Quinoa has the potential to provide a highly nutritious food source that can be grown on marginal lands not currently suitable for other major crops. Quinoa has gained international attention because of the nutritional value of its seeds, which are gluten-free, have a low glycaemic index 5, and contain an excellent balance of essential amino acids, fibre, lipids, carbohydrates, vitamins, and minerals 6. Quinoa has adapted to the high plains of the Andean Altiplano (>3,500вЂ‰m above sea level), where it has developed tolerance to several abiotic stresses 2, 3, 4. It was presumably first domesticated more than 7,000 years ago by pre-Columbian cultures and was known as the вЂmother grainвЂ™ of the Incan Empire 1. Quinoa (Chenopodium quinoa Willd., 2 nвЂ‰=вЂ‰4 xвЂ‰=вЂ‰36) is a highly nutritious crop that is adapted to thrive in a wide range of agroecosystems. These genomic resources are an important first step towards the genetic improvement of quinoa. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex.

Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. Unfortunately, few resources are available to facilitate its genetic improvement. Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security.

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