early like can be done with garlic. Because nobody seems to be talking about doing this, it looks like something I will have to experiment with.

One useful aspect of walking onions is that they are very cold hardy. They have survived several winters in the garden of my parents' Minnesota house without any effort given to protect them. Transferring some of this cold-hardiness to an onion with larger bulbs would be a worthwhile project.

[3] "If I remember right, two growers on this forum have reported obtaining true seeds from Egyptian onions, and successfully growing offspring from them. I think that in both cases A. cepa was flowering nearby."

This suggests that this onion will set seed when a genetically compatible onion is nearby. If the onions are not self-compatible, the population consisting of clones would normally prevent any fertilization. As this type of onion is derived from an inter-species cross, it may accept pollen from more than one species.

How to get bananas (Musa spp.) to set seed.

Normal bananas already set seed without our intervention, but unless you live in the tropics you're unlikely to encounter a normal banana. The bananas common in the stores outside the tropics are the result of a peculiar quirk of chromosomes.

Most banana species can readily hybridize. Some species have two copies of each chromosome (diploid), while others have four copies of each chromosome (tetraploid). If a diploid and tetraploid banana happen to cross, the resulting progeny will have three copies of each chromosome (triploid). Such a triploid banana will grow and mature normally, but will encounter a severe difficulty when it tries to make gametes.

It turns out that our common biology has a very hard time making gametes when the number of each chromosome is not divisible by two. In the case of the banana, a triploid plant will succeed in making a fruit, but it will fail to make any seeds.

Plant breeders get around this quirk by determining how many copies of each chromosome are found in different species/varieties of banana [1,2], then using this knowledge to intentionally create new triploid types that can be screened for useful traits. Our beloved store-bought-banana is a genetic dead end, but this doesn't prevent the generation of new varieties.

I like the idea of a banana that can grow in Minnesota, though I know it is a somewhat unrealistic idea. There are some banana species which can survive in more northern climates [3] and these provide the potential for breeding one that can survive in my Minnesota yard.

Most of the lovely plant diagrams in this post were derived from public-domain images hosted at botanicalillustrations.org. Some other diagrams are public-domain images from the same era that I found via google. I chose the original images which depicted the plants under discussion in the way I appreciated and then subtracted out the yellowed background of the page using my favorite image editor (GIMP)

Thursday, February 20, 2014

Making My Own Carrots

In 2013 I grew a batch of mixed bed (4ft x 6ft) of several carrot varieties, including a range of different colored forms. I had never grown carrots in my current garden, so I didn't know which varieties would work well and which would utterly fail. My main hope was that several types would prosper and I would get lots of mixed carrots to eat over the fall and winter seasons.

I harvested all the carrots during the second snowfall, digging and cleaning every single plant. There were plenty of largish carrots along with lots of small carrots. The brand of carrot culture that I applied (sow thinly and let the plants fight it out, without intervention) was particularly difficult for some varieties. A short, dwarf-rooted type ("Paris Market") almost disappeared in the resulting jungle. The red ("Atomic Red") variety from the Burpee Kaleidoscope mix tasted great, but performed poorly overall. The yellow ("Solar Yellow") and white ("Lunar White") ones from the same mix, on the other hand, did very well. The orange ("Bambino") and purple-skinned orange ("Cosmic Purple") ones from the same mix, came somewhere in between.

I ended up with several pounds of carrots and have been eating them all winter.

A secondary hope was that I would be able to save some of the largest carrots, those that agreed most with my local conditions and gardening style, for seed growing.   Over several years, this would let me develop a locally-adapted carrot variety of my very own.

Carrots are a biennial plant, producing flowers/seeds during their second year.   Since I wasn't confident in my carrots ability to survive in the ground all through the harsh Minnesota winter, I set some aside in the fridge for growing in the spring. For these, I trimmed the greens short, but left the growth point intact. The roots were then trimmed to fit into a quart-sized ziplock bag in the back of my fridge.

At the beginning of February, I checked in on the stored roots. Several had started to grow new shoots, while several others had rotted to mush. The rot took most of the orange ("Bambino") carrots, so it appears that color will be under-represented in the genetics of my developing population.

I decided that it was time to force the remaining roots, in fear of losing more to rot and so they could get an early start on the growing season. (Admittedly, the desire to see some green growth this deep in winter was a major factor in this decision.) I trimmed all the roots to about three inches long and placed them upright in a wide-bottom glass cylinder. I had enough roots such that they would cross-brace each other and remain upright in this container.

I happened to have a deep purple carrot ("Purple Haze", "Purple Dragon", or something) in the fridge, among leftovers from a farmers' market foray before my own carrots were ready… and I like purple, so I trimmed it like the others and added it to the forcing container.

If I am lucky, the roots will bloom early enough to let me grow the resulting seed this year, having been tricked into living their two year life-cycle in one year. If they don't bloom early, I will have had a nice windowsill plant for most of the winter and will have the seeds for next year.

In either scenario, the resulting next generation plants will contain a mix of F1s from the saved varieties. There are very few wild carrots ("Queen Anne's Lace") around where I live, so I shouldn't have any problems with weedy genetics getting mixed into my carrot population.   The next generation, a few years from now, should then show a riotous mix of traits as the various alleles segregate in the F2 progeny.

Part 2: Carrot flowers.
Part 3: Generation 2.

Sunday, February 9, 2014

Genetics of Squash Shape (2/2)

In my first blog post, I examined a small biology puzzle: the classical model of squash shape genetics (at left) didn't seem to match what I was seeing in my own garden.

The classical model involves two genes ('A' and 'B', respectively).   The dominant allele of both genes must be present (A_B_) to produce a disk-shaped squash.   If one gene is present in the dominant form and the other is in the recessive form (A_bb or aaB_), spherical-shaped squash will result.   If only the recessive alleles of both genes are present (aabb), then elongated squash will result.   After some digging, I found this model comes from a 1927 paper by Edmund W. Sinnott in the research journal, The American Naturalist.

This model predicts that crossing a (AABB) PattyPan to a (aabb) Zucchini should result in (AaBb) progeny plants with disc-shaped squash.   The progeny plants I grew, instead each produced intermediate/elongated-fat squash.   I assumed this meant my original PattyPan squash was a hybrid that contained both recessive alleles (AaBb) and so I then calculated the probabilities of producing (aabb) progeny from crossing the potential male parents (PattyPan and Zucchini) to the female parent (PattyPan).   The best probability I calculated was $$p = \frac{1}{16}$$.   I wasn't pleased with this result and decided I needed further data.

The magic of the internet then made its presence known: Ottawa Gardener was forwarded to my original post in a discussion of their recent post.   They had grown Zucchini, PattyPan, and some Pumpkins, then tossed some of the PattyPan squash to their chickens.   The next year when they moved the chicken run, up came a batch of hybrid squash.   Most appeared to be intermediate between the Zucchini and the PattyPan, with a few looking intermediate between the PattyPan and the Pumpkin.   (I've rearranged their photo to make the diagram at left.)

Because there are three potential male parents (and two offspring types), the calculations of probability get somewhat more intricate and I won't go into them here.   The detail I found most interesting was the recreation of the intermediate/elongated-fat shaped squash at the bottom-left.

Upon digging into the research literature further, I found a 1910 paper by R.A. Emerson, again in The American Naturalist.   In this paper, the author describes the result of crossing "White Scallop" (disc) and "Yellow Crookneck" (elongated) squash as being intermediate in shape.   This is contrary to the Sinnott model of shape genetics and is the result that both I and Ottawa Gardener observed in our gardens.

It seems like the Emerson result was never followed up on and the Sinnott result erroneously became the standard model of squash shape genetics that has been used in textbooks ever since.

I'm really happy to know that my garden results are consistent with results from others, but I still need more data.

The simplest model I've come up with requires there to be a third gene (C) that allows the first two genes (A & B) to produce disc-shaped squash.   Sorting out the genetics of a cross involving three genes is much harder than a cross involving one or two genes.   Fortunately, I've got several hundred F2 seeds from the F1 plants I grew.

I plan to grow several F2s this coming year and I've managed to find homes for a few more in others' gardens.   It may take several years of this to collect sufficient data to get an idea of what is going on.

Would you be willing to grow some of my experimental squash seeds, then send me photos/measurements of the fruit that grow?   Get a message to me and we'll work out how to get seeds to you.

Citations and notes :
1. Emerson RA.   The Inheritance of Sizes and Shapes in Plants.   1910, The American Naturalist 44: 739-746.   (https://archive.org/details/jstor-2455667)
• "Yellow Crookneck" x "White Scallop" -> F1 "intermediate".
• This matches the results I found in my garden

2. Sinnott EW.   Inheritance of Fruit Shape in Curcurbita pepo.   1922, Botanical Gazette 74: 95-103.   (https://archive.org/details/jstor-2470204)
• Sphere x Scallop -> F1 disc -> F2 (3 disc):(1 sphere).

3. Sinnott EW.   A Factorial Analysis of Certain Shape Characters in Squash Fruits.   1927, The American Naturalist 61: 333-344. (http://www.jstor.org/discover/10.2307/2456386)
• Sphere(#103) x disc -> F1 disc -> F2 (3 disc):(1 sphere).
• Sphere(#22) x disc -> F1 disc -> F2 (3 disc):(1 spheroid).
• Sphere(#103) x sphere(#22) -> F1 disc -> F2 (9 disc):(6 sphere):(1 elongate).

Part 1