genetics – 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.

Corny Ancestry

I love growing weird plants, and I’m endlessly fascinated by plant breeding and the extreme transformations humans have made in our crop plants over the history of agriculture.

Which is why growing teosinte, the wild ancestor of corn, was a no brainer. Even before I planted it, comparing the seeds is fascinating. teocornseed

Once growing you can see the similarity. Teosinte is on the left in the picture below, corn on the right.

The most dramatic difference between the two, I think, is the “ear” of teosinte, which is nothing more than a thin sprig of half-a-dozen seeds.

It is amazing to me that native Americans in Southern Mexico, with no knowledge of genetics, were able to transform this grass with a handful of tiny, rock-hard seeds into one of the single most productive crops in the world.

Jumping genes!

This spring, I noticed this striped flower in a stand of feral Hesperis matronis
Stripey flowers! And like almost all striped flower variants, almost certainly caused by transposons, aka jumping genes.

To understand transposons, you can think of genes as instructions. So when making a flower, a plant may be following a gene that says:

MAKE PURPLE PIGMENT

And so it does, and the flower is purple.

You can think of a transposon as a gene that says:

COPY ME!

And so the cell makes a copy of the transposon, and then that copy gets dropped somewhere else in the genome. And sometimes, that new copy of the transposon lands in the middle of a gene that does something important. Like, for example, a gene involved in pigment production. So you get this:

MAKE PUR COPY ME! LE PIGMENT

Which doesn’t make any sense. So now the gene for making the purple pigment doesn’t work. And if that happens in a cell in a flower petal, that part of the flower will be white. And as that cell divides, the new cells resulting from it will also have the transposon in place, making more white cells, producing a white patch or stripe in the flower.

When transposons were first discovered in corn by the great geneticist Barbara McClintock, they were thought to be an oddity, something unusual. As we’ve learned more, it turns out they are ubiquitous. Some 40% of the human genome is thought to be transposons. Usually they are invisible, and have been silenced to prevent their moving around and disrupting other genes. But sometimes they pop up in a flower and make themselves visible, in a beautiful, interesting way.

Joseph Tychonievich

Infographic with a BIG grain of salt

Infographics can be great: They’re bright colorful ways to make sometimes complex concepts visual and easy to understand. Sadly, “easy to understand” does not necessarily equal “accurate” and they can also be extremely misleading.

Take this beautifully made image from National Geographic. It is an older image — first posted back in 2011, but it makes the rounds on social media from time to time, and popped up in my facebook newsfeed a couple days ago.

Look at it! Oh no! We’re loosing all of our vegetable genetic diversity!

Or not. First, it is comparing apples to oranges. This image looks a commercially available varieties in 1903 and compares it to the number of varieties in one specific center for preserving genetic diversity. What happens if we compare the same metric? If you look at the number of varieties in the National Seed Storage Laboratory, that was founded in 1958… so in 1903, at the top of the graph, the number for all these vegetables would be… zero. If you look at the present day, the current umbrella organization for all the US government funded efforts to preserve genetic diversity of crop plants is GRIN, (Germplasm Resources Information Network) and if I do a quick search through that database using the keyword “tomato” I get… 9281 results. That is a pretty overwhelming improvement over 79 in 1983.

And what about commercially available varieties? To use tomato as an example again, in 1903, they found 408 varieties offered commercially. I just added up the varieties listed by just ONE seed company, Baker Creek Seeds, currently lists 287 different varieties of tomatoes. That is just ONE company. I have no doubt that if I added up all the varieties that are offered for sale in the giant pile of seed catalogs I get every spring it would be FAR more than the 408 on offer in 1903.

So… are we losing genetic diversity in our crop plants? Probably. There are lots of traditional varieties and land races that were never available commercially that have do doubt been lost, but to be honest, I think we’ve done a pretty good job at preserving the diversity. And certainly the USDA’s system of gene banks is an incredibly well run, impressive thing that deserves high praise indeed, for not merely preserving vast amounts of important genetic diversity but also working hard to characterize it and make it available to researchers and breeders so it can actually be put to work in the development of new and improved selections to try and feed the world.

So despite how colorful and easy to understand this infographic is, you don’t need to freak out about a massive loss of genetic diversity in our vegetable crops. Save that freaking out for all the wild species that have gone extinct or are about to go extinct thanks to habitat destruction and climate change world wide…

Cross-pollination making you cross?

No, your cucumbers have not hybridized with your melons.

I’ve been fielding different versions of the same question a LOT lately.
Three different people have sent pictures of “cucumelons” telling me they planted cucumbers next to their melons, and now the cucumbers look strange, so they’re concerned that they have cross pollinated with the melons. One person planted what was supposed to be a red raspberry next to their yellow raspberry, but the new plant is producing yellow fruit, so they think that it must be cross pollinating with their yellow plant, causing the fruits to turn yellow. Not to mention similar queries about tomatoes, peppers, and watermelons. It seems like every time a piece of produce turns out looking differently than what people expect, they blame pollen from the plant next to it.

I’m sure the highly educated readers of The Garden Professors know this already, but to clarify, there is a very simple reason why you don’t need to worry about one plant pollinating another plant and changing the quality of your produce UNLESS you are planning on saving seeds to grow for the next year.

When a flower is pollinated and starts developing into a fruit full of seeds, it is only the seeds themselves that combine the genetics of the two parents to develop into something new. Everything else – the flesh of a tomato, or cucumber or melon or raspberry – is produced solely by the mother plant, and the daddy of those seeds inside doesn’t matter a bit. Think about when a woman is pregnant… the identity of the father of the child inside her doesn’t change the character of the skin of her belly.

If you want to save seeds of your plant for next year, it is another matter, and you should be sure to isolate or (better yet) hand pollinate different varieties of the same species from each other to make sure they don’t hybridize unintentionally. You still don’t need to worry about your cucumbers and melons, however – they won’t hybridize by chance in your garden. If a plant doesn’t produce the right colored fruit or flower, most likely it was just mislabeled at the nursery. Grow a strange looking cucumber, chances are it was left on the plant too long. Cucumbers are harvested and eaten when young and immature, leave them too long and they get… strange looking. No need to blame it on the melons next to them.

There IS one exception to this, one common plant in the garden where the source of pollen makes a huge difference in what you harvest: Corn. Corn is the exception because what we’re eating is the seed itself, not the fruit produced by the mother plant surrounding the seed. That’s why if your sweet corn gets a dose of pollen from the field corn the farmer is grown next door, it comes out starchy and not sweet.

It also makes breeding colorful corn for fall decorations REALLY fun… Because when you see a multicolored ears of corn like this from my garden last year:

You can carefully pick out just the seeds showing the colors you like best, say the palest blues and pinks, sow them together the next year, and get something looking like this:

Or plant all the darkest kernels together and get this:

You don’t have to be crazy to work here, but it helps

Recently I spent a week in Oregon working on a Christmas tree genetics project along with my colleagues Chal Landgren( Oregon State University), Gary Chastagner ( Washington State University), and John Frampton (North Carolina State University). The objective of the project is to identify superior seed sources of Turkish fir and Trojan fir for use as Christmas trees around the United States. We refer to the project as the Cooperative Fir Genetic Evaluation or CoFirGE – remember, the most critical step in any experiment is coming up with a catchy acronym. CoFirGE began with a trip by my colleagues to Turkey where they collected seed from 100 fir trees across a range of sites in Turkey

Turkish fir growing in western Oregon

Why are we interested in these species? Both Turkish and Trojan fir are closely related Nordmann fir, which is widely used as a Christmas tree in Europe. These species make wonderful Christmas trees due to their symmetry and needle color. In addition they may be resistant to diseases, particularly Phytophthora root rot, that plague Christmas tree growers from Washington State to North Carolina.

So, what was going on in Oregon? After the seed were collected in Turkey they were sent to Kintigh’s nursery near Eugene, Oregon, where the seed were sown to produce seedling plugs. The next step of the project will be to send the seedlings out to cooperators in five locations (Pacific Northwest, Michigan, North Carolina, Pennsylvania, and Connecticut). This is tree improvement on a grand scale. In each region there will be two test plantings and each planting will include 30 reps of 100 seed sources or 3,000 trees. Multiplied by 5 regions and 2 plantations that’s 30,000 trees total that we will collect data on for the next 8-9 years.

30,000 seedlings ready to be sorted and shipped

Each seedling is individually labeled with a bar code for identification

Sorting into to boxes to send to cooperators around the country

But step one is getting the seedlings from the nursery to the out-planting sites. That means lots of tagging, sorting, and bagging. With help from technicians and students from WSU, OSU and NCSU and staff from Kintigh’s we were able to get all the seedlings sorted and bagged by mid-day on Thursday and start them on their journey to their new homes. Next step: Planting…

News flash – genes don’t explain everything!

Last week dedicated blog follower Ray E. sent me this link to a story in the Smithsonian magazine. It’s a fascinating look at adaptive responses by frog eggs and apparently is causing quite a stir in the evolutionary biology community. Phenotypic plasticity, which is the ability of an organism to modify its appearance or behavior based on environmental cues, is being hailed as a “revolutionary concept in biology.”

I don’t get it.

Anyone who’s studied plants for any length of time knows about this phenomenon. It’s why plants grow taller in the shade than they do in the sun. It’s why leaves inside a tree’s canopy are larger and thinner than those on the outer layer. In fact, it’s that darn phenotypic plasticity that can make data collection so difficult for those of us who do field research. Minimal differences in wind, water, soil chemistry, etc. in a research plot (or a garden, for that matter) are magnified once plants start responding to them.

This leads to one of my pet peeves about the state of biological research over the last few decades. If you look at the research that gets the big grant dollars, it’s either at the smallest scale (like molecular genetics) or the largest (like systems ecology). Those of us who are fascinated with how organisms work are pretty much left to our own devices to fund research. (The exceptions to this rules to a certain extent are human and veterinary medicine.)

While this may seem abstract to most of you, the funding imbalance filters down into the teaching function of colleges and universities. When I was doing my undergraduate and graduate degrees, my university had a bryologist (someone who studies mosses), an algologist (marine and freshwater algae), a botanist who specialized in diatoms, and so on. Most major universities had a reasonable number of faculty with expertise over distinct groups of organisms.

As these faculty retired, they were replaced by new faculty whose value was measured more by potential grant dollars than by replacing the loss of expertise. Thus, we have fewer entomologists or mycologists or even horticulturists, as universities scramble for the federal dollars (and substantial overhead) needed to support their institutions and obtainable by a small and select group of researchers. And university curricula reflect this shift, with the disappearance of distinct programs in botany and horticulture and plant pathology and weed science and crop science, as they are mishmashed into bland and unappealing “plant science” departments. Or worse, simply “biological sciences.”

So it’s no great surprise, I guess, that many evolutionary biologists are amazed at the “revolutionary concept” of phenotypic plasticity. I’m not sure many students – or their professors – spend as much time looking at and learning from organisms as they used to.

Today in Cucurbit News…

Cucumbers are one of the most widely-grown vegetables in the world. Baker Creek Heirloom Seeds (a great place to buy unusual and international veggie seeds) lists 51 varieties from North America, Southeast Asia, China, India, Mexico, and Europe. Dark green ones seem to be in the minority – yellow, white, orange and red skins in shapes round to elongated dominate.

Cukes traditionally have a few nutrients including some Vitamin A from carotenoids and beta carotene, but have never had the reputation as nutritional power house. Watery and gas-inducing, yes.

Researchers with the USDA have recently released a cucumber high in beta carotene. No "frankencuke" this; all the crossing was done by traditionally breeding methods (including bees and self-pollination). Lots and lots of crosses with a warty, round-ish chinese cuke (Cucumis sativus var. xishuangbannanesis) and some standard pickling cukes has resulted in a stable cultivar that has the smoother skin and proper proportions of marketable pickling cucumbers (there are lots of marketing standards associated with most fruits and veggies). But the big news is the orange interior, specifically the endocarp (the jelly-like stuff around the seeds) and the mesocarp (the fleshy part that is the whole point). It’s orange because it’s full of beta carotene (mesocarp is 2.7 micrograms per gram of fresh fruit compared to 0.02 micrograms per gram with a traditional white-fleshed variety. Even more impressive is the jump in endocarp beta carotene – from 0.16 micrograms per gram to 7.5 micrograms per gram). I don’t believe the USDA is going to release this particular line directly to the public, rather they’re offering the genetics (two recessive genes control the beta carotene content) to other breeders. This means other breeders can use it in their own breeding program to bring more nutritional value to their specific lines, at which point varieties will become available to growers/gardeners. Orange tzatziki!!!

from Staub, J.E., P.W. Simon, and H.E. Cuevas. 2011. USDA, ARS EOM 402-10 High β-Carotene Cucumber. HortScience 46:1426-1427.

(Linked, but my guess it won’t work if you don’t have a HortScience subscription or institutional access, sorry)

A word about GMOs from our visiting GP

I gave a talk to a group of gardeners last year about vegetable and community gardening. There was a wide variety of gardening experience represented, but one statement from a seasoned gardener bothered me a bit. And I think my response bothered him a bit too. I haven’t thought much about it until recently, when a high school English teacher I know told me a student expressed similar ideas in her class. The erroneous idea from my audience member was this: our tomatoes are being poisoned with ‘germetically modinified’…something something. The arguments have lost me beyond that (because there aren’t any). And really, there hasn’t been much talk about sex on this blog recently, so that should be remedied too. Therefore, I would like to take the platform offered by the Garden Professors to talk about plant breeding.

Fig. 1: Jaune flammee, which has at least one gene from at least one of its parents that causes the fruit to have very little lycopene.

Conventional” breeding is when a plant breeder selects parents and offspring and tests them for desirable characteristics (traits). It works the same way as breeding works in nature, except that we humans have a goal we’re working toward. Firm, 5-oz, disease-resistant, crack-resistant tomatoes, for example. In nature, the offspring that survive and reproduce the best in a given environment are ‘blindly’ selected and tend to stick around (Darwin, 1859). Male (sperm) cells are transferred to female (egg) cells by a plant breeder, or a bee, or the wind, or a beetle, or a fly or bird or bat or moth (etc.). The sperm and egg fuse to form an embryo, which grows to become what we’d call a plant. In both natural and artificial selection of tomatoes, no non-tomato DNA has been added, and no tomato DNA has been removed. By the classical definition of ‘genetic modification’, there has been none. I suppose this paragraph was only incidentally about sex, and probably a disappointment to some. Sorry.

Fig. 2. Tainan, a tiny heirloom

The confusion of the issue may lie with the Flavr Savr tomato. This was developed (yes, genetically modified) in the mid-90’s to resist softening during ripening. It has a couple bits of manufactured DNA in it to make this possible. The Flavr Savr is no longer grown or sold in the marketplace (that was SO 1990’s), and to my knowledge, no other transgenic tomatoes are either.

Fig. 3. Rutgers, historically much-cultivated and like all other tomatoes we can buy, bred conventionally.

Confusion may also lie with the plant hormone ethylene. Ethylene is made from incomplete combustion of fossil fuels, but it’s also made by plants. Keep your bananas away from your carnations, right? Bananas make ethylene gas, which causes carnations and snapdragons to senesce (die). Tomatoes make ethylene as they ripen. If you harvest tomatoes a bit early, but not too early, they are hard enough to ship but will still turn red later. If you expose these pre-ripened tomatoes to ethylene gas, they will ripen more quickly and uniformly. That’s what happens to a lot of the tomatoes in our stores. They are not genetically modified, they are treated with a plant hormone. That’s not unusual at all. Ethylene is used to ripen bananas, and to help make cucumber seeds (by eliminating male flowers from female parents). It’s used in growing ornamental plants quite a bit too (but not as much as many other hormones, and especially hormone inhibitors).

So please, if you are someone who tells anybody who will listen that the tomatoes in the store are GMOs, stop it. They’re not.

Is This Really a Good Idea?

Transgenic plants have been with us for well over a decade now. I have had the opportunity to work with many of the tools used for this technology, though most of that is far behind me (over 15 years now since I “ran a gel”) — I’m much happier being outside or even in front of a computer writing than in a lab. Fortunately I have a number of “lab rat” colleagues so I’m relatively up to date on what’s going on and what “gene-jumper” scientists can and can’t do.

To make a long story short, over these years transgenic plants have proven to be useful in some cases (by reducing the use of certain dangerous pesticides), and concerning in others (because some genes have escaped cultivation). I’m not going to go into the crazy ins and outs of the benefits and drawbacks of genetic engineering here except to give you my general opinion which is that every case needs to be handled individually. I do not believe that this engineering is, in and of itself, a bad thing. That said, I do believe that genetic engineering could get us into trouble if we’re not careful.So, with that little disclaimer I thought I’d mention something that I question — I’m not going to call it bad — but maybe it is. There’s an “artist” at the University of Minnesota — Eduardo Kac, who had some of his genetic material placed into a petunia so that some of the proteins from his body were expressed along with the petunias. I don’t have a picture of the petunia itself, but here on the St. Paul campus of the University of Minnesota you can see this structure, created by Kac, which is a graphic representation of a protein from the petunia.

(It was around 20 degrees outside when I took this shot — positively balmy compared to what it’s been like).

Anyway — as I said above — Though I have some concerns, I’m not opposed to using biotechnology for the “good of man.” Nor am I afraid that Kac’s creation is dangerous — from what I know it was kept in a closed system and the petunia was ultimately destroyed — not that it would have been particularly dangerous even if it had been released. But….to me anyway….This seems like a frivolous use of a powerful tool (that tool being the ability to move genes from one organism to another). I don’t know if I’d call it bad….but the words Wasteful and Inappropriate come to mind.

By the way, though I know less about it, it seems that Kac also transferred genes into a rabbit for the sake of art. But this is, after all, a horticulture blog so I thought I’d stick with plants!