Draft genome sequence of an inbred line of<i>Chenopodium quinoa</i>, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties

Yasui, Yukihiko; Hirakawa, Hideki; Oikawa, Tetsuo; Toyoshima, Masami; Matsuzaki, Chiaki; Ueno, Makoto; Mizuno, Nobuyuki; Nagatoshi, Yukari; Imamura, Toru; Manami, Miyago; Tanaka, Kojiro; Mise, Kazuyuki; Tanaka, Tsutomu; Mizukoshi, Hiroharu; Mori, Masashi; Fujita, Yasunari

doi:10.1093/dnares/dsw037

Cited by 88 publications

(96 citation statements)

References 82 publications

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“…Pseudomolecules (hereafter referred to as chromosomes, which are numbered according to a previously published single-nucleotide polymorphism (SNP) linkage map 13 ) were created by anchoring 565 scaffolds to the linkage map, representing 1.18 Gb (85%) of the total assembly length ( Table 1, Supplementary Data 1, Supplementary Data 2). This assembly represents a substantial improvement over the previously published quinoa draft genome sequence, which contained more than 24,000 scaffolds with 25% missing data 14 .…”

Section: Sequencing Assembly and Annotationmentioning

confidence: 96%

The genome of Chenopodium quinoa

Jarvis

Lightfoot

et al. 2017

Nature

567

644

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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 ...

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Section: Sequencing Assembly and Annotationmentioning

confidence: 96%

The genome of Chenopodium quinoa

Jarvis

Lightfoot

et al. 2017

Nature

567

644

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“…Its genomic complexity and polyploid nature have made molecular genetic analyses of the genetic mechanisms underlying its salt tolerance traits challenging. However, the draft genome of C. quinoa that was recently made available will be an excellent resource opening new paths to explore its stress adapted biology (Yasui et al, 2016). Also, the genome of the closely related non-halophyte Beta vulgaris (Amaranthaceae) and additional transcriptomes of the halophytic but non-salt gland subspecies B. vulgaris ssp.…”

Section: New Genetic Resources and Tools Provide Insights Into The Momentioning

confidence: 99%

Making Plants Break a Sweat: the Structure, Function, and Evolution of Plant Salt Glands

Dassanayake

Larkin

2017

Front. Plant Sci.

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Salt stress is a complex trait that poses a grand challenge in developing new crops better adapted to saline environments. Some plants, called recretohalophytes, that have naturally evolved to secrete excess salts through salt glands, offer an underexplored genetic resource for examining how plant development, anatomy, and physiology integrate to prevent excess salt from building up to toxic levels in plant tissue. In this review we examine the structure and evolution of salt glands, salt gland-specific gene expression, and the possibility that all salt glands have originated via evolutionary modifications of trichomes. Salt secretion via salt glands is found in more than 50 species in 14 angiosperm families distributed in caryophyllales, asterids, rosids, and grasses. The salt glands of these distantly related clades can be grouped into four structural classes. Although salt glands appear to have originated independently at least 12 times, they share convergently evolved features that facilitate salt compartmentalization and excretion. We review the structural diversity and evolution of salt glands, major transporters and proteins associated with salt transport and secretion in halophytes, salt gland relevant gene expression regulation, and the prospect for using new genomic and transcriptomic tools in combination with information from model organisms to better understand how salt glands contribute to salt tolerance. Finally, we consider the prospects for using this knowledge to engineer salt glands to increase salt tolerance in model species, and ultimately in crops.

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“…Betacyanins can be further modified by betalain-related glucosyltransferases that catalyse the 5-O-glucosylation of cyclo-DOPA (Sasaki et al, 2005) or alternatively the 5-O-or 6-O-glucosylation of betanidin (Figure 1a, Das et al, 2013;Vogt, 2002;Vogt et al, 1999). Recently, our group and others sequenced the quinoa genome (Jarvis et al, 2017;Yasui et al, 2016;Zou et al, 2017), and based on these genomic data, we identified the genes responsible for betalain biosynthesis including CqCYP76AD1, CqDODA and CqCDOPA5GT (Imamura et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Isolation of amaranthin synthetase from Chenopodium quinoa and construction of an amaranthin production system using suspension‐cultured tobacco BY‐2 cells

Imamura

Isozumi

Higashimura

et al. 2018

Plant Biotechnology Journal

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Summary Betalains are plant pigments primarily produced by plants of the order Caryophyllales. Because betalain possesses anti‐inflammatory and anticancer activities, it may be useful as a pharmaceutical agent and dietary supplement. Recent studies have identified the genes involved in the betalain biosynthesis of betanin. Amaranthin and celosianin II are abundant in the quinoa ( Chenopodium quinoa Willd.) hypocotyl, and amaranthin comprises glucuronic acid bound to betanin; therefore, this suggests the existence of a glucuronyltransferase involved in the synthesis of amaranthin in the quinoa hypocotyl. To identify the gene involved in amaranthin biosynthesis, we performed a BLAST analysis and phylogenetic tree analysis based on sequences homologous to flavonoid glycosyltransferase, followed by expression analysis on the quinoa hypocotyl to obtain three candidate proteins. Production of amaranthin in a transient Nicotiana benthamiana expression system was evaluated for these candidates and one was identified as having the ability to produce amaranthin. The gene encoding this protein was quinoa amaranthin synthetase 1 ( CqAmaSy1 ). We also created a transgenic tobacco bright yellow‐2 ( BY ‐2) cell line wherein four betalain biosynthesis genes were introduced to facilitate amaranthin production. This transgenic cell line produced 13.67 ± 4.13 μ m (mean ± SEM ) amaranthin and 26.60 ± 1.53 μ m betanin, whereas the production of isoamaranthin and isobetanin could not be detected. Tests confirmed the ability of amaranthin and betanin to slightly suppress cancer cell viability. Furthermore, amaranthin was shown to significantly inhibit HIV ‐1 protease activity, whereas betanin did not.

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Draft genome sequence of an inbred line ofChenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties

Cited by 88 publications

References 82 publications

The genome of Chenopodium quinoa

The genome of Chenopodium quinoa

Making Plants Break a Sweat: the Structure, Function, and Evolution of Plant Salt Glands

Isolation of amaranthin synthetase from Chenopodium quinoa and construction of an amaranthin production system using suspension‐cultured tobacco BY‐2 cells

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