Cross-breeding could create rice varieties that can survive flooding and fungi.
Japanese research teams have pinpointed the genes in hardy varieties of rice that help the plants to outgrow rising paddy-field waters and fend off fungal infections. Having these genes in more vulnerable rice varieties could save billions of dollars and feed millions more people.
The two papers are "very welcome at a time of increasingly difficult challenges to rice growing", says Michael Jackson, a plant physiologist at the University of Bristol, UK.
In the first study, published in Nature1 on 19 August, Motoyuki Ashikari, at Nagoya University in Japan, and his colleagues found two genes that help plants to keep their leaves above water when partially submerged. In the second study, published in Science2 on 20 August, a team led by Shuichi Fukuoka at the National Institute of Agrobiological Sciences in Tsukuba, Japan, has found a gene that helps some types of rice fight off fungal infection — and successfully isolated it from a linked stretch of DNA responsible for the terrible flavour of the wild varieties.
The Nature study focused on the threat posed by deep flooding, which affects more than 25% of global rice-producing land. Most rice plants (Oryza sativa) die if completely submerged for more than a few days. But some rice varieties can survive the conditions by rapidly shooting up in height. These plants are typically far less productive, however, so researchers have sought the genes responsible for flood tolerance in the hope of introducing them into high-yielding rice varieties.
In 2006, a team led by David Mackill at the International Rice Research Institute in the Philippines discovered similar flood-tolerance genes — a genetic cluster called Submergence 1 that allowed plants to survive for more than two weeks by entering a dormant state when completely submerged3 (see 'Rice made to breathe underwater').
Ashikari's team examined three genomic regions that they had found helped rice to grow. In the region that added the greatest growth boost, they mapped a pair of genes — dubbed SNORKEL1 and SNORKEL2 — that together can trigger growth of up to 8 metres in the face of rising water levels (see video).
Julia Bailey-Serres, a molecular geneticist at the University of California, Riverside, says that the Submergence and Snorkel genes can now be crossed into common rice varieties to protect crops exposed to different flooding scenarios. When flooding is deep and quick, Submergence genes might be best; but when floodwaters climb in a progressive and prolonged fashion, Snorkel genes will be more effective. "It provides two strategies and they both have their importance," she says.
Intriguingly, the same plant hormone, ethylene, stimulates both the escape strategies. "What has happened with natural selection apparently is that that pathway is where things are tweaked evolutionarily," says Bailey-Serres. The mutation in the Snorkel pathway probably came first, though, adds Ashikari. Some wild rice species possess Snorkel genes, whereas only domesticated breeds contain the Submergence genes, he says.
Flooding is not the only threat to the world's largest diet staple. Rice blast disease destroys around 10-30% of global rice crops — enough food to feed about 60 million people each year. Some rice plants are resistant to the pernicious fungus responsible the disease, but the rice from these plants often has undesirable qualities, such as lower stickiness and poor flavour, so they have not been introduced into widely consumed rice varieties. Some researchers have speculated that blast-immunity genes might directly confer terrible taste, but Fukuoka and his colleagues have shown that resistance and bad taste can be teased apart2.
The team cloned a gene called Pi21, and showed that plants with two rare deletions had around 10 times fewer blast lesions than wild-type rice, yet these same plants tasted awful. Fukuoka's group crossed the resistance gene into a tastier breed, and mapped the foul flavour to a point a few thousand nucleotides downstream of the Pi21 gene, indicating that Pi21 itself does not harm the rice's taste.
Both research teams are breeding more-durable rice varieties. No genetic engineering is required, says Ashikari, because all of these genes can be transferred by crossing. Once these new cultivars are made, however, they still need to be tested — both in the paddy and on the plate. "We need to see how these behave in field situations and how they can be used in a rice breeding programme," says Mackill.
Hattori, Y. et al. Nature advance online publication doi:10.1038/nature08258 (2009).
Fukuoka, S. et al. Science 325, 998-1001 (2009).
Xu, K. et al. Nature 442, 705-708 (2006).
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Frontiers in Plant Science (2019)