Thursday, January 29, 2015

The Trouble with Seeds (3/3)

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. There's also a third category of plants which have such long life-cycles that breeding projects become prohibitive.

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 Babington's leeks (Allium ampeloprasum var. babingtonii) to set seed.

Many alliums have forms which produce clonal bulbils in the flower head along with some flowers, but generally don't produce any viable seed. Research in garlic (A. sativum) has shown that you can often get seeds to mature if you extract the bulbils from the flower head at an early stage. The bulbils seem to draw nutrients away from the flowers and cause them to age too quickly for seeds to mature. When the bulbils are removed, the few flowers then get sufficient energy to grow and mature seeds. This process will probably work for Babington's leaks, or any other allium which produces bulbils and no seeds.

How to get Crosnes (Stachys affinis) to set seed.
[1] "Stachys palustris performed much better here than S. affinis this year - larger tubers, greater yields, no difference in flavor that I can detect. I've never grown either one before. Both set some seed, which is apparently common for S. palustris but not S. affinis. I wonder if I got some crossing."
If S. palustris shows self-incompatibility, the clonal Crosnes will generally fail to set seed. The plants would then be desperate for usable pollen, even from related species, in order to set seed. If they're crossed, the plants that grow from any of those seeds should be highly homogeneous, but distinct from either parent.

How to get Bur Oak (Quercus macrocarpus) to set seed, when very young.

Bur Oak trees can live for hundreds of years and generally don't start fruiting until they're 35+ years old. The wild trees produce very large acorns that are relatively sweet, requiring minimal processing to use as a food item. Domestication efforts could readily convert the species into a useful nut crop, but the long life cycle means it will generally have to be considered an intergenerational project.

Grafting methods are routinely used to increase fruit production or control the growth of fruit trees. Such grafting methods might also be applied to the Bur Oaks. When a host oak tree goes into bloom, the hormonal signals flowing through its sap will encourage the grafted Bur Oak to also go into bloom. There are numerous shrub oak species (Q. cornelius-mulleriQ. dumosaQ. durataQ. palmeriQ. sadlerianaQ. turbinellaQ. vaccinifolia, or Q. wislizeni) that mature much younger than the Bur Oak. One of these might be ideal as a host for grafted seedlings. The shorter life of the host oak would mean that you could plant as many as you need to host whatever number of Bur Oak seedlings you're working with. This process should shorten the 35+ year breeding cycle of the Bur Oak down to 2-3 years, making it a much more reasonable project to take on.

Most of the lovely plant diagrams in this post were derived from public-domain images hosted at 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 did some coloring or color correction using my favorite image editor (GIMP)

Thursday, January 22, 2015

Hybrid Sterility and Speciation

1. Burbank's Fragaria x Rubus.
Luther Burbank (1849-1926) was a widely renown botanist and scientist. He bred numerous interesting plants. He liked to attempt wide crosses; crosses between distantly related species. One of the more unexpected crosses he attempted was the cross between a strawberry (Fragaria spp.) and a raspberry (Rubus spp.) (fig. 1). To the then (and now) commonly held Victorian ideal of plant species, this cross shouldn't have had a chance at all of working. However, the cross appeared to succeeded and fruit developed. The plants that developed from the seeds grew with a combination of characters from the parents, thus showing their hybrid nature. The hybrids flowered abundantly in the second year, but no fruit was ever produced. Burbank found that at most a few seedless drupelets (fruit segments like in a raspberry) would form and so he abandoned the project.

There is a lot that Luther Burbank didn't know about plants. His exuberance for performing crosses and doing selections let him produce some wondrous results, but his lack of knowledge was a limitation.

Chromosomes were discovered in the 1880s, but the process of meiosis wasn't made clear until 1905-1911. The dates suggest it is possible that Burbank was aware of meiosis, even if he wasn't aware of the consequences for his work. Fortunately, such knowledge is now widespread and biologists are well aware of the consequences.

2. Meiosis and failures of meiosis.
Strawberries and raspberries show a diversity of genome sizes, but they all have a basic chromosome count of 7. They species range from diploid with 14 chromosomes to decaploid with 70 chromosomes. An even number of chromosomes is found in all cases, as this is required for the formation of gametes (fig. 2A).

If two species with different chromosome counts are crossed, the resulting hybrid can have an uneven number of chromosomes and will be generally unable to generate gametes (fig. 2B). (Example: 2n x 4n => 3n; this is how seedless watermelons are made.)

If two species with the same number of chromosomes are crossed, but the chromosomes are too unrelated, the resulting hybrid will also fail to generate gametes (fig. 2C). In this case the hybrid will have an even number of chromosomes, but they won't line up during meiosis and the result will be a haploid with an increased basic chromosome count. This can be caused by a high level of structural rearrangements in the chromosomes of strawberries vs. raspberries, even if the genes are otherwise compatible.

Because Burbank performed the cross with whatever strawberry and raspberry plants were convenient and the cytogenetics of the parent plants wasn't examined, either of the above scenarios could be responsible for the hybrid infertility that he saw.

I have one raspberry (Rubus occidentalis, isolated in my yard in Minnesota) and one strawberry (Fragaria vesca, isolated in central Wisconsin) in my collection and I think I will set about crossing them during this year. Both species have been examined in detail and happen to be diploid with 14 chromosomes, so the first incompatibility mechanism isn't a concern.

3. Meiosis after allotetraploidy.
The second incompatibility mechanism can be overcome by inducing tetraploidy in the hybrid. This would be done using Colchicine or Oryzalin, herbicideal compounds that interfere with cell division and result in a doubling of the number of chromosomes in treated tissue. Induction of tetraploidy generally produces one branch that has larger fruit, thicker stems, and other visible features to distinguish it from the original diploid parts of the plant. Because this tetraploid would contain two full copies of genomes from different species, it would be referred to as an allotetraploid.

4. Tragopogon spp. hybrids.
This process has been observed to happen naturally. Three species of Tragopogon (T. dubius, T. porrifolius, and T. pratensis) were introduced into the Pacific northwest region of the USA in the early 1900s from Europe. By the 1950s, scientists realized there were two new species of Tragopogon to be found in the region (T. mirus and T. miscellus). The new species were fertile allotetraploid hybrids between pairs of the introduced species. The hybrid species have even been recreated in the lab. In this case, it appears the allotetraploids came about because the parent species occasionally produce aberrantly diploid gametes which merged to form the fertile allotetraploid. The precise pathway is different than what I expect would be going on with the strawberry/raspberry cross, but it is a wonderful case-study for hybrid speciation.

If everything works out, it will be a few years before I have a fertile strawberry/raspberry cross. I wonder what the fruit would taste like? I'll keep you informed as it goes.


Tuesday, January 13, 2015

Astrobiology : Mars & Isotopic Analysis

Two stable isotopes of carbon are found, carbon-12 (12C) and carbon-13 (13C). Carbon-12 is the vast majority, at 98.89% abundance. Individual samples of carbon from different sources can vary strongly from the general abundance ratio, depending on where they came from.

The reactions of biology tend to prefer the lighter form of carbon, so over time biological sources of carbon tend to become relatively enriched in carbon-12 vs. carbon-13. A consequence of this is that carbon samples from a living source are distinct from carbon samples from a geological source.

We've examined the carbon ratios from many sources here on Earth. We've now also examined the carbon ratios from a few sources on Mars. A study was published in the December 2014 edition of Meteoritics & Planetary Science that discussed the examination of carbon ratios in a recently recovered Martian meteorite called Tissint.

There are significant differences in the carbon pattern between Earth and Mars. I put together the above figure from one in references #1 and #2, to better compare the known carbon ratio differences by sample type.

The carbon ratios found in carbonates on Mars suggest they are of inorganic origin. Those from freshwater or marine sources on Earth have ratios consistent with their known biological origin.

The red data-points are from organic material found in Tissint. They compare very well to the blue data-points from coal here on earth. On both planets, atmospheric carbon is relatively reduced in carbon-12 compared to the organic material. This is pretty good evidence that the organics in the meteorite came from some living thing, just as the organics in coal did.

The carbon could still have come from contamination here on Earth, after the meteorite landed. To test for this, the researchers examined the isotopic ratios of the hydrogen in the sample. Mars is enriched in deuterium relative to Earth and this same enrichment was found in the examined organic material.

This research happens to be the best direct evidence so far for the existence of life on Mars (at some point in the past). This still isn't entirely conclusive physical evidence. For that we will have to go to Mars and either find an unambiguous macro-fossil, or culture some micro-organism from one of the brine-water seeps we've been looking at from space.

I've been convinced that there was in the past (and is most likely today) living organisms on Mars, from theoretical considerations about how life works, and how it must have spread in the early solar system. However, I wasn't really expecting to see any convincing physical evidence any time soon.

  1. Tissent Carbon ratios:
  2. Earth Carbon ratio: 
  3. Mars Carbon ratio:
  4. Organics on Mars:

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.