Cool Research – Page 2 – The Garden Professors™

Love notes of genetics and physiology for Valentine’s Day

A St. Valentine meme compliments of my "friend" the self-styled Rev. Apostle, and Bishop to the Stars, Joel L. Watts. — A St. Valentine meme compliments of my “friend” the self-styled Rev. Apostle, and Bishop to the Stars, Joel L. Watts.

Ahhh….’Tis the time of year when we celebrate romantic love in homage to a 3rd Century priest who came up a head short for performing unsanctioned Christian weddings. (It is also of note that St. Valentine, or Valentinius as his friends called him, is the patron saint of bee keepers but, strangely, not of birds, flowers, or trees).

In celebration, many suitors, partners, spouses, fling-seekers, and woo-wishers will flock to florists, grocery floral counters, and even gas stations to purchase flowers, namely roses, that have likewise been beheaded.

Those roses, with all of their tightly wound petals, look nothing wild-type roses. Modern roses are the product of many centuries of breeding that started independently in China and the Mediterranean region.

So if the wild-type rose has a single row of five petals, how do breeders get all of those extra petals? They can just come from nowhere, you know.

The simple answer is that tissue that turns into stamens in the wild-type flower are converted to petal tissue. While early (and even contemporary) plant breeders may not understand the mechanism responsible for the doubling (gene expression), research is showing that the same gene is responsible for the doubling in both the Chinese and Mediterranean set of species/subspecies.

In a nutshell, what happens is that the different regions of the flower – sepals, petals, stamens, carpel – develop in response to the expression of a set of genes. It isn’t just the genes acting alone, though; it is their interaction in the tissues that makes the difference. These genes are grouped by the floral part they affect and are grouped as A-Function, B-Function, C-Function, and E-Function.

If you want to learn a whole lot more about it than I can ‘splain (it has been a few years since my last plant physiology class), this paper thoroughly explains the gene expression and evolution of the flower. Their figure depicting the flower model is informative, yet simple. I’ve included it (and its accompanying caption) below.

The ABCE model of floral organ identity. Sepals are produced where A function acts alone, petals where A and B functions overlap, stamens where B and C functions combine, and carpels where C function acts alone. In the eudicot genetic model Arabidopsis thaliana, APETALA1 (AP1) and APETALA2 (AP2) are the A-function genes, APETALA3 (AP3) and PISTILLATA (PI) together specify B function, C function is specified by AGAMOUS (AG), and multiple SEPALLATA genes provide E function. http://www.pnas.org/content/107/52/22570

In the paper “Tinkering with the C-Function: A Molecular Frame for the Selection of Double Flowers in Cultivated Roses” researchers show that in lines from both regions of the world produced double flowers as a result in a reduction of expression of the C-Function gene AGAMOUS (RhAG) leads to double flowers. In Arabidopsis (every plant lab bench jockey’s favorite model plant), this reduction shifts expression of the A-Function genes toward the center of the plant, turning stamens into petals and carpels into sepals.

Now, one question I get from time to time is “why don’t these roses smell like the old-fashioned roses?” One answer is that as we breed for looks, we are breeding out genes responsible for scent oil production. So Shakespeare was actually wrong when he said that “a rose by any other name would smell as sweet.” That isn’t true these days.

So, I wish you a perfectly lovely Valentine’s Day, no matter how you celebrate. Just remember to whisper sweet nothings of floral gene expressions in your sweetheart’s ear. And remember to stop and smell the roses – if it is a variety that has a decent scent.

Add one species, get four new ones

Here’s an interesting twist on the whole native, non-native discussion… sometimes the introduction of new species of plants can trigger the evolution of new species of insects! Sometimes, in fact, a whole bunch of them, as is described in the coolest new research paper I’ve read in ages (Actual paper, behind a pay wall) (A brief Summary)

Introduce apples, trigger the evolution of four new species of insect

Basically, there is a fruit fly, Rhagoletis pomonella, native to Eastern North America that lays its eggs on the ripe fruits of native hawthorns. It is part of a whole group of species of flies that each go after a different kind of fruit – blueberries, snowberries and dogwoods each have their own species of closely related fly. When Europeans arrived and introduced non-native apple trees, the hawthorn fly started laying eggs on the apples as well, and got the name of apple maggot. But here’s the crazy bit: The hawthorn flies didn’t just expand their diet, they actually evolved to a new race, a new species in the making, that live exclusively on apples.

These flies have very brief life spans, so the adults must emerge at exactly the right time or there won’t be ripe fruit to lay their eggs on. But apples and hawthorns ripen nearly a month apart, so the apple targeting flies have evolved to emerge several weeks earlier than the original hawthorn flies. In addition to diverging in time of emergence, the two types of flies have changed their preferences in smells. The original fly is attracted to the smell of hawthorns, and avoids the smell of apples, while the new flies show the exact opposite behavior, each homing in on their target host, be it new or old.

The final piece of these two types of flies becoming two different species is that they each now mate only on the fruit of their tree of choice. This is important, because now the apple and hawthorn flies don’t interbreed due to their preference of mating location, and being a reproductively isolated group is the most commonly accepted definition of a species. Now the two types of flies will continue to diverge, as the lack of interbreeding means more and more genetic differences between the two populations will build up over time.
All of this is very cool, and has been long understood. Here’s the EVEN COOLER part from this new research: The divergence of one kind of fruit fly into two is cascading through the ecosystem. There are three species of parasitioid wasps that lay their eggs on the hawthorn fruit fly that have diverge into new forms that specialize in the new apple fruit fly. Just like the fruit flies, the timing of their life cycle, their preference and avoidance of the smell of the ripe fruit, and their mating habits have shifted to create different apple and hawthorn specific races. So where there was one fruit fly and three wasps, the introduction of the European apple has lead to the evolution of one additional fruit fly, and three new wasps.

I’m not sure what import this has, if any, in the ever raging native-versus-exotic debate in horticulture, but it sure is cool – the evolution of new species happening right before our eyes.

Joseph Tychonievich

Ray’s 2015 Tomatoes

I thought I’d share some of the new varieties of tomatoes I’m growing this year, along with some old favorites.

First up is a picture of a new variety from Dr. Harry Klee’s research at the U. of Florida called Garden Gem, along with Blush from Artisan Seeds.

Garden Gem is a new hybrid, poised to take the fresh market grocery store tomatoes on. Same disease resistance, same shipping quality, but with much improved flavor. Dr. Klee describes the research at his site:

The first step in a flavor improvement program starts with a simple question: what do people like and what’s in the varieties that people do like? In order to answer this question, we took a giant step back to “heirloom” tomatoes.

Blush has been around for a few years, an open pollinated variety with a great history of breeding, since 8 year old Alex was instrumental in choosing its parent lines.

The year that the cross that created Blush was made, Alex participated in setting up crosses for our annual winter crossing list. He chose 3 of the 19 crosses to be made that year, after the other 16 had been established (by a PhD-holding plant breeder with big plans). The striking outcome is that about 90% of the value from that year came from Alex’s 3 crosses. The progeny from his crosses continue to permeate most everything we are doing.

Both have something in common in that one of the progenitors for each is a variety called Maglia Rosa.

Note also the meatiness of Garden Gem … I think it will make a great all-purpose variety for the home gardener for canning and sauces, as well as fresh eating.

Another aspect, which you can’t tell very well from the picture of Garden Gem, is the faint yellow striping in the skin, and some later fruits that have a hint of a nipple on the blossom end.

GardenGemGreenTiger — Top Garden Gem Next Maglia Rosa Bottom Green Tiger

Next up, another Garden Gem, followed by Maglia Rosa, and then Green Tiger. See hints of vestigal “nipple” alluded to earlier in the Garden Gem.

Cute little feller … a Currant Tomato. Actually, a different, but very close relative, and source of much research and study, since it still grows wild in the Andean mountains … PITA to pick, but great “conversation piece” when used as a garnish. Solanum pimpinellifolium

We grew these as part of a variety trial a few years back … more for the novelty. But when we did a Brix test that year, it was the highest recorded.

A little odd, since the flavor is not in the least “sweet” … coulda been just more concentrated. Dunno, really.

AuntRubyGermanGreen — Aunt Ruby’s German Green Heirloom

Aunt Ruby’s German Green. One of my long term favorites. It’s a more tangy than sweet heirloom variety that stays green when ripe.

Green Zebra … an open pollinated variety bred by Tom Wagner and introduced in 1983 according to Wikipedia.

Green when ripe, and with yellow striping. Dunno why most of mine this year are exhibiting a lobed shape, rather than perfectly round.

I may have to buy new seeds next year.

Another hybrid from the research lab of Dr. Harry Klee of the University of Florida. This one is named Garden Treasure.

I don’t have any information about its progenitors, like its companion Garden Gem.

Beautiful, baseball-sized fruit. Very slight indication of green shoulders, and with the same faint yellow stripe as Garden Gem. Also a heavy fruit, very meaty.

And very good flavor. Pretty good balance between tart and sweet. I can see these being popular with fresh market growers.

I sourced the seeds from Dr. Klee’s efforts by making a small donation to his research program at the University of Florida. The idea was brought to my attention by his colleague, Dr. Kevin Folta in this blog post.

We can look forward to new, satisfying varieties that merge the best of production traits with the historical successes that delighted the senses. These are new heirlooms, and they open an exciting peek of what is coming in plant genetic improvement.

Here are more details of the story and the individual varieties! I hope you order some seeds and give your feedback to Dr. Klee so he can build your ideas into the future of tomatoes!

I often complained about the flavorless red things that you find in grocery stores, so here was a way to support researchers working to overcome that.

And Dr. Klee is not alone. Rutgers University went about restoring the old fresh market hybrid varieties that gave “Jersey Tomatoes” their deserved reputation.

Read about Ramapo, Moreton, and a processing tomato at the Rutgers site Rediscovering the Jersey Tomato .

And there are other research programs at Purdue, University of Michigan and Israel conducting similar efforts. No doubt there are others.

The future of good tasting grocery store, and fresh market tomatoes seems bright.

Scientific Beekeeping

Honey bee (Apis mellifera), Courtesy of Charles Sharp at Wikimedia Commons

When I first moved to the country in the late nineties, one of the first things I wanted to do (after establishing several vegetable gardens to indulge my tomato obsession) was to become a beekeeper.

So I took a six week course sponsored by West Virginia University, read the full documentation available from the University of Maryland and Penn State as well as back issues of beekeeping magazines, and checked with some hobby beekeepers in the area.

Unfortunately, at that time, honeybees were being devastated by an invasive species … the Varroa mite (Varroa destructor), and the amount of effort needed to keep colonies free from them discouraged me, and the message I was getting from experienced hobby beekeepers was one of “be prepared”, and “I’m, regretfully, giving it up because of the effort involved.”

Basically … too much work … not something I was willing to commit to.

But I never lost my fascination with them (and other bees and wasps, for that matter.)

Then in 2006, I started hearing about Colony Collapse Disorder, or CCD, and it was while researching it, that I found the site of Randy Oliver, a biologist who also made his living beekeeping.

The site is Scientific Beekeeping.

From his About tab.

I started keeping bees as a hobbyist around 1966, and then went on to get university degrees in biological sciences, specializing in entomology. In 1980 I began to build a migratory beekeeping operation in California, and currently run about 1000 hives with my two sons, from which we make our livings.

In 1993, the varroa mite arrived in California, and after it wiped out my operation for the second time in 1999, I decided to “hit the books” and use my scientific background to learn to fight back.

The site is not a beginner’s “how to”, but a way to share what he has learned with others:

What I try to do in my articles and blogs is to scour scientific papers for practical beekeeping applications, and to sort through the advice, opinion, and conjecture found in the bee magazines and on the Web, taking no positions other than to provide accurate information to Joe Beekeeper.

(If you’ve been following my blog posts here, then you’ll probably recognize the pattern of places that rise quickly in my judgment, as ones I like)

The site has become my “go to” source for all things related to honeybees, and I recommend it to others who want to stay abreast of the subject.

Scientific Beekeeping

Nature’s Poisons

It’s more than a little bit intimidating to be a part of the Garden Professors team, since I have no advanced degrees, and my undergraduate degree is in Mathematics, with no formal training in Botany, Horticulture or Plant Science at all.

I am, however, an avid and active hobby gardener; I read a lot; and I have a life-long love of learning and sharing what I’ve learned with others, which led to a nine-year stint as a county Extension Educator, implementing a county wide mosquito management program for West Nile, with additional responsibilities for pesticide education and consumer horticulture.

So, what I hope to do with my space here on the GP site, is share some of the other blogs that I read on a regular basis … ones I’ve learned to trust for either the expertise, or writing style, or some additional insight into plants or gardening, or issues that arise in gardening circles.

First up this week … Natures Poisons, a blog written by Dr. Justin Brower a forensic toxicologist – that’s someone who is employed CSI-like, to investigate possible crimes related to toxicology.

His blog isn’t directly related to his profession, however … as Dr. Brower explains:

I also like plants and gardening, and seeing how there are thousands of plant based poisons, there’s no shortage of material.

Some things I will write about:

•Nature’s Poisons – all types chemical and biological
•Interesting poisonings – recent and historical
•Old uses of Nature’s Poisons

So he’s a gardener, like me, and the rest of you folks who follow the GPs.

I like the blog, not only for the wit and wisdom, but also because it puts a realistic perspective around the idea of “natural” … something which we gardeners often mistakenly equate with benign.

Plants make chemicals to protect themselves from being eaten, and the science behind that, and our use, and avoidance of them, is fascinating.

To get you started exploring the blog, here’s one of my favorite posts there discussing Horseradish, or Armoracia rusticana

Not only do you learn a lot about glucosinolates, and other chemicals in horseradish, but also a peek into the mind of a scientist.

Back inside the warm confines of the house, I cut off the tops of the horseradish roots, rinse off the dirt under water, and scrub them clean with a wash rag.

The “typical” method of preparing horseradish is to grate or grind the horseradish with an equal amount of water, wait a few minutes for the allyl isothiocyanate to build up to the desired hotness, then quench the reaction with a tablespoon or two of vinegar. Throw in a pinch of salt, and you’re done.

You’re always cautioned to do this in a well ventilated area or outdoors.

But screw that.

One, it’s cold outside, and two, and most importantly, I’m a Scientist.

If you like the blog, you’ll likely also like this book by Amy Stewart … Wicked Plants.

Enjoy!

Walnut warfare

Recently, a question about using black walnut chips for mulch was posted on our Garden Professors Facebook group page. As gardeners know, black walnut has a reputation as a chemical warfare species that will kill anything growing underneath it – a phenomenon called allelopathy. So it’s logical to wonder about the lethality of walnut chip mulches.

To get a good feel for the science behind black walnut’s allelopathic abilities, I was fortunate to find a relatively recent review on the topic (Willis, R.J. 2000. Juglans spp., juglone and allelopathy. Allelopathy Journal 7(1):1-55.). This well-written review includes a fascinating section on the historical background of walnut allelopathy, which was first mentioned in 36 BC by the Roman author Varro. But the science of allelopathy really started less than 100 years ago, when a Virginia researcher noticed the injury caused to tomato plants growing near black walnut (Juglans nigra) in his home garden. Subsequent experiments by him and others suggested that the orangish hydroquinone juglone leaching primarily from leaf litter and hulls.

Source: Wikipedia.

The research results on walnut, juglone, and allelopathy have been nothing if not inconsistent. For every report of toxicity in an exposed species, another report found no effect. In fact, much of the supposed allelopathy might instead be due to walnut’s highly competitive root systems, which could suck up available water and nutrients over a vast expanse of soil.

Source: Flickr user davidburn

There are a number of other factors that help account for ambiguous results:

1) Juglone is not the only secondary metabolite produced by walnut species. They are loaded with a number of untested phenolics, flavonoids, alkaloids, terpenes and other quinones which could have allelopathic activity.
2) Juglone concentrations vary greatly among walnut species. They also have seasonal variability in the same individual.
3) Light conditions, rainfall, soil chemistry, and many other abiotic factors can influence juglone levels.
4) Organic matter and clay particles in soils can bind juglone, reducing its movement within the soil.
5) Microbial activity breaks down juglone.

Carefully controlled laboratory experiments can demonstrate juglone allelopathy to a number of plant species, especially at the seedling stage. However, there is little evidence from landscape level research to suggest that allelopathy is the reason that plants are damaged by being in proximity to walnut trees. In fact, the author of the review study concludes that even though Juglans species provides the best known and most widely accepted example of allelopathy, there is “still is no unambiguous demonstration of its effect” as “no one has as yet demonstrated that juglone is actually taken up by plant roots.”

Source: Wikipedia

Where does this lead us in our discussion of walnut mulch toxicity? Fresh hulls and leaves appear to be the primary source of allelopathy, but not the wood. And even these sources may be quickly neutralized by soil conditions. Therefore, a walnut chip wood mulch should pose no danger at all to landscape plantings.

One tree’s leaves… over 400 kinds of bacteria!

Okay… this bit of research just blew my mind.

Researchers took leaf samples from just ONE tree in Panama, and identified over 400 different kinds of bacteria making their home there. Sampling 57 different tree species, the total number of bacteria types ballooned to over 7,000. You can read more about the study here.

A few trees. A nearly inconceivable number of microorgansims

That’s a lot. I love this kind of research because it just reinforces how LITTLE we know about this world we live in. Our world is filled with a massively diverse microbiome that we know virtually nothing about. Research is ongoing, and hopefully in the coming years we’ll begin to understand more about how these unseen organisms influence the world we live in. I’ll be fascinated to learn more.

In the mean time, any mention of microorganisms in a gardening context instantly raises questions of the efficacy of products containing (supposedly) beneficial fungi and/or bacteria for our soil. The huge, barely understood diversity of bacteria living in every aspect of our world is a good indication of why the research on adding specific microorganisms to soil generally show no impact, or only an impact in certain specific circumstances. This stuff is complex, and we’re just barely beginning to learn about it. Hopefully in the future we’ll begin to learn how to manipulate the microorganisms that live with our plants, but I wouldn’t expect it to happen over night. Right now, I’m just following the basic rule of adding organic matter to my soil to make a good home for the organisms that live there, and following the research as it opens a window to this unseen world all around us.

How NOT to do an experiment

Over on Facebook I follow some groups who find provocative topics, and today’s “science fair” post was so over the top that I had to share it here.

Here’s the original post. Now the accompanying text about microwaves is whacky enough on its own (and well worth reading), but my primary interest is with the experiment. This exemplifies why there are basic rules for doing science.

This starts out okay – identical pots, the same type of media (I assume), similar sized plants – but then things go downhill:

1) Replicates are important. There is one treatment and one control, meaning that it’s impossible to run any kind of statistical analysis. Ideally between 10-20 replicates of the control and the experimental treatment are used in this kind of experiment. That’s 20-40 plants total.

2) Variable control is important. Plants in a windowsill are subject to light and temperature gradients. That makes analysis more complicated unless one has an extremely long windowsill so that all plants are treated uniformly. And then our researcher prunes the tops of the plants – yet another variable.

3) Consistency between treatments is important. It appears that the pot on the left is wetter than the one on the right – the media is darker. If it’s not draining well – for whatever reason – then you’ll have a hypoxic root environment. Plants don’t like that.

4) Objectivity is important. It’s difficult (impossible, really) for any researcher to be completely objective. Ideally, the pots would have been watered by another person and then labelled in such a way that the person recording the data would have no clue which was which.

I think it’s really important to get kids excited about science. But it’s just as important giving them guidelines about doing science in a way that advances their own understanding about how the world works. Otherwise, it’s just more fodder for the aluminum hat crowd.

Phosphorus and Big Macs

Minnesota, and I were cruising through old pictures and files and getting all sentimental about the cool stuff we used to do. A lot of it was never published just because after we were done with one thing we were just too damn excited to move on to the next. Anyway, one of the neatest experiments that we never wrote up was a phosphorus experiment. Here’s what it looked like to the casual observer.

Now let me explain the neat part to you a little. Inside those boxes, underneath three of the six plants in each container, are vials set up like this – three vials per plant (the black tubes provide air to the vials).

Each plant had one root placed into each of the three vials – one vial contained 1 ppm phosphorus, one vial contained 10 ppm phosphorus, and one vial contained 30 ppm phosphorus. The tub itself was also filled with one of these three solutions (1, 10, or 30 ppm phosphorus) as seen below.

At the end of the experiment we weighed the roots filling each vial, as well as weighing all of the roots from each plant. Here’s what we found for the individual vials.

As you can see, more phosphorus in a vial meant that the plant would devote more energy to growing roots there – but also notice that the 10 ppm solution has the greatest mass of roots overall. Here’s what we saw when we looked at the total size of all of the roots from plants for the different solutions.

As you can see, the roots from the plants in the 10 ppm solution are the largest (shoots showed the same trend). So here’s the way I see it (this is the Big Mac part). I love Big Macs. If I see a McDonald’s I want to go in there – I gravitate towards McDonald’s to get Big Macs. But too many Big Macs aren’t good for me. They might even stunt my growth! It’s the same for phosphorus. Roots do grow towards phosphorus (this isn’t technically correct, but it works for my analogy so I’m sticking with it!), but that doesn’t mean that a tremendous amount of phosphorus is actually good for them. In fact, it might even stunt their growth! This could be for a variety of reasons, but most likely because the phosphorus would interfere with the uptake of other elements.

Moss-tacular!

Mosses are soft, green, and tough as nails, as shown in a recent article in the Proceedings of the National Academy of Science (prestigious, high impact journal with a rather unfortunate acronym).

Dr. Catherine La Farge and associates, from the University of Alberta, visited a remote glacier on Ellesmere Island, Nunavut while studying the wild, wide world of arctic bryophyte systematics. Bryophytes are ancient, non-vascular, non-flowering plants – mosses and liverworts, mostly.

Long story short, they harvested bits of moss that had been trapped in ice for about 400 years and were now exposed. Several species were collected, taken back to the lab, ground up, placed on growing media in a growth chamber, and they soon had mosses galore.

This is fascinating on several levels, as pointed out by the authors. One is the power of totipotency – the ability of a cell to “de-differentiate into a meristematic state that can then reprogram the cell for development of the organism” a la stem cells. Another is the mosses’ ability to “shut down” when dry and “revive when conditions are favorable” (like not frozen in ice for 400 years?!)

The article also graphs the disturbingly accelerating rate of retreat of the Teardrop Glacier, where the mosses were collected. Aargh. The window of favorable conditions may not be open long for these little wonders.