Genome size variation in Chenopodium quinoa (Chenopodiaceae)

Kolano, Bożena; Siwinska, Dorota; Pando, Luz Gómez; Szymanowska-Pułka, Joanna; Małuszyńska, Jolanta

doi:10.1007/s00606-011-0534-z

Cited by 34 publications

(20 citation statements)

References 25 publications

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“…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.…”

Section: Sequencing Assembly and Annotationsupporting

confidence: 81%

The genome of Chenopodium quinoa

Jarvis

Lightfoot

et al. 2017

Nature

589

706

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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 Annotationsupporting

confidence: 81%

The genome of Chenopodium quinoa

Jarvis

Lightfoot

et al. 2017

Nature

589

706

View full text Add to dashboard Cite

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“…Quinoa is an allotetraploid (2 n = 4 × = 36) with an estimated genome size of 1.45–1.50 Gb (Kolano, Siwinska, Gomez, Szymanowska‐Pulka, & Maluszynska, ). Recently, Jarvis et al.…”

Section: Introductionmentioning

confidence: 99%

“…Quinoa is an allotetraploid (2n = 4 × = 36) with an estimated genome size of 1.45-1.50 Gb (Kolano, Siwinska, Gomez, Szymanowska-Pulka, & Maluszynska, 2012). Recently, Jarvis et al (2017) published a more complete sequence of the quinoa genome with 1.39 gigabases (Gb), generating increased interest on quinoa genetics and genomics research.…”

Section: Introductionmentioning

confidence: 99%

Effect of high temperature on pollen morphology, plant growth and seed yield in quinoa (Chenopodium quinoa Willd.)

Hinojosa

Matanguihan

Murphy

2018

J Agronomy Crop Science

106

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Quinoa (Chenopodium quinoa Willd.) has gained considerable attention worldwide during the past decade due to its nutritional and health benefits. However, its susceptibility to high temperatures has been reported as a serious obstacle to its global production. The objective of this study was to evaluate quinoa growth and pollen morphology in response to high temperatures. Pollen morphology and viability, plant growth and seed set, and several physiological parameters were measured at anthesis in two genotypes of quinoa subjected to day/night temperatures of 22/16°C as a control treatment and 40/24°C as the heat stress treatment. Our results showed that heat stress reduced the pollen viability between 30% and 70%. Although no visible morphological differences were observed on the surface of the pollen between the heat‐stressed and non‐heat‐stressed treatments, the pollen wall (intine and extine) thickness increased due to heat stress. High temperature did not affect seed yield, seed size and leaf greenness. On the other hand, high temperature improved the rate of photosynthesis. We found that quinoa has a high plasticity in response to high temperature, though pollen viability and pollen wall structure were affected by high temperatures in anthesis stage. This study is also the first report of quinoa pollen being trinucleate.

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“…Its grain has an excellent balance of carbohydrates, lipids, and proteins with essential amino acid compositions optimal for human nutrition (Popenoe et al 1989). Chenopodium quinoa is an allotetraploid species with 2 n = 4 x = 36 chromosomes and relatively small genome (1.487 pg/1C or 1,453.8 Mb; Kolano et al 2012), which shows disomic inheritance for most qualitative traits (Ward 2000). Although recent studies of the quinoa genome have provided some insight into its origin and composition of its repetitive genome fraction (Mason et al 2005; Maughan et al 2006; Kolano et al 2008, 2011), retrotransposable elements were not analyzed so far.…”

Section: Introductionmentioning

confidence: 99%

Isolation and characterization of reverse transcriptase fragments of LTR retrotransposons from the genome of Chenopodium quinoa (Amaranthaceae)

2013

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Key messageHigh heterogeneity was observed among conserved domains of reverse transcriptase (rt)isolated from quinoa. Only one Ty1-copia rtwas highly amplified. Reverse transcriptase sequences were located predominantly in pericentromeric region of quinoa chromosomes.AbstractThe heterogeneity, genomic abundance, and chromosomal distribution of reverse transcriptase (rt)-coding fragments of Ty1-copia and Ty3-gypsy long terminal repeat retrotransposons were analyzed in the Chenopodium quinoa genome. Conserved domains of the rt gene were amplified and characterized using degenerate oligonucleotide primer pairs. Sequence analyses indicated that half of Ty1-copia rt (51 %) and 39 % of Ty3-gypsy rt fragments contained intact reading frames. High heterogeneity among rt sequences was observed for both Ty1-copia and Ty3-gypsy rt amplicons, with Ty1-copia more heterogeneous than Ty3-gypsy. Most of the isolated rt fragments were present in quinoa genome in low copy numbers, with only one highly amplified Ty1-copia rt sequence family. The gypsy-like RNase H fragments co-amplified with Ty1-copia-degenerate primers were shown to be highly amplified in the quinoa genome indicating either higher abundance of some gypsy families of which rt domains could not be amplified, or independent evolution of this gypsy-region in quinoa. Both Ty1-copia and Ty3-gypsy retrotransposons were preferentially located in pericentromeric heterochromatin of quinoa chromosomes. Phylogenetic analyses of newly amplified rt fragments together with well-characterized retrotransposon families from other organisms allowed identification of major lineages of retroelements in the genome of quinoa and provided preliminary insight into their evolutionary dynamics.

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Genome size variation in Chenopodium quinoa (Chenopodiaceae)

Cited by 34 publications

References 25 publications

The genome of Chenopodium quinoa

The genome of Chenopodium quinoa

Effect of high temperature on pollen morphology, plant growth and seed yield in quinoa (Chenopodium quinoa Willd.)

Isolation and characterization of reverse transcriptase fragments of LTR retrotransposons from the genome of Chenopodium quinoa (Amaranthaceae)

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