Chenopodium polyploidy inferences from Salt Overly Sensitive 1 (SOS1) data

Walsh, Brian M.; Adhikary, Dinesh; Maughan, Peter J.; Emshwiller, Eve; Jellen, Eric N.

doi:10.3732/ajb.1400344

Cited by 52 publications

(46 citation statements)

References 42 publications

(46 reference statements)

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“…Single-gene sequencing studies previously identified pools of North American and Eurasian diploids as candidate sources of the A and B sub-genomes, respectively [20][21][22] , with hybridization occurring somewhere in North America. To understand genome structure and evolution in quinoa further, we sequenced, assembled, and annotated the A-genome diploid C. pallidicaule (commonly called cañahua or kañiwa) and the B-genome diploid C. suecicum 21 (Fig.…”

Section: Evolutionary History Of Quinoamentioning

confidence: 99%

The genome of Chenopodium quinoa

Jarvis

Lightfoot

et al. 2017

Nature

Self Cite

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: Evolutionary History Of Quinoamentioning

confidence: 99%

The genome of Chenopodium quinoa

Jarvis

Lightfoot

et al. 2017

Nature

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589

706

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“…In hexaploid wheat, transcriptome assemblies in ancestral diploid species were used to classify the genes predicted from a de novo genome assembly into the A, B, and D genomes 72 . This was not possible in quinoa because the donor diploid species of the B-genome has yet to be identified, 23 and no genome or transcriptome data of the A-genome species were available. Nevertheless, the fact that we could identify several putative homeologous genes suggests that we were successful in capturing the two subgenomes at least to a certain extent.…”

Section: Resultsmentioning

confidence: 99%

“…Quinoa is an allotetraploid species (2 n = 4 x = 36 with a genome size of 1,448 Mbp) 21 , 22 that consists of two distinct genomes, A and B 23 . Genetic mapping of quinoa has been conducted using amplified fragment length polymorphism (AFLP) markers, 1 simple sequence repeat (SSR) markers, 1 and array-platform markers 24 .…”

Section: Introductionmentioning

confidence: 99%

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

Yasui

Hirakawa

Oikawa

et al. 2016

DNA Res

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Chenopodium quinoa Willd. (quinoa) originated from the Andean region of South America, and is a pseudocereal crop of the Amaranthaceae family. Quinoa is emerging as an important crop with the potential to contribute to food security worldwide and is considered to be an optimal food source for astronauts, due to its outstanding nutritional profile and ability to tolerate stressful environments. Furthermore, plant pathologists use quinoa as a representative diagnostic host to identify virus species. However, molecular analysis of quinoa is limited by its genetic heterogeneity due to outcrossing and its genome complexity derived from allotetraploidy. To overcome these obstacles, we established the inbred and standard quinoa accession Kd that enables rigorous molecular analysis, and presented the draft genome sequence of Kd, using an optimized combination of high-throughput next generation sequencing on the Illumina Hiseq 2500 and PacBio RS II sequencers. The de novo genome assembly contained 25 k scaffolds consisting of 1 Gbp with N50 length of 86 kbp. Based on these data, we constructed the free-access Quinoa Genome DataBase (QGDB). Thus, these findings provide insights into the mechanisms underlying agronomically important traits of quinoa and the effect of allotetraploidy on genome evolution.

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“…The SOS1 gene tree resolves the Chenopodium species studied in three clades, the first comprising of 'Vulvaria' and 'Auricomum' clade, the second clade A of American species and the third large clade is divided into B, C and D clades comprising of polyploids and one Eurasian C. ficifolium. Two distinct lineages of alloploids have been identified of which one is of American tetraploids with homeologs in A and B clades while Eastern Hemisphere hexaploids including C. album (6x) had three distinct genomes with one homeolog each of B, C and D clades [27].…”

Section: Genome Analysis and Origin Of Polyploidy Taxamentioning

confidence: 99%

“…Further evidence for the Eastern Hemisphere hexaploids comprising of three different genomes has come from phylogeny based on two introns of single copy nuclear Salt Overly Sensitive 1 (SOS1) locus [27]. The SOS1 gene tree resolves the Chenopodium species studied in three clades, the first comprising of 'Vulvaria' and 'Auricomum' clade, the second clade A of American species and the third large clade is divided into B, C and D clades comprising of polyploids and one Eurasian C. ficifolium.…”

Section: Genome Analysis and Origin Of Polyploidy Taxamentioning

confidence: 99%

The taxonomic riddle of Chenopodium album L. complex (Amaranthaceae)

Ohri

2015

Nucleus

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C.album L. complex is a heterogenous assemblage of many taxonomic entities of cosmopolitan distribution. This is because many weedy and semi-domesticated forms have arisen due to hybridization and polyploidy. These distinct forms have been perpetuated by their breeding system characterized by high level of selfing and also by the phenological differences. The interrelationships in this aggregate of various taxa are now beginning to be explored. This is mainly because of the economic importance of many semi-domesticated forms providing nutritious leafy vegetable and grains and the economic impact of weedy forms on other crops. The work done on cytology, genome size estimation and molecular markers on various populations and cytotypes has provided tangible results in explaining genetic relationships among different types as well as in unraveling the genomic constitution and origin of polyploid forms. The studies show a great diversity of morphological types and three ploidy levels (2n=18, 36, 54) in C.album complex. The 4x type from North West India is genetically different from 2x and 6x types. The 6x types have been shown to be allopolyploids based on karyotypes, genomic in situ hybridization, flavonoid profiles and SOS1 homeologs.

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Chenopodium polyploidy inferences from Salt Overly Sensitive 1 (SOS1) data

Cited by 52 publications

References 42 publications

The genome of Chenopodium quinoa

The genome of Chenopodium quinoa

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

The taxonomic riddle of Chenopodium album L. complex (Amaranthaceae)

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