- How livestock help feed the world.
- The latest CWR newsletter from PGR Secure.
- “…humans have inadvertently been probing the environmental envelope of carbon-based life for thousands of years simply by experimenting with pickling, salting, smoking, and refrigeration.”
- A better way for museums to preserve rice plants. In other news, museums interested in preserving rice plants.
Rewarding excellence in Indian rice breeding
India’s Directorate of Rice Research has just recognized the Paddy Breeding Station of Tamil Nadu Agricultural University (TNAU) as the best rice breeding station among India’s 107. The Vice-Chancellor of the university said that:
“The landmark varieties that have been developed through Pure Line Selection by this station triggered the growth of rice production in the State. The first variety — GEB 24 (Kichili Samba) — released during 1921 played a significant role in the development of rice cultivars over the years, not only in India, but world-wide.”
With help from the irrepressible Nik and his local version of IRRI’s all-knowing germplasm database we can actually kind of quantify that. It turns out that out of the 11 IRRI releases in 2011 (IR155-165), only IR157 (an irrigated japonica) doesn’t have GEB 24 in its pedigree. Just for that, it would seem to be a very well-deserved award. But I’m also told they helped IRRI build up its collection in the early days.
What about the other direction of use, though? Well, IR8 starts to feature, by itself, in the pedigrees of TNAU varieties in the early 70s (e.g. in CO38 and CO40), then by the early 80s there are 5 IRRI lines involved in the development of CO43. But by the 90s there are a couple dozen IRRI lines in the pedigree of CO47. So the flow of germplasm has been two-way.
In more ways than one. Apparently, IRRI are in the process of restoring to TNAU some of their CO varieties, which they had lost for one reason or another, but had taken the precaution of sending to Los Baños. Good collaboration all around. Great to see the achievements recognized in the popular press, if not necessarily the collaboration. But then that’s what we’re here for.
LATER: Further delving into the database by our friends at IRRI reveals that TNAU sent material quite regularly to IRRI from 1961 to 1987, with a peak of 952 accessions in 1978. But “only 40% of TNAU’s CO varieties conserved in the IRRI genebank came directly from TNAU. 30% came via CRRI and 30% via other organizations. TNAU obviously shared their material widely.”
The how and why of indicators of agricultural biodiversity
Let us assume, for the sake of argument, that one crop variety does disappear every single day. The question still remains: does it matter? After all, the variety that was just lost yesterday might be very similar to one that’s still out there today. That’s part of the reason why a group of French researchers has just come up with “A new integrative indicator to assess crop genetic diversity,” which is the title of their paper in Ecological Indicators. 1
Christophe Bonneuil and his co-workers thought that, given the data, they could come up with something more powerful and more widely applicable than richness (i.e. the number of different varieties) or the standard diversity indicators (i.e. various combinations of richness and evenness). So they started with number of varieties, but then they factored in the relative extent to which each was grown in their study area, the departement of Eure-et-Loire in France (which is the evenness bit), how genetically distinct each was (which is the bit which addresses the pesky question of how different the variety that disapeared today is from all the other ones left behind), and how much genetic diversity there was inside each.
They got the data on genetic differences among varieties by comparing genebank samples of all the wheat types grown in Eure-et-Loire from 1878 and 2006 at 35 microsatellite loci, and data on acreage of each variety at different points in time from various archival sources. Internal genetic diversity was set at one of three values derived from the literature, depending on whether the variety was a landrace, an old commercial line or a modern pure line.
They put all that together into this monster indicator of allelic diversity in the landscape,
and then calculated it for different times periods, and got this:
That shows a decrease in diversity as landraces are replaced with modern varieties, but, interestingly, something of a resurgence after the mid-1960s, as more diverse germplasm is introduced into breeding programmes. The indicator has been on a downward trend just lately, as the genetic relatedness of the most frequent varieties has increased. 2 Overall, it’s maybe a 50% drop since 1878. Not entirely dissimilar to the iconic 75% figure, and at least this wasn’t plucked out of thin air.
Interesting enough, but check out the trend in number of varieties over the same period:
Totally different. Pretty much an upward trend, albeit with some stuttering. Certainly no evidence from these data of massive erosion of diversity. Maybe the findings of Jarvis et al. (2008) that simple richness can be a useful indicator of diversity should be applied with caution if you’re not just dealing with landraces.
But how significant is it really that the value of this particular indicator of diversity, for all its fanciness, has decreased? Has anyone actually suffered as a result? I don’t know, but a second paper I came across this week suggests how one could find out. Roseline Remans and others associated with the Millennium Villages Project have a study out in PLoS ONE which adds yet another — different — nuance to diversity. 3 Their index considers not just how many different crops are grown on a farm, but also how different they are in their nutritional composition. Think of it as the nutritional analogue of the inter-varietal genetic diversity term in the French indicator. The more different in nutritional composition two crops are, the more complementary they are to local diets, the more important it is that both are there, the higher the resulting “functional” diversity index. And in fact the authors did find a positive relationship between their diversity indicator and nutritional status, at least at the village level.
Easy to imagine (though perhaps less easy to actually implement) a further refinement of Bonneuil et al.’s indicator which additionally integrates nutritional data, to yield an indicator of crop genetic and functional diversity. And, of course, once you have such a super-indicator, it might actually be possible to reward people on the basis of their success in maintaining it at high levels. Which, as it happens, is the subject of yet another paper I happened across last week. 4 But maybe that’s a paper too far for now. 5
Nibbles: Kenyan blog, Beer, CGIAR squared, Horse domestication
- And Kenya’s best agriculture blog is…Tracking The Scent! Congrats Kio Wachira!
- Drinking beer as an agricultural act.
- CRP4 needs a new name.
- Meanwhile, here’s another example of CGIAR centres working together. Not clear if it’s in a CRP, though, and if so what it is called.
- Horse domesticated once, but with occasional restocking.
Brainfood: Species prioritization, In situ costs, Mycorrhiza, Crop diversity indicator, Diet diversity indicator, Ag & Nutrition, Chestnut blight, Oyster translocation, Maize introgression, Italian asses, New hosts for pests
- Species vulnerability to climate change: impacts on spatial conservation priorities and species representation. Yes, you can focus on sensitive species, but it comes at the cost of representativeness.
- Estimating management costs of protected areas: A novel approach from the Eastern Arc Mountains, Tanzania. Those are $ costs per pixel on the map, which I’ve never seen before. Don’t think they took into account the effects of climate change, though. Maybe they should get in touch with the Aussies above?
- The use of mycorrhizal inoculation in the domestication of Ziziphus mauritiana and Tamarindus indica in Mali (West Africa). It would help.
- A new integrative indicator to assess crop genetic diversity. Includes varietal richness, spatial evenness, between-variety genetic diversity, and within-variety genetic diversity. Not much left, really. Anyway, remember this from last week? Anyone out there going to put 2 and 2 together?
- Assessing Nutritional Diversity of Cropping Systems in African Villages. A new tool! Different from the integrative indicator above! Anyone going to put 4 and 2 together?
- Agriculture-Nutrition Pathways Recognising the Obstacles. “The pathways between agriculture and nutrition seem to be laden with impediments, particularly in the form of intricate household preferences.” Those pesky preferences.
- The chestnut blight fungus world tour: successive introduction events from diverse origins in an invasive plant fungal pathogen. Asia to N. America to Europe, but more than once. All very complicated. The surprising thing is that low diversity and low admixture have nevertheless still resulted in success in disparate places. What fiendish molecular or biochemical mechanism is behind this? Only more research will show, natch.
- Translocation of wild populations: conservation implications for the genetic diversity of the black-lipped pearl oyster Pinctada margaritifera. Introducing some wild individuals near farms leads to more diverse farmed populations, right? Nope. The farmed populations are way diverse already and if anything the diversity is moving the other way.
- Maize x Teosinte Hybrid Cobs Do Not Prevent Crop Gene Introgression. That’s because the hybrid cobs break apart much more easily than maize.
- Detecting population structure and recent demographic history in endangered livestock breeds: the case of the Italian autochthonous donkeys. Microsatellites confirm existence of 8 breeds of Italian donkey, though there is also significant substructuring within each by farm. This apparently calls for a “synergic management strategy at the farm level,” which basically means using the breed as the unit of conservation but being careful about inbreeding.
- Evolutionary tools for phytosanitary risk analysis: phylogenetic signal as a predictor of host range of plant pests and pathogens. Work out host susceptibility by looking at existing pest preferences and phylogenetic distance from the stuff the pest is known to like.