Speedy rice

Here’s a time-lapse video of the long-term continuous-cropping experiment at IRRI. I didn’t dare turn the music off in case someone was going to tell me something interesting about it all. They didn’t, which makes it just interesting eye-candy. In my opinion, the video would also benefit if it gave some sense of the passing of real time — maybe an animated timeline?

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.1 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 Science2 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.

  1. 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. []
  2. 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 []

Snorkel rice

ResearchBlogging.orgYoko Hattori and colleagues report in Nature1 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 gene2, 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 gene3 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.

  1. 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 []
  2. 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

  3. The combination of the two would make for an interesting experiment. []

Pesticide brigades

It is well established that brown plant hopper outbreaks in rice are caused by the use of pesticides. So why do farmers and their advisers spray even more when there is an outbreak?

According to this post on the Ricehoppers blog, it might be because plant protection services (in Vietnam) operate like fire brigade services, equipped for rapid response and control. And because, for the people leading these services, it is better to do the wrong thing (spray) then to be perceived as not acting (and perhaps lose their job).

Perhaps, like modern fire brigades, plant protection services will be able to shift their emphasis to prevention. And, like modern fire-ecologists, learn to let the occasional outbreak run its course.

Darwin’s kitchen

By Jacob van Etten

It’s January 2009, the Darwin storm breaks loose. A taste of things to come is the publication of a revived and illustrated version of Emma Darwin’s recipe notebook. When authors Dusha Bateson and Weslie Janeway heard about the booklet in the Cambridge University Library they were “very concerned they wouldn’t be able to get a book out of it.” Yet they tried out every recipe and converted dust into gold by publishing them in a colourful cookbook.

Weslie Janeway says:

One of the things that is very clear is that people ate much more seasonally then – although we see the beginnings of modern food supply. For example, they married in 1839, and the railroads were being built. And it began to be possible to have fish away from the coast. Rice was arriving from the rice plantations in America. Basically, they had root vegetables all winter.

The recipe for boiling rice is in Charles Darwin’s own hand.