Quinoa genome sequenced

09 February 2017
Posted by Chris Smith.

The Incas called it the "mother grain" while middle class residents of Cambridge and Canberra call it lunch. But, for many, the quinoa plant - or Chenopodium quinoa to give it its proper name, which can tolerate extremes of salt, drought and temperature yet still produce nutritious seeds, could be a future lifeline. Now scientists have decoded its genome to reveal where this extraordinary crop came from, and how it can handle such harsh conditions.

Archaeological evidence suggests that quinoa was once widely cultivated. On a plateau around Peru's Lake Titicaca, nearly 4 kilometres above sea level where temperatures vary from below freezing to a scorching 38 degrees Celsius, these plants flourished and fed the pre-Columbian inhabitants of the region.

But eschewed by the Spanish invaders, quinoa then fell out of fashion for a few hundred years. More recently, amid concerns fuelled by a rising human population, grim climate change predictions and fears about food security, interest in quinoa is growing again.

The reason is the plant's remarkable resilience, evolved over millennia of tolerating some of the harshest conditions on Earth. It grows on some of the world's poorest, salt-polluted soils, tolerating a huge range of humidities and temperatures. Nevertheless, the seeds it produces are plentiful, protein-rich, gluten-free and have a low glycaemic index. They also taste great.

The downside is that some of the more productive quinoa varieties deter predators by coating their seeds with mildly toxic bitter-tasting soapy compounds called saponins. These can be washed off, but, in a water-poor environment, this would defeat the object of growing the plant in the first place. Also, some of the plants with the greatest environmental resilience characteristics are not the highest yielding.

This is where the genome sequence of the plant can help. Publishing the results in Nature, KAUST plant scientist Mark Tester and his team have painstakingly unpicked the genetic code of quinoa and a number of its close relatives.

The job has been challenging because quinoa doesn't just have one genome, like a human, it has two, which are dubbed A and B. This is the result of a hybridisation event - like a genetic merger - between two different ancestors of the plant a few million years ago. Piecing together which sequences go with which genome, particularly in areas when the DNA message repeats itself many times, is extremely tough.

Now Tester's team have achieved this though, they are making hay, if not quinoa, while the genetic sun shines. The quinoa plant, they now know, has about 1.3 billion genetic letters in its DNA code spelling out more than 44,000 genes spread across 18 chromosomes.

They don't yet know what all of those genes do, but the genome serves as a road map, enabling plant breeders and other scientists to identify the key regions responsible for conferring specific traits on the plants. By comparing plants that add greater or lesser amounts of saponins to their seeds, for instance, they've already been able to single out the genetic region responsible, making it much easier to breed the trait out.

"Rather than having to wait 3 months for the plant to grow and then test the seeds, we can test a small amount of leaf tissue in a plant just a few days old [to see if it has the saponin genes]," says co-author Sandra Schmoeckel.

In the same way, the genome sequence generated by the team means that scientists will be able to map out many of the "markers" that highlight other beneficial traits in the plants, like salt and temperature tolerance, so they can select for these during breeding and crossing experiments or through the use of GM technology.

Importantly, by working out how quinoa does it, it might even be possible to move the genes responsible into other key crop plants, to reinforce rice, soy or cereals, although this is still some way off. "It's an intriguing possibility," observes University of Georgia plant scientist Andrew Paterson, who was not involved in the study. "But it's far from trivial!"

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