The introns in FLOWERING LOCUS T-LIKE (FTL) genes are useful markers for tracking paternity in tetraploid Chenopodium quinoa Willd.

Štorchová, Helena; Drabešová, Jana; Cháb, David; Kolář, Jan; Jellen, Eric N.

doi:10.1007/s10722-014-0200-8

Cited by 42 publications

(39 citation 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. 1a, Table 1).…”

Section: Evolutionary History Of Quinoamentioning

confidence: 99%

The genome of Chenopodium quinoa

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et al. 2017

Nature

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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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“…One clade contained the New World diploids—BYU accession numbers 835 ( C. dessicatum ), 843 ( C. neomexicanum ), 921 ( C. standleyanum ), 1005 ( C. hians ), and 1302 ( C. pallidicaule )—while the other contained the Eurasian diploid, C. ficifolium (BYU accession number 943). We designated the New World variant as A‐genome and the Eurasian variant as B‐genome, following the convention previously set in Walsh et al (unpublished data, 2014) and Storchova et al (2014). These two distinct variants shared 91.5% identity on average.…”

Section: Resultsmentioning

confidence: 99%

“…in South America. Quinoa is an allotetraploid pseudocereal (AABB, 2 n = 4 x = 36; Maughan et al, 2004; Ward, 2000) that was recently demonstrated to carry subgenomes of New World (AA) and Old World (BB) origin (Walsh et al, unpublished data, 2014; Storchova et al, 2014). Its confamilial relatives include several commercially important plant species, such as amaranth ( Amaranthus L.), spinach ( Spinacea oleracea L.), beet ( Beta vulgaris L.), and garden orache ( Atriplex hortensis L.).…”

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Characterization of the Granule‐Bound Starch Synthase I Gene in Chenopodium

et al. 2015

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Chenopodium L. is a relatively under-studied genus that includes the cultivated seed crop quinoa (C. quinoa Willd.). Quinoa is an allotetraploid (2n = 4x = 36, AABB genomes) that is cultivated by subsistence farmers and commercial growers in the Andean regions of South America. Approximately 60% of a quinoa seed is starch, a glucose polymer that is an important carbohydrate energy source in the human diet. Seed starch is normally composed of amylose and amylopectin in a 1:3 ratio. The accumulation of the amylose fraction of starch is controlled by a single dominant gene in quinoa, GBSSI. We report the sequencing and characterization of the GBSSI gene in 18 accessions of Chenopodium, including Andean quinoa and the related Mesoamerican chenopod domesticate, C. berlandieri subsp. nuttalliae Saff. Two distinct homeologs (GBSSIa and GBSSIb) were identified in the tetraploid accessions, and 19 different alleles were identified, including three null mutants-one in an accession of quinoa and two in a waxy landrace of C. berlandieri subsp. nuttalliae. Expression analysis of the null mutants revealed that GBSSIa and GBSSIb were both strongly expressed late in seed development.GBSSI sequences were used to analyze the phylogenetic relationships between quinoa and other members of the Chenopodium genus. This study and the discovery of Chenopodium GBSSI null-mutants will assist in the development of new Chenopodium crops with novel starches.

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“…() reported a draft assembly of the cañahua genome (accession PI 478407). Quinoa is an allotetraploid (2 n = 4 x = 36), presumably resulting from a relatively recent (3.3–6.3 mya) polyploidization event between North American and Eurasian diploids representing the A and B subgenomes of modern quinoa, respectively (Štorchová et al., ). Although cañahua is not believed to be the direct A‐genome donor of quinoa, it is a related A‐genome diploid.…”

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The genome of Chenopodium pallidicaule: An emerging Andean super grain

et al. 2019

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Premise Cañahua is a semi‐domesticated crop grown in high‐altitude regions of the Andes. It is an A‐genome diploid (2n = 2x = 18) relative of the allotetraploid (AABB) Chenopodium quinoa and shares many of its nutritional benefits. Cañahua seed contains a complete protein, a low glycemic index, and offers a wide variety of nutritionally important vitamins and minerals. Methods The reference assembly was developed using a combination of short‐ and long‐read sequencing techniques, including multiple rounds of Hi‐C–based proximity‐guided assembly. Results The final assembly of the ~363‐Mbp genome consists of 4633 scaffolds, with 96.6% of the assembly contained in nine scaffolds representing the nine haploid chromosomes of the species. Repetitive element analysis classified 52.3% of the assembly as repetitive, with the most common repeat identified as long terminal repeat retrotransposons. MAKER annotation of the final assembly yielded 22,832 putative gene models. Discussion When compared with quinoa, strong patterns of synteny support the hypothesis that cañahua is a close A‐genome diploid relative, and thus potentially a simplified model diploid species for genetic analysis and improvement of quinoa. Resequencing and phylogenetic analysis of a diversity panel of cañahua accessions suggests that coordinated efforts are needed to enhance genetic diversity conservation within ex situ germplasm collections.

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The introns in FLOWERING LOCUS T-LIKE (FTL) genes are useful markers for tracking paternity in tetraploid Chenopodium quinoa Willd.

Cited by 42 publications

References 30 publications

The genome of Chenopodium quinoa

The genome of Chenopodium quinoa

Characterization of the Granule‐Bound Starch Synthase I Gene in Chenopodium

The genome of Chenopodium pallidicaule: An emerging Andean super grain

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