Category: Articles

Longer pieces; we’d call them essays if that didn’t sound pretentious.

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Climate change: Diversity the mother of invention?

Our man with the factor 30 sunscreen and the big umbrella writes:

Climate change is the new black. Everyone’s talking about, if you haven’t experienced it, well frankly you haven’t lived. We’ve heard this week that 39% of the world will have novel climates in 2100 (via Eco-Justice Blog). The concept of “novel” climates is a little abstract, but the authors of the study did a good job of bringing attention to the fact that new solutions are needed to adapt to climate change. It’s not always just a question of transferring existing technologies and practices. Without alienating the good people who invited me to write this, I’m afraid that for these areas conventional crop improvement of some of the hardiest crops is perhaps the most rational means of confronting this. (No alienation here: Ed.) Either that or give up on agriculture in these regions and intensify in the less affected regions.

But the study leaves 61% of climates where change is predicted, but to a climate already found currently on the earth. That’s a calming thought, as long as of course we have faith in the conventional climate models and hope the doomsday scenarios don’t come true. This opens up a world of opportunities for agricultural biodiversity, where an eternal optimist like me could even think something good might come of it. After all, adversity is the mother of invention. Perhaps the building blocks for agriculture adapted to the Brazilian cerrados will come from landraces used by farmers from the Sahel belt in Niger.

What do we need to do?

We need to get out of the abstract paradigm that we’ve constructed of ex situ collections, leading to crop breeding of blanket solutions, followed by a less than optimal delivery of new seed technologies. Farmers have exchanged seeds informally for millennia, and the rich diversity of landraces is testament to the fact that this works, especially in the face of change. We need to go back a hundred years, and direct all our 21st century advances in international diplomacy and treaties, communication technologies and truly use our ex situ collections to redeploy diversity and stimulate a diversification of agricultural systems.

Why? Well for starters studies point to climate change impacts being highly localized. To over-simplify, deploying a new seed technology across an entire region would result in improved adaptation for some, but a failure to capitalize on an opportunity for others. Of course, that’s the flip side of diversity: how to avoid sub-optimal use of diversity? How can we help a farmer to use the most adapted seed, maximizing the opportunity without being over-exposed to risk? Plenty of valid research questions.

Of course, we need to do a lot more and diversity is unfortunately not capable of confronting climate change alone. But I’m interested to hear ideas of how we might operationalise the redeployment of agrobiodiversity, especially in marginal areas.

From Andy Jarvis. If you have ideas, leave a comment.

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Mapping underutilized genomes

It seems you can hardly open a newspaper these days — or open a news website — without reading that someone somewhere has mapped yet another genome, whether human, Neanderthal, sheep, mouse or bee. It hasn’t received any press coverage at all, but the taro (Colocasia esculenta) genome has now been added to the list. CIRAD scientists working in Vanuatu, in the South Pacific, and others just announced this at the recent meeting of the International Society for Tropical Root Crops held in Kerala, India.

One thing to note is that these are not all really genome mapping projects. Despite the many headlines to that effect, scientists are not mapping the Neanderthal genome. What they’re doing is sequencing it — or a small bit of it. There is a difference.

Sequencing means determining the (correct!) order of all the DNA bases — the letters of the genetic code — of an organism. Besides some very fancy hardware and software, you need the DNA of just one individual to do this. Mapping is both rather less and rather more.

Less, because it only aims to determine the relative location of some major landmarks of the genome. That is, not the order of all the letters in the book of life, but rather the relative positions of the pages where some choice quotations can be found.

More, because some of those genomic landmarks may be close to genes associated with predisposition to a disease or some other interesting trait. To find that out you need DNA from whole families, or populations, rather than a single individual — in the case of taro, the family was all the progeny from a couple of crosses between local ni-Vanuatu varieties. You trace the inheritance of the trait you’re interested in together with that of specific “markers” (any observable variation in the DNA sequence), and, hey presto, if you’re lucky you have a much more readily documented proxy for the trait.

With the new genome map, we now have genetic proxies for things like the yield and dimensions of the underground corm of taro. This edible aroid is an important staple in Oceania and parts of South and South East Asia, Africa and the Caribbean, but there are few breeding programmes around the world, which is why it often ends up on lists of so-called “neglected and underutilized species.” This map should make it easier to screen the hundreds of seeds that can result from crossing two varieties and select only the best individuals for further testing (this is called marker-assisted selection). It should therefore stimulate people to set up taro improvement programmes.

These are much needed. Mainly vegetatively propagated by farmers, taro is genetically fairly uniform in many places, making it susceptible to pests and diseases. It was almost wiped out in the South Pacific country of Samoa in the mid-1990s by taro leaf blight, a fungal disease. It has recovered at least in part because a regional project (called TaroGen) was set up by Pacific countries with support from Australia to breed — in collaboration with farmers — and disseminate resistant varieties.

Biotechnology means GMOs to many people, but this is a case where biotechnology is facilitating conventional breeding — nothing to do with genetic engineering. It may not have made the news like other mapping projects, but the new genome map means taro breeding should prove a little bit easier in the future.

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Future prospects for European crop varieties

Last time I looked at the state of seed availability in Europe and how it got that way: a one-size-fits-all approach that suits industrial growers and their breeders well enough but that leaves gardeners and specialist growers out in the cold. This time, what are they doing about it.

This whole discussion began with the prosecution of the Kokopelli Association in France for selling seeds of unregistered varieties. That provoked disbelief and a note that change was being discussed. So it is. The version I saw of the “Draft Commission Directive establishing the specific conditions under which seed and propagating material of agricultural and vegetable species may be marketed in relation to the conservation in situ and the sustainable use of plant genetic resources through growing and marketing” is due to come into force on 1 April 2007

I shall refrain from the obvious joke.

The provisions of the draft are somewhat complex, and in boiling them down I will almost certainly get something wrong. But in essence, a “conservation variety” or “amateur variety … with no intrinsic value for commercial production” can be sold within a “bio-geographic region” without having to be registered under the previous seed marketing directives. There are many other conditions hedged about, like the colour of the labels and the minimum size of the packages. Two stick out. The total seed sold for each conservation variety shall not exceed 0.1% of the seed of that species used each year in the country concerned. And marketing is limited to the bio-geographic region of origin or adaptation of the variety.
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How the European Common Catalogue destroys biodiversity

Charities know that it is a good idea to forge a bond between those who have and those who have not — the better to make those who have, give. So winsome children and kindly old people show us that we are all part of one big happy family, and families help one another, don’t they? But what if those who are normally the position of having, and giving, become those who need?

All of which is a roundabout way of saying that as far as agricultural biodiversity is concerned, Europe is probably more in need of help than anywhere else. Elsewhere, as in Europe, intensive agriculture and monocropping are destroying existing biodiversity. But elsewhere, unlike Europe, farmers, gardeners and ordinary folk who just want to grow themselves a bit of food have a bit of choice. If they can find the variety they want, they can buy it (or obtain it by barter, whatever) and grow it. In Europe that is not legal.
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Unlocking the future of keys

Hawaiian taro farmers – they call it kalo there – know the difference between the varieties Haokea and Mana ‘ōpelu, and thanks to a nifty piece of software now so can everyone else. A researcher in Fiji, say, can quickly see whether they might be the same as the ones she’s working on half an ocean away (at least outwardly, see forthcoming article on genomes).

The software makes use of a different kind of taxonomic key. The usual kind of key that people use to identify things is called a dichotomous key, and it has been an essential part of the taxonomist’s toolkit pretty much since Linnaeus. It consists of a series of questions about what an organism looks like, each of which can have one of two answers, wherein lies the dichotomy. Are the petals red or purple? If red, are the leaves pinnate or palmate? If purple, does the stem have thorns or not? And so on. If you answer all the questions – and there can be a lot – you’re rewarded with the name of the organism you’ve been trying to identify.

That can be a big if. The dichotomous key has been a very successful tool, but it does have some major drawbacks. What happens, for example, if the part of the organism you’re being asked about – flowers, say – is not available? And what happens if you’re not quite sure about the difference between the two choices presented, say between pinnate and palmate leaves in the example above. You could try the key one way and then the other and see what answer makes the most sense, but that will be very time-consuming. Keys can also simply be badly made (or badly translated), or out of date.

Recognizing that something must be done, and that, with the necessary computer tools just beginning to become available, it now could be done, scientists at the CSIRO Division of Entomology in Australia started developing the DELTA software suite in 1971. This is based on the use of the DELTA format (DEscription Language for TAxonomy), a method of recording taxonomic descriptions for computer processing that has since been adopted as a standard for data exchange by the International Working Group on Taxonomic Databases. One of the DELTA programs can be used to prepare conventional dichotomous keys. But another, called Intkey, can produce “interactive keys.”

Also called “multi-access,” these are keys where characters can be used in any order. You put into the program the information you have about the organism you are trying to identify. The software does the rest, finding the best overall matches based on the descriptions it has in its database, with a measure of how likely each match is. It also suggests what other characters to look for to narrow down the options further. No inflexible series of often ambiguous questions, coming to an abrupt halt when you find you don’t have the bit of plant you need. No going back to the start if you get something wrong or are not sure of one of the answers you gave. Much better all round. But difficult to do without a computer if you’ve got lots of options and lots of characters, which is why Linnaeus didn’t go the interactive way.

Lately, the Centre for Biological Information Technology at the University of Queensland, Brisbane Australia has developed another interactive identification system, called Lucid. PACINET, a regional taxonomic capacity building partnership in the Pacific in which I’m involved, recently organized a training course in the use of Lucid here in Fiji. PACINET is affiliated with the BioNET-International global network in taxonomy. Lucid proved pretty simple to learn and use. Participants were able to put together prototype identification systems in just a couple of days, for example for the reptiles of Fiji.

The names of the organisms at the end of keys – whether dichotomous or interactive – are usually the Latin names of species, but they don’t need to be. They could just as well be the names farmers use to refer to their taro – or kalo – varieties. Honolulu’s Bishop Museum has developed a website on Hawaiian taro varieties using Lucid. The museum doesn’t conserve kalo germplasm, just the information about the local varieties. I can’t think of a single genebank that is using an interactive identification system to manage their collections. They should be. Then if a new variety turns up, they could very quickly determine if something similar to it is already being conserved. They could also work out if two or more varieties they are conserving, perhaps with different local names, are actually very similar, at least in appearance. You could do all this with standard database software, of course, but an interactive identification system makes the whole process so much easier, and so much more fun.