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.
Frank and the giant peach
While Luigi was getting excited about giant parsley, frequent tipster Dirk Enneking sent word of giant peaches, a much tastier quarry. The great plant explorer Frank Nicholas Meyer traveled widely in the east and sent many collections back to the USDA, his employer. ((Among his many finds is the famous Meyer Lemon, recently reborn as a foodies’ favourite.)) He wrote a wonderful account of his Agricultural Explorations in the Fruit and Nut Orchards of China, published in March 1911 (and, gloriously, available thanks to Google.) Meyer describes the diversity of Chinese peaches, singling one out for special praise.
The best of them all is the “Fei Tau,” or Fei peach, Feitcheng being the name of the village where the orchards are located. These peaches grow to a large size, often weighing over 1 lb apiece, and are of a soft, pale-yellowish colour externally, with a slight blush on one side. The meat is white except near the stone, where it is slightly red. The fruit is a clingstone, with a very large, pointed stone. The skin is very downy. The fruit ripens in the early and middle part of October and has an excellent flavor, being sweet and aromatic. It possesses extraordinary keeping and shipping qualities, keeping until February if wrapped in soft tissue paper. Its shipping qualities are such that it is carried in baskets, slung on poles across the shoulders of coolies, from Feitcheng to Peking, a journey of eight days on foot. So famous is this peach, that it is sent every year as a tribute or present to the imperial court at Peking; and even right on the spot where this fruit grows the most perfect specimens retail at from 10 to 15 cents in Mexican money, a price which is about two-thirds of the average daily wages of the Chinese field laborer.
I want to try one of those! How many of the varieties Meyer mentioned are still available in China?
Whether you think Meyer’s comment says more about low wages than high prices, the fact impressed Meyer enough to note it. But why were they using “Mexican money”? Meyer describes lots more peach diversity.
Some of these peaches are blood red and when cut through look more like a beet root than anything else. One variety in Shansi is even called the “Rho Tau,” or beef peach, so much does it resemble meat.
He also mentions flat peaches, red and white, which by the sound of it resemble the ephemeral “Saturn” peaches that briefly show up in the fruit-shops of Rome and can perfume a large room with their scent.
Meyer points out that the Chinese genetic diversity had, and in 1911 still has, a lot to offer growers in the US, and that, after all, was his job, to plunder the resources of another sovereign state and bring them back to improve US agriculture. But has anyone calculated the contribution of Chinese peaches like the ones Meyer noted to peaches in the US and elsewhere? It would be a fascinating and tasty case study.