Genomics

Keen insights from quinoa

Technological advances have allowed scientists to sequence the complex quinoa genome. This highlights the ongoing expansion of genomics beyond major crops to other plants that have relevance for global food security. See Article p.307

In 2006, one of us estimated that, given ongoing technological advances, 200 domesticated plants would be sequenced within 14 years1. Genomics has already outstripped this prediction, with most major crop plants, domesticated animals and model organisms having now been sequenced. Nonetheless, the genomes of many organisms that are valuable to local communities and have potentially high salience to a world challenged by issues of food security remain to be tackled. One example of such an organism is the Andean crop quinoa (Chenopodium quinoa). On page 307, Jarvis et al.2 report a high-quality genome sequence for this species.

Archaeological evidence3 indicates that quinoa was domesticated some 7,000 years ago in the high plateau around Lake Titicaca in the Andes (Fig. 1), becoming a major food crop for Andean civilizations that preceded the Inca3,4. Quinoa was prized for its nutritional qualities and adaptability to diverse environments, growing at an exceptional range of altitudes (from sea level to 4 kilometres above it), temperatures (from −8 °C to 38 °C), humidities and soil conditions5. By the mid-twentieth century, quinoa had fallen out of fashion, being cultivated mainly by isolated native communities in the Andean highlands. It wasn't until the 1970s that the plant's nutritional and commercial potential began to be more widely appreciated6, but increased scientific input into breeding programmes will be needed if the full potential of this crop is to be realized.

Figure 1: Quinoa plants grown at high altitude.
figure1

David Jarvis/Ivan Gromicho

Jarvis et al.2 have sequenced the genome of Chenopodium quinoa.

With this aim in mind, Jarvis et al. sequenced the approximately 1.5-gigabase-long genome of C. quinoa. This species, like many plants, is polyploid — it has four copies of each of its nine chromosomes, because it arose by hybridization of two ancestral diploid species (which have two sets of chromosomes). The ancestors, dubbed A and B, each contributed two sets of nine chromosomes to the polyploid progeny. The authors used single-molecule, real-time sequencing in combination with a range of sophisticated mapping techniques to properly interleave otherwise-isolated DNA sequences with one another.

This integration of sequencing and mapping techniques led to the assembly of 439 sequence 'scaffolds' that together covered 90% of the genome and that aligned into 18 groups, matching the 18 basal chromosomes (one set of 9 derived from each ancestor). This feat is particularly impressive given that, as the authors note, a remarkable 64% of the quinoa genome consists of repetitive DNA, making it challenging to find the islands of unique sequence that are necessary to piece together the jigsaw puzzle of its chromosomes.

A combination of transcript analysis and ab initio prediction (in which the genome is searched for sequences characteristic of genes) suggested that the genome contains 44,776 genes. Of an existing database of 956 known quinoa genes, 97.3% were found in the current sample, indicating that the sequence covers nearly the whole genome.

Next, the authors generated draft (less in-depth) sequences for other members of the Chenopodium genus: 15 genetically different quinoa strains (accessions); five and two accessions, respectively, of polyploid relatives C. berlandieri and C. hircinum; and two diploid plants, C. pallidicaule and C. suecicum, which are descended, respectively, from the suspected A and B progenitors of quinoa. These data provided insight into the radiation and domestication of Chenopodium species.

Comparison with quinoa's two suspected diploid progenitors revealed that nine of the basal C. quinoa chromosomes more closely resemble the A genome progenitor C. pallidicaule, which derives from the New World. The other nine resemble the Eurasian B genome progenitor C. suecicum. These data provide further support for the existing theory7 that the Eurasian progenitor dispersed across the ocean prior to formation of the polyploid C. quinoa, 3.3 million to 6.3 million years ago.

A constraint on the widespread acceptance of quinoa as a major crop for human consumption is the bitter-tasting compounds called saponins that coat quinoa seeds. These compounds deter pests, but destroy red blood cells and so must be removed before consumption — a process that uses water- and labour-intensive techniques. Certain 'sweet' quinoa lines produce very low levels of saponins. However, these strains are not yet widely cultivated in the Andes, at least in part because of increased predation by birds and other pests, which results in lower yields.

In their final experiments, Jarvis et al. identified a DNA sequence associated with the presence or absence of saponins. The candidate sequence is a small genomic region encoding two transcription factors that are involved in saponin biosynthesis. Only one of these, AUR62017204, is expressed in seeds, with its expression in sweet quinoa lines producing a truncated protein that presumably results in reduced saponin production.

The authors' genome sequence overcomes key obstacles to the study and use of quinoa, but challenges remain. For example, proof that an AUR62017204 variant confers 'sweetness' will require demonstration that introduction of this variant into wild-type quinoa reduces saponin production. Such introduction could be achieved either as part of an engineered genetic construct (which has not been done, to our knowledge) or by replacing the wild-type sequence with the sweet variant using genome editing (a possibility that involves some time and cost).

Using the information gained from the genome to improve quinoa production will require invigorated breeding efforts. Likewise, identification of the defences used by quinoa and other members of the Amaranthaceae family of plants to achieve stress tolerance in a range of environments will require much fundamental research. The transfer of these abiotic stress defences — or of other traits — from quinoa to other crops is an intriguing possibility, but far from trivial.

Nonetheless, the ability to rapidly gain insights into the biology and evolution of characteristics of interest in particular organisms will lead to new agricultural possibilities. For example, if diagnostic DNA markers for a trait of interest or genome editing can be used to speed up the breeding of commercially viable sweet quinoa varieties, it could provide an economic opportunity for farmers in the Andes and beyond, increasing food production in challenging environments. Sequencing the genomes of other neglected food crops8 could lay the foundations for further contributions to global food security.Footnote 1

Notes

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Correspondence to Andrew H. Paterson or Alan L. Kolata.

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Paterson, A., Kolata, A. Keen insights from quinoa. Nature 542, 300–302 (2017). https://doi.org/10.1038/nature21495

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