- New Agriculturist is out. Among many cool things, check out the piece on crossing rice with a wild relative to make it perennial.
- Nestle finds 33 elite coffee trees in Indonesia, evaluates 6, will use these to produce seedlings by somatic embryogenesis. What could possibly go wrong?
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: Traditional knowledge, Opium poppy, Fish, Bees, Earthworms, Wild horses, Camel, Fearl rabbits, Guinea savannah, Kava
- “In the face of climate change, keeping diverse, resilient ecosystems is one of the strongest tools for adaptation.”
- Getting high in Eden.
- Chinese ate freshwater fish 40,000 years ago.
- British MPs finish cleaning their moats, decide to save the honeybee.
- Worm power!
- LEISA 25:2 is out.
- Przewalski’s horse gets first ever reverse vasectomy.
- Early farmers used camel-drawn carts.
- Using Google Earth to map bunnies in Australia. And then kill them.
- Farming the savannah. What could go wrong?
- Stressed out? Try kava. With audio goodness.
Collecting seeds in Botswana
The Guardian had the nice idea to embed a reporter in a seed collecting trip by the Millennium Seed Bank’s leadership and local partners in Botswana, but the end result is a bit disappointing. Despite Tim Adams’ valiant attempts to bring out the fascination, romance and thrill of plant hunting, along with the logistical challenges and politics of it all, I was just not engaged, I’m sorry to say. Maybe it was the glib, slightly sarcastic, slightly condescending tone. Or maybe I’m just misreading the thing. Maybe I’m just over-reacting to the now ritual comparison of Kew’s operation with the totally different Svalbard Global Seed Vault. Maybe I should just shut up and let you read the piece and decide for yourself.