Genetic Resources and Crop Evolution

, Volume 58, Issue 5, pp 727–739 | Cite as

Development and use of microsatellite markers for genetic diversity analysis of cañahua (Chenopodium pallidicaule Aellen)

  • A. Vargas
  • D. B. Elzinga
  • J. A. Rojas-Beltran
  • A. Bonifacio
  • B. Geary
  • M. R. Stevens
  • E. N. Jellen
  • P. J. MaughanEmail author
Research Article


Cañahua (Chenopodium pallidicaule Aellen) is a poorly studied, annual subsistence crop of the high Andes of South America. Its nutritional value (high in protein and mineral content) and ability to thrive in harsh climates make it an important regional food crop throughout the Andean region. The objectives of this study were to develop genetic markers and to quantify genetic diversity within cañahua. A set of 43 wild and cultivated cañahua genotypes and two related species (Chenopodium quinoa Willd. and Chenopodium petiolare Kunth) were evaluated for polymorphism using 192 microsatellite markers derived from random genomic cañahua sequences produced by 454 pyrosequencing of cañahua genomic DNA. Another 424 microsatellite markers from C. quinoa were also evaluated for cross-species amplification and polymorphism in cañahua. A total of 34 polymorphic microsatellite marker loci were identified which detected a total of 154 alleles with an average of 4.5 alleles per marker locus and an average heterozygosity value of 0.49. A cluster analysis, based on Nei genetic distance, clearly separated from wild cañahua genotypes from the cultivated genotypes. Within the cultivated genotypes, subclades were partitioned by AMOVA analysis into six model-based clusters, including a subclade consisting sole of erect morphotypes. The isolation by distance test displayed no significant correlation between geographic collection origin and genotypic data, suggesting that cañahua populations have moved extensively, presumably via ancient food exchange strategies among native peoples of the Andean region. The molecular markers reported here are a significant resource for ongoing efforts to characterize the extensive Bolivian and Peruvian cañahua germplasm banks, including the development of core germplasm collections needed to support emerging breeding programs.


Cañahuaf Genetic diversity Microsatellite markers Population structure 



This research was supported by grants from the McKnight Foundation, as well as the Ezra Taft Benson Agriculture and Food institute and Holmes Family Foundation. We gratefully acknowledge the advice and support provided by Dr. Alejandro Bonifacio, PROINPA Foundation, Bolivia and are grateful to Dinesh Adhikary, Nathan Mahler, Joshua Raney, and Shawna and James Daley for technical support in developing the microsatellite protocols. We are also grateful to David Brenner of the USDA NC-7 (Ames, IA) and Dr. Angel Mujica of the National University of the Altiplano (Puno, Peru) for providing seed for this study.


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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • A. Vargas
    • 1
    • 2
  • D. B. Elzinga
    • 1
  • J. A. Rojas-Beltran
    • 2
  • A. Bonifacio
    • 2
  • B. Geary
    • 1
  • M. R. Stevens
    • 1
  • E. N. Jellen
    • 1
  • P. J. Maughan
    • 1
    • 3
    Email author
  1. 1.Department of Plant & Wildlife SciencesBrigham Young UniversityProvoUSA
  2. 2.Fundacion PROINPACochabambaBolivia
  3. 3.Department of Plant & Wildlife SciencesBrigham Young UniversityProvoUSA

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