The genome of Chenopodium pallidicaule: An emerging Andean super grain

Hayley Mangelson, David E. Jarvis, Patricia Mollinedo, Oscar M. Rollano-Penaloza, Valeria D. Palma-Encinas, Luz Rayda Gomez-Pando, Eric N. Jellen, Peter J. Maughan

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


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.

Original languageEnglish
Article numbere11300
JournalApplications in Plant Sciences
Issue number11
StatePublished - 1 Nov 2019

Bibliographical note

Funding Information:
The authors would like to thank PROINPA Foundation for the generous donation to the Universidad Mayor de San Andrés, La Paz, Bolivia, of 10 cañahua lines belonging to the “Programa de mejoramiento genético de cañahua.”

Publisher Copyright:
© 2019 Mangelson et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America


  • Amaranthaceae
  • Andean crops
  • Chenopodium pallidicaule
  • Hi-C
  • proximity-guided assembly


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