The genome of Chenopodium quinoa

Abstract

Quinoa (Chenopodium quinoa Willd., 2n = 4x = 36) is a highly nutritious crop that is adapted to thrive in a wide range of agroecosystems. It was presumably first domesticated more than 7,000 years ago by pre-Columbian cultures and was known as the 'mother grain' of the Incan Empire 1 . Quinoa has adapted to the high plains of the Andean Altiplano (> 3,500 m above sea level), where it has developed tolerance to several abiotic stresses [2][3][4] . 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 the potential to provide a highly nutritious food source that can be grown on marginal lands not currently suitable for other major crops. This potential was recognized when the United Nations declared 2013 as the International Year of Quinoa, this being one of only three times a plant has received such a designation.Despite its agronomic potential, quinoa is still an underutilized crop 7 , with relatively few active breeding programs 8 . Breeding efforts to improve the crop for important agronomic traits are needed to expand quinoa production worldwide. To accelerate the improvement of quinoa, we present here the allotetraploid quinoa genome. We demonstrate the utility of the genome sequence by identifying a gene that probably regulates the presence of seed triterpenoid saponin content. Moreover, we sequenced the genomes of additional diploid and tetraploid Chenopodium species to characterize genetic diversity within the primary germplasm pool for quinoa and to understand sub-genome evolution in quinoa. Together, these resources provide the foundation for accelerating the genetic improvement of the crop, with the objective of enhancing global food security for a growing world population. Sequencing, assembly and annotationWe sequenced and assembled the genome of the coastal Chilean quinoa accession PI 614886 (BioSample accession code SAMN04338310) using single-molecule real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio) and optical and chromosome-contact maps from BioNano Genomics 9 and Dovetail Genomics 10 . The assembly contains 3,486 scaffolds, with a scaffold N50 of 3.84 Mb and 90% of the assembled genome contained in 439 scaffolds (Table 1). The total assembly size of 1.39 gigabases (Gb) is similar to the reported size estimates of the quinoa genome (1.45-1.50 Gb (refs 11,12)). To combine scaffolds into pseudomolecules, an existing linkage map from quinoa 13 was integrated with two new linkage maps. The resulting map (Extended Data Fig. 1) of 6,403 unique markers spans a total length of 2,034 centimorgans (cM) and consists of 18 linkage groups (Supplementary Table 7), corresponding to the haploid chromosome number of quinoa. Pseudomolecules (hereafter referred to as chromosomes, which are numbered according to a previously published single-nucleotide polymorphism (SNP) linkage ...

Morphological Traits Defining Breeding Criteria for Coastal Quinoa in Chile

“…These ecotypes correspond to (i) Inter Andean valleys quinoa (in Colombia, Ecuador, and Peru); (ii) Highlands quinoa (in Peru and Bolivia); (iii) Yungas quinoa (in Bolivian subtropical forest); (iv) Salares quinoa in salt flats (in Bolivia, northern Chile, and Argentina); and (v) Coastal quinoa, from lowlands or sea level (in central and southern Chile) (Risi and Galway 1984;Fuentes et al, 2012). The expansion routes from the Titicaca Lake have been supported with genetic data as revealed with the use of molecular markers and genomic resources of the quinoa genome (Fuentes et al, 2009Jarvis et al, 2017).…”

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing

“…This has been used to vastly improve the lettuce (Lactuca sativa) genome (Reyes-Chin-Wo et al, 2017), and it offers the future possibility of improving fragmented plant genome assemblies to chromosome scale. Combinations of new long-range sequencing technologies are also powerful and have been used to sequence, e.g., a desiccation tolerant grass (VanBuren et al, 2015) and quinoa (Jarvis et al, 2017). However, these long-range sequencing technologies rely on previous extraction of high quality, high molecular weight DNA, which can be an additional challenge in many plants due to both cell walls and secondary metabolite content.…”

Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

“…Indeed, the sequencing and assembly methods required to achieve a high level of contiguity are well within reach of many laboratories, including those working with trees (Neale et al, 2014), minor crops (Clouse et al, 2016;Jarvis et al, 2017), or ecological systems (Martínez-García et al, 2016;Olsen et al, 2016;Tang et al, 2016;Vining et al, 2017). If a research group invests in mate-pair or long-read sequencing at high depth, it is natural to proceed to genome assembly, even though the assembly may never be used for map-based cloning or genetic analysis in the traditional sense.…”