Author: Robert Hijmans

Posted on

Maize mystery solved

ResearchBlogging.org Joost van Heerwarden and co-workers ((van Heerwaarden J, Doebley J, Briggs WH, Glaubitz JC, Goodman MM, de Jesus Sanchez Gonzalez J, & Ross-Ibarra J (2010). Genetic signals of origin, spread, and introgression in a large sample of maize landraces. Proceedings of the National Academy of Sciences of the United States of America PMID: 21189301)) have solved a problem in our understanding of maize domestication. Previous work had shown that maize originated from Balsas teosinte, Zea mays subspecies parviglumis, a wild species that occurs in low and mid-elevation regions of south-west Mexico ((Matsuoka Y, Vigouroux Y, Goodman MM, Sanchez G J, Buckler E, & Doebley J (2002). A single domestication for maize shown by multilocus microsatellite genotyping. Proceedings of the National Academy of Sciences of the United States of America, 99 (9), 6080-4 PMID: 11983901)). This made the Rio Balsas area, where parviglumis occurs, the most likely area of maize domestication. This was corroborated by Piperno et al.‘s ((Piperno DR, Ranere AJ, Holst I, Iriarte J, & Dickau R (2009). Starch grain and phytolith evidence for early ninth millennium B.P. maize from the Central Balsas River Valley, Mexico. Proceedings of the National Academy of Sciences of the United States of America, 106 (13), 5019-24 PMID: 19307570)) discovery of 8,700 years old maize remains in that area; the oldest evidence of maize unearthed to date.

The problem was that the maize land races genetically most similar to parviglumis are not found there. They occur in the Mexican highlands. And that’s awkward, particularly because highland maize has a rather different set of ecological adaptations than lowland maize.

Van Heerwaarden et al. say this is a paradox caused by the role of another wild species: Zea mays subspecies mexicana. This species occurs in the highlands, and it is inter-fertile with cultivated maize. The tricky thing is that because the two wild species, parviglumis and mexicana, both referred to as teosinte, are closely related, more closely to each other than to their cultivated cousin, geneflow from mexicana makes the genes of highland maize look more like those of parviglumis!

This means that you cannot directly identify the most ancestral maize populations from genetic similarity with their putative ancestor. Instead, Van Heerwaarden et al. estimated ancestral gene frequencies from cultivated maize populations, without direct reference to the wild species. And, Bingo! Western lowland populations are indeed more ancestral than the highland populations. Maize did originate in the lowlands, and from there it spread to the highlands and to other parts of the Americas.

Posted on

Taxonomists to keep jobs until 2515

The second edition of Arthur Chapman’s report “Numbers of Living Species in Australia and the World” was launched this week.

The total number of described species in the world is estimated at just under 1,900,000 — well above the 1,786,000 in the previous report that was published in 2006 ((The figure for Australia, just under 150,000, is much lower than in the previous report; largely due to revised estimates of the number of insects.)). Chapman’s estimate of the total number of species is close to 11 million. A staggering 83% remain undescribed.

And not because taxonomist aren’t beavering away:

About 18,000 new species are being described each year (16,969 in 2006 and 18,516 in 2007). About 75% of the new species described in 2007 were invertebrates, 11% vascular plants and nearly 7% were vertebrates.

That is an impressive feat. But at this rate it will take until 2515 to describe all the species currently alive. Unfortunately, many of them will be extinct by then.

Posted on

Upstream blast

ResearchBlogging.org Blast is one of the worst rice diseases. I believe that, thanks to the breeders, most modern varieties have decent levels of resistance. After all, they can be used in varietal mixtures to protect traditional glutinous rice varieties from blast. ((Zhu, Y., Chen, H., Fan, J., Wang, Y., Li, Y., Chen, J., Fan, J., Yang, S., Hu, L., Leung, H., Mew, T., Teng, P., Wang, Z., & Mundt, C. (2000). Genetic diversity and disease control in rice. Nature, 406 (6797), 718-722 DOI: 10.1038/35021046 Also see this post.)) Unfortunately, much of this resistance is not durable, because the pathogen overcomes it with time.

For a long time, durable resistance has been known to exist in some Japanese varieties. But these varieties have not been useful for resistance breeding, as the resistant parent also brought along undesired characteristics: the offspring always had poor eating quality.

Shuichi Fukuoka and colleagues have found out why. They report in Science ((Fukuoka, S., Saka, N., Koga, H., Ono, K., Shimizu, T., Ebana, K., Hayashi, N., Takahashi, A., Hirochika, H., Okuno, K., & Yano, M. (2009). Loss of Function of a Proline-Containing Protein Confers Durable Disease Resistance in Rice Science, 325 (5943), 998-1001 DOI: 10.1126/science.1175550
see also Normile, D. (2009). New Strategy Promises Lasting Resistance to a Rice Plague Science, 325 (5943), 925-925 DOI: 10.1126/science.325_925)) that it is because of a tight genetic linkage. Resistance is conferred by the Pi21 locus, and:

The eating quality of plants carrying the elite cultivar’s chromosomal sequence from a point less than 2.4 kb downstream of the Pi21 locus was equivalent to that of the elite cultivar, and the plants showed a high level of blast resistance. In contrast, plants carrying the donor chromosomal sequence up to 37 kb downstream of the Pi21 locus showed inferior eating quality.

By crossing in just the right bit of the chromosome, and making sure that the neighboring areas do not tag along, resistance can now be transferred, without spoiling the taste.

Posted on

Nomenclatura

The NYT reports that most cultures use the same categories to classify plants, such as trees, vines, herbs, bushes. People also consistently use two-word combinations for specific organisms within a larger group. At least that is what Cecil Brown found after studying 188 languages. It would be interesting to compare the kinds of labels used for crops and crop varieties across cultures. Has anyone done that?

The article also says that we are “losing the ability to order and name and therefore losing a connection to and a place in the living world.” The other day, Jacob commented on “Los tomates ya no saben a nada” by saying that he has “had more and less tasty Spanish tomatoes this summer. The thing is that you can’t “see” taste when you buy (the variety is not indicated)” ((There are of course many tomatoes that look very unlike the next one, but perhaps these haven’t made it to the Spanish retailers yet; or the difference he tasted had little to do with varieties)).

Should we try to get more variety names in shops, markets, restaurants? The slow/organic/local food movement puts a lot of emphasis on where things are grown, but less on what is grown. Also think Starbucks & co.: coffee from Sumatra, Ethiopia, Antigua; but what variety? And why always arabica? Can’t they serve a nice barako? ((You can get a good barako coffee or ice cream in Cafeño in San Juan, Batangas, Phillipines. And on the way back to Manila have a pako salad at Kusina Salud.))

Posted on

Snorkel rice

ResearchBlogging.orgYoko Hattori and colleagues report in Nature ((Hattori, Y., Nagai, K., Furukawa, S., Song, X., Kawano, R., Sakakibara, H., Wu, J., Matsumoto, T., Yoshimura, A., Kitano, H., Matsuoka, M., Mori, H., & Ashikari, M. (2009). The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water Nature, 460 (7258), 1026-1030 DOI: 10.1038/nature08258)) that they have identified two genes involved in the awesome elongation of deep water rice; the type of rice that can grow in several meters deep water. The genes, baptized SNORKEL1 and SNORKEL2, can now be identified with molecular markers and crossed into popular rice varieties. The BBC has a nice video comparing — I assume — genetically otherwise nearly identical rice varieties with and without the genes.

The avid reader will remember the runner-up entry in The Competion about the sub-1 gene ((

Kenong Xu, Xia Xu, Takeshi Fukao, Patrick Canlas, Reycel Maghirang-Rodriguez, Sigrid Heuer, Abdelbagi M. Ismail, Julia Bailey-Serres, Pamela C. Ronald & David J. Mackill, 2006. Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442: 705-708. doi:10.1038/nature04920
)), that is used by IRRI to make rice flood-proof. Some of these new sub-1 varieties, such as Swarna-sub1 are already grown by farmers in India and Bangladesh.

Interestingly, sub-1 does the very opposite of SNORKEL. Sub-1 shuts the plant off to stop elongation, so that it saves its energy, and can recover later. This works great with flash floods if the water recedes after a week or two. But if the water stays for longer than that, the crop dies. With stagnant deep water, a variety with the SNORKEL gene could be a better bet.

If farmers know beforehand that the water is going to be very deep (because it happens most years), they probably already plant deep water varieties (or plant later or do some other smart thing). Deep water rice is somewhat in decline, because of low yield, but it is grown on a very large area, probably about 3.5 million ha worldwide, mostly in India, Bangladesh, Myanmar, Thailand, Indonesia, Vietnam and Cambodia.

However, if flooding is rare it could be more profitable, though risky, to plant other than deep-water varieties. For their earliness, yield, quality, or what not. Adding either the sub-1 or the SNORKEL gene ((The combination of the two would make for an interesting experiment.)) to those varieties would be an insurance policy for flood years. But which gene to choose? And in what variety? And where to grow it? Not an easy question, but we have been trying to answer it.