And talking of horses. It’s kinda amazing to think that the dog and the horse, eventually domesticated at different times and in different places in Eurasia, can trace their lineages back to ancestors which co-evolved as hunter and prey on the grasslands of a continent — North America — which was at the time completely cut off from the rest of the world, and to which they were re-introduced, again quite independently, millions of years later.
Nibbles: Desert garden, Funding, Vegetables, Communication, Ecosystem services, Bees, Native grasses, Soil, Raspberries, Ancient ag trade, Soybeans, Ag origins
- “See how beautiful you can make with small water!”
- IRRI redux.
- The problems of vegetable production in Africa, in microcosm.
- “This is a local production, storage and distribution system, a huge exhibit of biodiversity.’’
- PNAS special issue on ecosystem services.
- Bee books.
- Switch to switchgrass.
- More than you probably want to know about earthworms.
- Evil Fruit Lord questions Scotland-China raspberry deal.
- Ancient crop DNA recovered from underwater amphorae. Totally amazing.
- Nutritionist introduces soybeans to Afghanistan.
- Early PNG agricultural site added to UNESCO World Heritage list.
Grey horses understood
An easy way to mark yourself as a novice is to call a white horse white. They’re greys. I don’t know why, but there it is. ((Probably specifically to enable horsey types to act superior.)) Today, thanks to a paper in Nature Genetics, I do know why they’re grey. ((Gerli Rosengren Pielberg, Anna Golovko, Elisabeth Sundström, Ino Curik, Johan Lennartsson, Monika H Seltenhammer, Thomas Druml, Matthew Binns, Carolyn Fitzsimmons, Gabriella Lindgren, Kaj Sandberg, Roswitha Baumung, Monika Vetterlein, Sara Strömberg, Manfred Grabherr, Claire Wade, Kerstin Lindblad-Toh, Fredrik Pontén, Carl-Henrik Heldin, Johann Sölkner, Leif Andersson (2008). A cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the horse Nature Genetics, (), – DOI: 10.1038/ng.185)) Turns out they are over-expressing two genes on horse chromosome 25, thanks to a duplicated bit of DNA 4600 base pairs long. And that’s true in more than 800 greys from 8 different breeds. the duplication has not been found in any non-grey horses.
Greys generally start off with dark hair, but gradually lose the dark pigment, leaving them with white hair and, usually, black-skin. Alas, greys also often develop melanomas that reduce their lifespan, and also show depigmentation of the skin like viteligo in humans. So what’s going on? Leif Andersson and his colleagues suggest that maybe the two genes, called STX17 and NR4A3, may be speeding up the rate of division of pigment cells in the skin and the hair follicles. In the skin, this leads to melanomas. In the hair follicles it depletes the stem cells.
Nibbles: Overexploitation, development, coat colour, water
- TRAFFIC says many traditional medicines are being over-exploited in Cambodia and Viet Nam. Via .
- New model of development more important than new green revolution, says IICA head.
- Baa baa black sheep, have you any genes?
- Food crisis, energy crisis; what about the water crisis? IWMI resurrects 2007 report. More here.
Growing bigger rice grains
The Indiana Joneses of domestication are better served by a DNA sequencer than a bullwhip, but they’re digging up stuff that’s every bit as exciting as a crystal skull. ((Yeah, right. If you’re a complete crop dork.)) Latest case in point, a paper published online in Nature Genetics today by Takeshi Izawa and colleagues at the National Institute of Agrobiological Sciences in Tsukuba, Japan. ((Shomura, A., Izawa, T., Ebana, K., Ebitani, T., Kanegae, H., Konishi, S., Yano, M. (2008). Deletion in a gene associated with grain size increased yields during rice domestication. Nature Genetics. DOI: 10.1038/ng.169)) They’ve discovered that a single mutation — the loss of just 1212 DNA code letters — was a fundamental step in the domestication of rice.
Agroarchaeologists have always had a fun time sitting in armchairs, waving their arms and saying things like “and then people would select for larger grains”. But really, how much heritable variation is there in grain size in a variety? Not a lot, given that 100-seed weight is sometimes sufficiently invariable as to be a diagnostic characteristic.
Domesticated rice definitely has larger grains, and more of them, than Oryza rufipogon, the ancestor of both indica and japonica modern rices. There’s still some argument over whether the two types were truly independently domesticated, but if not they have certainly been evolving separately since domestication. So Izawa et al. crossed Nipponbare (that’s it, below), a large-grained japonica, and Kasalath, a thin-grained indica, and looked for genetic differences associated with differences in the width of the rice seeds.
They found several, of which one, called qSW5, because it is a quantitative trait locus for seed width on chromosome 5, explained almost 40% of the natural variation in seed width. They then created a variety that contained the crucial bit of Kasalath chromosome 5 in a background of Nipponbare genes. That revealed a greater number of rows of specialized cells in the outer glume, a known determinant of grain size. Cloning the gene and putting it into thin-grained Kasalath resulted in larger grains.
They also looked for the qSW5 gene in more than 100 japonica and indica landraces, and found a clear link between the Nipponbare version of the gene, with the deletion, and wider grains.
A final piece of evidence. In a field trial, Nipponbare with the Kasalath gene yielded 10% less, while Kasalath with the Nipponbare gene had heavier grains.
All of which leads Izawa to comment that “qSW5 is a domestication-related gene in rice” and to suggest “the possible use of the defective qSW5 allele for a breeding program of new indica cultivars”.
The deletion in the qSW5 gene that results in fatter grains is a functional nucleotide polymorphism (FNP). It is good to see the researchers refer to it as “defective” even though we don’t actually know how it might be selected against in the wild-type population. In a neat coda to the main study, the researchers looked at two other FNPs associated with domestication, one that controls the taste and texture of cooked rice grains and one that keeps the rice grains attached to their stalk. ((This loss of shattering is often a diagnostic of domestication.)) With the wild rice alleles for comparison, they examined 142 rice landraces to see which varieties had the old — i.e. unselected — version of each of the three FNPs.
Most of the indica landraces carried the original alleles. A distinct group of japonica varieties had all three FNPs. This supports the idea of two independent domestications. ((Astonishing! We were blogging about the geography of rice (albeit in a slightly different context, exactly one year ago today.)) And among the japonicas, there were some landraces that had only one or two of the FNPs, suggesting that there are true “heritage” varieties with a longer independent history. I’m sure those are properly conserved in genebanks.