Monday, 27 October 2008

Purple GM tomatoes? Yeah right

I don't exactly make a secret of my opposition to genetically modified foods, so you wouldn't expect me to be impressed by a piece in today's Guardian trumpeting the wonders of a new GM tomato. But actually I was bloody boiling mad after reading the piece. Not because of the GM tomato itself (nobody is trying to force me to eat it) but because the report is a gross and cynical misrepresentation.

"Tomatoes that have been genetically modified to be rich in antioxidants can give protection against cancer, a team of British scientists has found.

Researchers at the John Innes Centre in Norwich created the crop of purple tomatoes by altering them with genes from snapdragon flowers. In tests, mice that were prone to cancer lived almost a third longer if their diet was supplemented by the modified tomatoes.

The findings, which appear in the journal Nature Biotechnology, pave the way for a new generation of "functional foods" that could potentially offer protection against serious diseases.

Derek Burke, former chair of the UK's regulatory committee on GM, said: "This is a truly positive outcome from genetic modification of plants, and a real help to people wanting to improve their diets." "

It's not that the health claims being made here are untrue. Purple fruits and veg are rich in anthocyanin which is already known to have health benefits and may indeed be useful in fighting cancer, which is why most of my pea-breeding projects focus on producing purple peas. These findings are not new, and I don't dispute them.

The suggestion, however, that this is a wonderful new breakthrough only made possible by genetic engineering is complete and utter bollocks.

To the general public who are used to seeing only red tomatoes in the shops, the idea of a purple tomato may seem quite novel (and for sure they have nice pictures of it and it looks very pretty). But for those who browse heirloom seedlists they're not exactly new. I seem to recall seeing a packet of exquisitely purple toms from the SSE floating around in Patrick's box at the Oxford seed swap. Admittedly I haven't seen any with the intensity of purple shown in the GM ones, but the point is that if tomatoes can naturally produce anthocyanin then they can be selectively bred to produce larger amounts of it. No gene splicing from the flower borders required.

So I really have to ask ... what the hell is the point? Normal red tomatoes are naturally rich in lycopene which is another nutritional wonder-pigment. Orange tomatoes are generally rich in beta-carotene which makes Vitamin A. You are already doing plenty of good to your health if you eat red and orange tomatoes.

More or less any fruit or veg with purple colouring is already packed with anthocyanin. Blackberries, blueberries, blackcurrants, jostaberries. Red cabbage. Aubergines (egg plants). Cherries. Purple sprouting broccoli. Red wine.

Which begs the question, why go to all that trouble to splice anthocyanin into tomatoes? It adds nothing to western diets. It uses an expensive patented technology which the consumer will ultimately have to pay for. And it's being presented to the public in a cynical haze of hype and spin.

Whatever the motivations of the team who developed this tomato, who may have had good reasons, I am disgusted with the way the report is being carried in the media. It looks to all intents and purposes like a propaganda campaign on behalf of the industry. GM technology getting the credit for something that nature is producing perfectly well by herself. A cynical attempt to sell the idea of GM foods to the general public on the basis that most people don't know much about the science of plant pigments and won't realise it's a marketing wheeze.

I find it quite scary that the former chair of the UK's regulatory committee on GM is trumpeting this tomato as a nutritional advance. I wonder what planet these people are on and whether they read anything other than Monsanto brochures.

Want to get the benefit of this amazing cancer-eradicating anthocyanin stuff? Then take my advice. Eat more blueberries.

EDIT: Here we go, it has already been done. Many thanks to Graham for pointing me to this excellent discussion about a purple-blue tomato bred by Oregon State University using conventional methods. It has an exceptionally high anthocyanin content (as well as the usual carotenoids) and is derived from crosses with wild tomato species. All in the public domain and being freely shared among breeders.

Friday, 17 October 2008

Daughter of the Soil - now with added dotcom

I mentioned before that there was going to be a little change in the way I post my Heritage Vegetable Reviews this year. Instead of going on the blog, they'll be going on their own permanent pages on the Daughter of the Soil companion website (whooooo - swish eh?)

I've kept a bit quiet about this companion site because I needed some time to get it up and running properly, but I've been working on it behind the scenes over the summer ... very slowly because I'm still a bit of a dunce with the page layout software. Though actually the biggest trouble is that I keep thinking of more things I want to add to it, making loads more work for myself.

The companion website can be found (not entirely surprisingly) at It's not a replacement for the blog, which carries on as normal, it's just attached to and interlinked with it. Where the blog is ever-changing (or it would be if I got my backside into gear), the website aims to organise some of the existing content of the blog into a stable and static form to make it easier to find things. Much as I value my regular readers, it's clear that a large proportion of visitors here are coming through Google looking for information about specific things. I want to have a centralised place for all my reviews and informative articles so people can browse them more easily. There's so much material on this blog now, even I haven't got a clue where to find half of it.

Over time, I will be adding goodies and resources to the website which are NOT on the blog.

One biggish project I've done so far (not yet complete but hopefully still useful) is a reference chart of heritage vegetable varieties briefly describing individual characteristics of a whole load of varieties I've grown in my garden. There are clickable links to pictures for each trait listed. So for example you can click on the description of a Ne Plus Ultra pea flower or a ripe Green Tiger tomato and see a picture of one. I'm hoping this will evolve into a really useful quick reference guide for anyone seeking heritage vegetable information.

I've put all my reviews on their own permanent pages, with a centralised index page. There are a few I haven't got round to posting yet, and I'm still making fancy new pages for some of the older reviews, but most of the links are up and running. These are the new Heritage Vegetable Reviews for 2008 that I've posted so far:

Climbing French Bean: Major Cook's - wonderful scrummy bean of WW1 vintage, soon to be available from the Heritage Seed Library.
Pea: Carouby de Mausanne - a very old French mangetout variety with very purty flowers.
Pea: Gravedigger - a gorgeously sweet and juicy mid-height pea, soon to be available from the Heritage Seed Library.
Pea: Irish Preans - a mega-tall one (also from HSL) with bicolour flowers and huge olive green seeds. Said to be a cross between a pea and a broad bean but I'm afraid it most certainly isn't.
Pea: Salmon-Flowered - a real oddity from the HSL which I believe to be a relic of the antique 'crown pea'.
Tomato: Green Tiger - already posted here on the blog as I try to draw attention to this lovely supermarket escapee.
Tomato: Orange Strawberry - see my Goddess Tomato post below for a taste of this oxheart beauty.

There will also eventually be a section about plant breeding, but all I've got on there at the moment is the data table for my Yellow Sugarsnap Project which is only really of interest to nerds like myself.

NB The blog URL is not changing. This is additional to, not instead of, the existing URL.

Thursday, 16 October 2008

The joy of Mendelian segregation ... illustrated!

Nature makes order from randomness.

The photo above shows one of the pods from my Yellow Sugarsnap Project with peas segregating for seed colour. The pod is from one of my F2 hybrid plants (the second generation after the original cross) so the peas inside are F3. As immaculate as this alternating pattern is, it's entirely random.

I've just spent three days typing up descriptions of all my little packets of F3 seed from the Yellow Sugarsnap Project into a nice tidy table, and even as I handled each of my sixty-two seed packets (each plant's seeds carefully saved separately) and stared at them hour after hour I didn't notice the pattern. I noticed that some of the packets of seed are very uniform while others show a bit of variability. I thought that factor might be significant, so for each one I wrote down how variable the seeds were, and which traits they varied for. Sometimes it was size or colour, but more often it was a case of a few wrinkly seeds showing up in a batch of smooth ones. I dutifully jotted all this down but I still didn't notice the pattern. D'uh!

And then I was asked to do a little recorded talk about Mendel and his peas for a University of Bath podcast, just a very brief grounding in the history of genetics for psychology undergraduates. Not trusting myself to not screw it up, I did some refresher-research on Mendel. And in doing so I thought very hard about his experiments, and how he'd been the first person to notice the recurrence of 3:1 ratios in inherited traits. And it was only then that I twigged that there was a pattern in the seeds I'd collected from my pea project. So I raked them all out of the box and sorted them into different groups, and ker-ching! There it was. A beautiful and very obvious ratio.

As like as two peas in a pod? These F3 seeds from my Yellow Sugarsnap Project vary from smooth to wrinkled in the same pod, as well as varying for colour.

As a romantic idle speculation, I wonder whether Mendel found the same thing in his peas and got the initial idea for dominant/recessive segregation from it. Peas have this wonderful advantage over pretty much all other vegetables, that certain traits show up visibly in the seeds. If Mendel had been experimenting with tomatoes or brassicas this wouldn't happen because the seeds all look very similar no matter how different their genes are. He would have to actually grow the plants to see the differences between them. But with peas being the way they are, he must have seen a pattern very similar to what I have here.

The pattern is this: a number of my seed packets from the F2 plants have perfectly uniform round peas, with no wrinkles. A similar number have all wrinkled peas, with not a single round one among 'em. But a larger number have got variability for wrinkliness. And in every one of these cases they have, roughly speaking, a quarter wrinkled and three-quarters round. There are no other ratios. None of the packets have mostly wrinkled with just a few round, or even half and half. They all have an approximate 3:1 ratio in favour of round peas. A Mendelian ratio in other words. In fact there are two Mendelian ratios at the same time. The packets of round or predominantly round seed outnumber the packets of wrinkled seed by about 3:1, while the ratio of round to wrinkled within each of the variable seed packets is also 3:1.

I sorted the seed packets into types. On the left are all the seeds which are completely round with no wrinklies. On the right are the ones with all wrinklies and no roundies. In the middle are the packets which show a mixture of types. There are roughly twice as many in this middle group, as you can see.

Wrinkliness is one of the traits Mendel experimented with, and he found it to be recessive to roundness. This is now known as the R locus. The round-seeded allele is R and its wrinkle-seeded alternative is r. My original cross was between Golden Sweet (RR) and Sugar Ann (rr), so the resulting F1 hybrid must have had a genotype of Rr. Recombining those Rr genotypes in the F2 generation can go any of four ways, with visible effects in the seeds, like this:

Genotypes in the F2 plants can clearly be assigned to their four respective groups.

Why does seed wrinkliness matter? Well, it's a very useful trait for pea breeders to look out for because it's a rule-of-thumb indicator of sweetness. Sugars shrink more than starches do within pea seeds, so the sweeter ones tend to end up more wrinkly. A high sugar content doesn't guarantee a good flavour (as I found in my taste tests with these) but it helps.

It's obviously very useful to be able to identify the seeds which are likely to produce plants with sweet-tasting peas before you've sown them. If I want to breed a sweet-tasting variety I can just pick out and sow the wrinkly seeds and not the round ones, which will greatly increase my chance of getting what I want. This is a really unusual situation, and only works because the desirable trait shows up in the seed itself in an obvious way, when most other traits don't – you have to grow the plants to find out what their genetic make-up is, and even then you can't always tell. It's only because wrinkliness is recessive that I can be confident it will breed true.

Let me explain from a practical point of view. Dominant traits are a pain in the backside for plant breeders to work with. Say I wanted to breed a new pea with purple flowers, based on a cross between a purple-flowered and a white-flowered variety. Purple flowers show straightforward dominance in peas, so I would get ALL purples in the F1 generation followed by an F2 generation which was three-quarters purple and a quarter white. So I would obviously proceed by saving seed from all the purple-flowered F2s and removing the whites. When I sow the seeds from the purple-flowered plants, will they simply produce more purple-flowered plants? No, only a third of them will be true-breeding for purple. The rest will still have the recessive white-flower allele lurking in their DNA, hidden by its dominant purple twin. Although they look like true purples on the outside, those plants will again produce a 3:1 ratio of purples to whites. Unfortunately there's no way to tell which are true-breeding and which aren't, other than by growing them and removing all the whites in each generation until they eventually stop showing up.

Recessive traits, by contrast, are a joy. They show up in smaller proportions of course, but once you have a plant with the requisite pair of recessive alleles it should breed true from then on without any further mucking about.

That's why the sweet-wrinkly seeds showing up in a Mendelian ratio is such a godsend. Laying all these peas out on my desk in their individual packets, I can see their exact genotype for the R gene at a glance. The round seeded ones are RR and will breed true for roundness. The wrinkled ones are rr and will breed true for wrinkliness. The ones that are mostly round with a few wrinklies are Rr or rR (which amount to the same thing) and will continue to show variability in their offspring.

This is incredibly handy. Not only can I identify the sweet ones without having to grow them all and taste them, I can see which of them are true-breeding for sweetness/wrinkliness. If I want to be sure of getting a full complement of wrinkliness in my plants for ever after, I can instantly pick out the ones with the fully recessive genotype and Bob will be my uncle.

The reason this is possible is because this segregation for seed type is showing up within different peas on the same plant. Compare that to the situation with flowers. If some of the plants were obliging enough to produce a load of purple flowers and a smattering of whites all on the same plant, that would be great. I would know those were not true-breeding for purple. But they don't. They produce all purple flowers and keep the whites hidden in their genome to pass on to their offspring unseen.

OK, so we've established that the plants which produce only smooth, rounded seeds must be RR, and because they have a matching pair of alleles their offspring will also be RR. The technical name for this is homozygous. Exactly the same is true of the plants which produced only wrinkled seed. They are also homozygous, because their genotype must be rr and so all their offspring will be rr too.

The plants which produced a mixture of round and wrinkled types have to be heterozygous. Instead of a matched pair of alleles they have one of each type. That means that when they make seeds they will randomly pass on the four possible combinations to their offspring: RR or rr (which are both homozygous and will breed true) or Rr or rR (which are heterozygous and won't). The heterozygous seeds will express their dominant allele and hide their recessive one, so they will look the same as the RR seeds, and so once again there will appear to be a ratio of 3 rounded to 1 wrinkly.

Note that it's the plants which produced these seeds which are heterozygous, not the seeds themselves. Half the seeds in the heterozygous batch will actually be homozygous, but the other half remain heterozygous and will produce variable offspring which are half homozygous and half heterozygous, and so on ...
These seed packets are all siblings from the Yellow Sugarsnap project ... I still can't get over the amazing diversity made by this one simple cross!

With the two quarters of homozygous seeds separating out like this, you can see that in each generation half the heterozygosity is lost. If continued for a few generations it will all but disappear. That's how new varieties are stabilised.

In practical terms, what does that mean for these packets of variable seeds from the heterozygous F2 plants? Well, I know that I have all four classes mixed up here in approximately equal amounts, and I can see which seeds are homozygous (true-breeding) for wrinkliness, because they're wrinkled. Unfortunately I can't see which ones are homozygous for round seeds, because they look exactly the same as the heterozygous ones. Hence this 3:1 ratio of round to wrinkled. If I were to sow all these seeds, I would find the same 3:1 ratio in the next generation too, and onward.

Finally, a little reminder that all I'm looking at here is the R locus, the gene controlling wrinkliness. That's just one of many thousands of genes in every pea. Segregation is taking place at every other locus at the same time! If I select identical-looking wrinkled peas, I can assume they will be true-breeding for wrinkliness but they may differ enormously in other traits.

Wow, my head feels weird now.