Conservation Genetics

, Volume 10, Issue 2, pp 369–377 | Cite as

Assessment of genetic diversity patterns in Chilean quinoa (Chenopodium quinoa Willd.) germplasm using multiplex fluorescent microsatellite markers

  • F. F. Fuentes
  • E. A. Martinez
  • P. V. Hinrichsen
  • E. N. Jellen
  • P. J. Maughan
Research Article


Quinoa (Chenopodium quinoa Willd.) is a staple seed crop in the Andean region of South America. Improving quinoa productivity is a primary food-security issue for this region, and has been part of the impetus for the establishment of several new quinoa breeding programs throughout the Andean region. Chilean quinoa has been characterized as morphologically diverse and bifurcated into coastal and highland ecotypes. The success of emerging breeding programs will rely heavily on the development of core germplasm collections and germplasm evaluation—especially of the coastal quinoa ecotypes that are often neglected in traditional breeding programs. Thus, the objective of this study was to characterize and quantify the genetic diversity within 28 Altiplano and 31 coastal Chilean accessions of quinoa using microsatellite markers. To facilitate the analysis, we also report the development of seven sets of fluorescent multiplexed microsatellite PCR reactions that result in genetic information for 20 highly polymorphic microsatellite loci. A total of 150 alleles were detected among the quinoa accession, ranging from 2 to 20 alleles per locus and an average 7.5 allele/locus. Both cluster (UPGMA) and principal component analyses separated the accessions into two discrete groups. The first group contained quinoa accessions from the north (Andean highlands) and the second group consisted of accessions from the south (lowland or coastal). Three accessions from Europe were classified into the southern quinoa group. The data obtained in the diversity analyses highlights the relationships within and among northern and southern Chilean quinoa accessions and provides the quinoa scientific community with a new set of easy to use and highly informative genetic markers.


Chenopodium quinoa Genetic diversity Multiplex fluorescent SSR Highland quinoa Coastal quinoa 



This research was supported by grants from CORFO and FIA institutions. We gratefully acknowledge I. von Baer (Baer Seed Company) for seed contribution, the assistance of the Chilean national seed bank (INIA), and BYU Environment for Mentoring Grant funding that helped with student support.


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Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • F. F. Fuentes
    • 1
  • E. A. Martinez
    • 2
  • P. V. Hinrichsen
    • 3
  • E. N. Jellen
    • 4
  • P. J. Maughan
    • 4
  1. 1.Departamento de Agricultura del DesiertoUniversidad Arturo PratIquiqueChile
  2. 2.Centro de Estudios Avanzados en Zonas Áridas (CEAZA)Universidad de La SerenaLa SerenaChile
  3. 3.Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación La PlatinaINIA Santa RosaChile
  4. 4.Department of Plant & Wildlife SciencesBrigham Young UniversityProvoUSA

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