I’ve blogged about ProMED before a couple of times. It’s advertised as a “global electronic reporting system for outbreaks of emerging infectious diseases & toxins.” But it is actually a bit more than that, as a recent piece on cassava brown streak disease revealed. There have recently been some stories in the Ugandan popular press about this disease. And one of the early ones made it to ProMED. That’s useful enough, but it also elicited a reply from Prof. Mark Laing of the School of Biochemistry, Genetics, Microbiology and Plant Pathology, University of KwaZulu-Natal in Pietermaritzburg, South Africa. He noted that “that there is hope on the horizon versus both cassava mosaic disease (CMD) and cassava brown streak virus (CBSV)” and quoted a couple of breeding programmes that are having some success. That’s really how you want an early warning system to work. It should not only give warning of the problem, but also get people to discuss possible solutions. It doesn’t seem all that complicated to set up. Is it too much to hope for that there’ll be something along these lines for genetic erosion before I crawl away to my well-earned retirement?
Livestock genetics symposium online
DAD-Net informs us that the presentations given at the symposium on Statistical Genetics of Livestock for the Post-Genomic Era, held at the University of Wisconsin-Madison, USA, on May 4-6, 2009, are now available online in the form of both PDFs and videos. Quite a resource.
Making that haystack smaller
Germplasm collections can be very large, and that can put off potential users. What breeder really wants to screen thousands of accessions, when only a dozen might end up being useful? It’s not surprising, therefore, that people have looked for short-cuts. One approach is to make a “core collection.” You use the available data on the collection to select a sub-set which you hope will contain most of the original genetic diversity in a fraction (20%, say) of the total number of accessions. And then you evaluate that subset, rather than the whole collection, and use the results to delve back into the remaining 80% of the material, with hopefully a better chance of finding what you’re looking for.
That’s been done for lots of large collections now, with a certain amount of success in increasing their use — and usefulness. But breeders are not really satisfied. They want to shorten the odds even more. And the application of Geographic Information Systems (GIS) technology in something called the Focused Identification of Germplasm Strategy (FIGS) provides a potentially effective way of doing just that.
Jeremy described recently over at Bioversity how FIGS was used to increase the chances of finding a needle in a haystack by “start[ing] with a smaller haystack.” The haystack was 16,000 wheat accessions. The needle was resistance to powdery mildew.
It works like this: take 400 genebank samples known to have some resistance to powdery mildew and use the geographical location where they evolved and were collected to determine the environmental profile that can be associated with resistance. Then apply that profile to a further 16,089 samples with location data, using the profile as a template to identify those that were found in places that share the conditions associated with resistance. The result is a group of 1320 wheat varieties, mostly from Turkey, Iran and Afghanistan. This much more manageable subset was screened by growing them with diverse strains of powdery mildew. About 16% of the samples (211 of 1320) showed some resistance.
These varieties then moved to the next phase, molecular screening for the presence of different alleles of the Pm3 gene. More than half (111 of the 211) had Pm3 resistance, some in previously unknown forms. In the end the group isolated and identified 7 new functional alleles of the Pm3 gene. It took scientists 100 years to find the first 7 Pm3 alleles. FIGS doubled the number in a fraction of the time.
Very good. But is it always going to work? Another recent paper — in fact, a series of papers — counsels caution.
Nibbles: Kerr reports, Monsanto shares, Thailand patents
- Kerr Center for Sustainable Agriculture mourns loss of agricultural biodiversity, issues report.
- Monsanto “shares with farmers the science behind the technology.” Nice of them.
- Thailand patents (transgenic) jasmine rice to “keep foreigners out of our paddy fields.” So much to say about this, so little time.
PBR dedicated to Tony Brown
Volume 31 of Plant Breeding Reviews is dedicated to Anthony H.D. Brown, the distinguished Australian conservation geneticist. Tony has been making fundamental contributions to the theory of crop genetic resources conservation through his work on sampling strategies, core collections and on farm conservation for forty years. But he has also worked tirelessly in the field, as the following little snippet makes clear:
If you happened to be one of the few vehicles driving the remote dirt Peninsula ‘‘highway’’ in Cape York, north Queensland, in July of 1983, you may have seen three collectors (Ted Hymowitz from Illinois and Jim Grace and Tony from CSIRO) sprawled on the lawn outside the Lakeland pub below the billboard saying ‘‘Ice Cold Beer.’’ This was no early knock off; they actually were sampling rare, tiny Glycine tomentella plants. The billboard had nothing to do with site selection; a collector must check all habitats. The roadside pub, a lone building in the rural landscape, was a haven for the thirsty traveler, and it surrounds a haven for wild plants that grazing animals would otherwise decimate. Thus, sampling strategies for germplasm collection adapt to reality.
You can read the full dedication courtesy of Google Preview. Well worth it. You get to know one of the giants of the field, and there’s a refresher course in the history of crop genetic resources and agrobiodiversity conservation thrown in for good measure.