Genetic diversity

April 19, 2012April 20, 2012

Blight is right: genetic uniformity was to blame

The Southern Corn Leaf Blight epidemic that struck the US in 1970 is usually seen as a canonical example of the dangers of genetic uniformity. I use it that way myself, often. Certainly yield losses in 1970 seemed very high, higher than the average 12% “expected from all diseases of corn”. But could we all be wrong? A commenter thinks so.

[W]as it a major problem? Over twenty years ago I gave a seminar at CIMMYT. I had prepared a slide showing the year on year average yield increase ((I don’t know whether he really means year on year increase; somehow, I doubt it. What would be the point?)) in maize in the USA for about 70 years‚ but leaving off the actual years. … I challenged the audience to identify the blight year (1970). Nobody could. … Try this on colleagues and students.

I did, and it is true, 1970 does not look all that extraordinary against the trend.

A more interesting graph is this one, in which the rising trend in average yield is removed from the actual yield each year.

Now 1970 is a little more visible, though I agree it still doesn’t look catastrophic. I mean, compare that with 1988 and 1993. There is one huge difference. In 1988 drought was widespread, while in 1993 floods devastated many farms and yields in the northwest corn belt. Weather in 1970 was just fine, thank you. Weather is clearly a very important factor in annual yields, and it interacts with pests and diseases in complex ways, but it seems pretty clear that the yield loss of 1970, while not as drastic as in other years, was certainly not the result of wayward weather.

The commenter asked “are we making too much of a fuss about the Leaf Blight”? I don’t think so, obviously, so I asked Professor Darrel Good, of the University of Illinois. He knows more about maize yields than almost anyone (and is responsible for the graphs above). He said:

I have not seen any specific analysis of 1970, but am pretty sure that the decline in corn yield was in fact attributed to the outbreak of southern corn leaf blight. Hard to quantify that impact relative to weather. It is a similar phenomenon as the aphid damage to the soybean crop of 2003. ((A pest recently arrived in the US from the soybean’s native China, and a rabbit hole I am not now going to explore.)) These rare events are not captured in our models.

In some respects, pests and diseases are as unpredictable as weather. In industrialized agriculture, genetic diversity within a crop is unlikely to provide much protection against the vagaries of weather. ((Subsistence agriculture is almost certainly different.)) But genetic diversity definitely can protect against unpredictable pests and diseases, not just in maize, and not just against Southern Corn Blight.

April 16, 2012April 13, 2012

Brainfood: Pollinator threats, Predicting drought tolerance, Markets and conservation, Groundnut oil composition diversity, European wheat landraces, Dung beetles, Livelihoods, Phenology

Impact of landscape alteration and invasions on pollinators: a meta-analysis. Habitat alteration and invasions equally bad on visitation rates, invasive animals more bad than invasive plants, and disturbance of the matrix more than fragment size. But there are some differences among vegetation types.
The determinants of leaf turgor loss point and prediction of drought tolerance of species and biomes: a global meta-analysis. Osmotic potential at full turgor could be used to predict drought tolerance across species. Cut a long story short, that simplifies down to salty cell sap, give or take. Good for choosing crop wild relatives to use in breeding for drought tolerance?
Market-based instruments for biodiversity and ecosystem services: A lexicon. If you want to tell your tradable permits from your reverse auctions. And really, who doesn’t?
Phenotypic and molecular dissection of ICRISAT mini core collection of peanut (Arachis hypogaea L.) for high oleic acid. Much diversity in oleic acid (O) to low linoleic acid (L) ratio found. Breeders alerted.
Phenotypic diversity and evolution of farmer varieties of bread wheat on organic farms in Europe. There wasn’t much of it, over 3 years.
A Comparison of Dung Beetle (Coleoptera: Scarabaeidae) Attraction to Native and Exotic Mammal Dung. They really know their shit.
Small-scale farming in semi-arid areas: Livelihood dynamics between 1997 and 2010 in Laikipia, Kenya. Life continues to be a bitch, there’s no other way to say it. But when will the people who measure livelihoods measure the diversity of people’s assets as well as their size?
Climate-associated phenological advances in bee pollinators and bee-pollinated plants. About 10 days over the past 130 years, most of the change since 1970, and bee plants keeping pace with bees.

April 13, 2012April 20, 2012

Biodiversity is more than a matter of breeding

One of the great problems in talking about biodiversity is that it has so many different meanings. ((At which point the average lazy English writer would insert the Humpty Dumpty quote and move on. Next would come the Samuel Johnson quote, and then we can get back to the story.)) That makes it easy to misunderstand one another, and to make mistakes.

So, for example, we pointed out that having great diversity in your pedigree does not confer any diversity in the here and now if all the offspring of those highly diversified matings are genetically identical. Our friend Mike Jackson was quick to point this out, and he recently followed up with a link to an IRRI annual report for 1997-98. Delivering Diversity to the Field amplifies the confusion, talking about the huge increase in the number of ancestors in a variety’s pedigree ((Confusingly calling them all “parents”.)) and telling us that “these varieties have also increased the danger of genetic vulnerability to major disease or insect pest outbreaks”. Modern varieties, then, are more diverse because they have many “parents” and more vulnerable because they are more uniform. ((No point, here, in picking more holes in that article; we leave that as an exercise for the reader.))

All this is important because it addresses something that Bruce Chassy brought up in response to our criticism of his effort to debunk an anti-GMO paper by bringing biodiversity into the picture. Chassy wrote:

Biodiversity has taken on an almost spiritual meaning. I do not mean to in any way diminish the importance of biodiversity but sometimes when people start believing they stop thinking.

Amen to that. Chassy goes on to illustrate, as follows:

The American Chestnut comes to mind as species that was diverse and widespread through diverse ecosystems in the US. Three billion trees, 25-30% of all trees in the Eastern US, were nonetheless wiped out by a single disease, Asian bark fungus (Cryphonectria parasitica) in a few short decades. Just a few scattered individuals remain of this once common tree. Biodiversity did not save them.
On the other hand, the Quaking Aspen (Populus tremuloides) is propagated by root and shoots. A grove of these Aspen is essentially a giant monoclone; the specie itself appears to have very little biodiversity. They have survived for perhaps 100s of millions of years and have been called the largest living organisms since all the trees in a grove are connected by roots and can be thought of as part of one distributed organism. Lack of diversity appears not to have hurt this specie.
A number of common crops are propagated clonally as well. Naval oranges, bananas, potatoes, pineapples, apples are examples. Why doesn’t biodiversity matter to these crops? Because they were produced by plant breeders and are propagated commercially before being planted by farmers.

Where to begin?

At the beginning. Biodiversity can exist at several different levels. A landscape contains different species from different kingdoms. Populations of a single species will differ from one another. And individuals in a population will differ genetically from one another. So all those chestnuts may have been “diverse” but not where it counted, in their susceptibility to Chestnut blight, although at least one resistant individual has been found. As for Quaking Aspen, some groves are indeed large clones (as are groves of many other trees) but groves differ greatly from one another, and aspens will reproduce sexually, for example after fire, increasing the genetic diversity among stands. Aspens are also threatened by many pests and diseases.

I could make the same points with regard to vegetatively propagated crops and obligate out breeders. Clubroot, anyone?

One measure of diversity is the probability that two individuals chosen at random will share some specified quality, but it really matters what that quality is. Could be something as simple as a specific sequence of DNA. Could be a specific protein coded by the DNA (which can be identical even if there are differences in the DNA). Could be something as complicated as susceptibility to a disease, or resistance to drought. It’s complicated. But that’s no excuse for wilfully misusing an important concept.

April 10, 2012November 29, 2017

Nibbles: Anna Laurent, Sequencing, Gossypium, Capsicum, Native Americans, Journal, Genebank, Hairy fruit, JIC, Tasty tulips

Design guru talks botany. Latest plant getting the treatment is the Hawaiian Cotton Tree. Which, despite its name, really is a (remote) cotton wild relative.
What has Next Generation Sequencing ever done for me? And what you should know about how it works.
And here’s an example of it at work: different cultivated cotton species have behaved differently, genetically speaking.
That used ancient DNA, this one didn’t, but I guess a future one on chiles might. LATER: Ooops, just realized this is old. So what was it doing in my RSS feed?
Speaking of chiles, here’s a couple of more things on Native American agriculture.
Free access to the first issue of volume 20 of Journal for Nature Conservation for the next 12 months.
Rebuilding the genebank in Ivory Coast.
Discovering the wonders of the coconut. Their headline, not mine.
The latest news from the John Innes Centre’s genebank.
Fancy a tulip? To eat, that is.

April 9, 2012

Nibbles: Baby ginger, Livestock, Teaching, Organic seeds, Pawpaw, Citrus, Ethiopia

Baby ginger, if you can offer tropical conditions and want to make money.
ILRI beefs about the lack of interest in livestock in the run-up to Rio+20.
Teachers! A resource! What Are Seed Gene Banks and How Do They Work?
Farmer unthreatened by GMOs grows organic seed for others.
Botanist documents flowers of (one kind of) pawpaw.
Woman takes a trip down memory lane during visit to citrus field genebank.
Ethiopians improve their food security with roots and tubers. Wot, no bananas?