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. Maughan
Research Article

Abstract

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.

Keywords

Cañahuaf Genetic diversity Microsatellite markers Population structure 

References

  1. Achigan-Dako EG (2008) Phylogenetic and genetic variation analyses in cucurbit species (Cucurbitaceae) from West Africa: definition of conservation strategies. Cuvillier Verlag, GöttingenGoogle Scholar
  2. Bohonak AJ (2002) IBD (isolation by distance): a program for analyses of isolation by distance. J Hered 93:153–154PubMedCrossRefGoogle Scholar
  3. Bonifacio A (2003) Chenopodium sp.: genetic resources, ethnobotany, and geographic distribution. Food Rev Int 19:1–7CrossRefGoogle Scholar
  4. Di Gaspero G, Peterlunger E, Testolin R, Edwards KJ, Cipriani G (2000) Conservation of microsatellite loci within the genus Vitis. Theor Appl Genet 101:301–308CrossRefGoogle Scholar
  5. Dray S, Dufour AB (2007) The ade4 package: implementing the duality diagram for ecologists. J Stat Softw 22:1–20Google Scholar
  6. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620PubMedCrossRefGoogle Scholar
  7. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491PubMedPubMedCentralGoogle Scholar
  8. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform 1:47–50Google Scholar
  9. Flores R (2006) Evaluación preliminar agronómica y morfológica del germoplasma de cañahua (Chenopodium pallidicaule Aellen) en la estación experimental Belen. Universidad Mayor de San Andrés, La PazGoogle Scholar
  10. Friedt W, Snowdon RJ, Ordon F, Ahlemeyer J (2007) Plant breeding: assessment of genetic diversity in crop plants and its exploitation in breeding. In: K. Esser UL, W. Beyschlag, J. Murata (eds). Springer, Berlin, pp 151–178Google Scholar
  11. Gade D (1970) Ethnobotany of cañahua (Chenopodium pallidicaule), rustic seed crop of the altiplano. Econ Bot 24:55–61CrossRefGoogle Scholar
  12. Gaitan-Solis E, Duque MC, Edwards KJ, Tohme J (2002) Microsatellite repeats in common bean (Phaseolus vulgaris): isolation, characterization, and cross-species amplification in Phaseolus ssp. Crop Sci 42:2128–2136CrossRefGoogle Scholar
  13. Galwey NW (1989) Exploited plants—Quinoa. Biologist 36:267–274Google Scholar
  14. Groben R, Wricke G (1998) Occurrence of microsatellites in spinach sequences from computer databases and development of polymorphic SSR markers. Plant Breed 117:271–274CrossRefGoogle Scholar
  15. Gumerman G (1997) Food and complex societies. J Archaeol Meth Theor 12:105–139CrossRefGoogle Scholar
  16. Höglund J (2009) Evolutionary conservation genetics, 1st edn. Oxford University Press, New YorkCrossRefGoogle Scholar
  17. Huelsenbeck JP, Andolfatto P (2007) Inference of population structure under a Dirichlet process model. Genetics 175:1787–1802PubMedCrossRefPubMedCentralGoogle Scholar
  18. IPGRI, PROINPA, IFAD (2005) Descriptores para cañahua (Chenopodium pallidicaule Aellen). Instituto Internacional de Recursos Fitogenéticos, Roma, Italia; Fundación PROINPA, La Paz, Bolivia; International Fund for Agricultural Development, Roma, ItaliaGoogle Scholar
  19. Jarvis DE, Kopp OR, Jellen EN, Mallory MA, Pattee J, Bonifacio A, Coleman CE, Stevens MR, Fairbanks DJ, Maughan PJ (2008) Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.). J Genet 87:39–51PubMedCrossRefGoogle Scholar
  20. Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129PubMedCrossRefGoogle Scholar
  21. Mallory MA, Hall RV, McNabb AR, Pratt DB, Jellen EN, Maughan PJ (2008) Development and characterization of microsatellite markers for the grain Amaranths. Crop Sci 48:1098–1106CrossRefGoogle Scholar
  22. Marin W (2002) Distanciamiento entre surcos y plantas en dos ecotipos de kañawa (Chenopodium pallidicaule Aellen) en el Altiplano Norte. Universidad Mayor de San Andrés, La PazGoogle Scholar
  23. Marti N, Pimbert M (2007) Barter markets for the conservation of agro-ecosystem multi-functionality: the case of the chalayplasa in the Peruvian Andes. Int J Agr Sustain 5:51–69Google Scholar
  24. Mason SL, Stevens MR, Jellen EN, Bonifacio A, Fairbanks DJ, Coleman CE, McCarty RR, Rasmussen AG, Maughan PJ (2005) Development and use of microsatellite markers for germplasm characterization in quinoa (Chenopodium quinoa Willd.). Crop Sci 45:1618–1630CrossRefGoogle Scholar
  25. Morchen M, Cuguen J, Michaelis G, Hanni C, SaumitouLaprade P (1996) Abundance and length polymorphism of microsatellite repeats in Beta vulgaris L. Theor Appl Genet 92:326–333PubMedCrossRefGoogle Scholar
  26. Muller K, Borsch T (2005) Phylogenetics of Amaranthaceae based on matK/trnK sequences data: evidence from parsimony, likelihood, and bayesian analysis. Ann Missouri Bot Gard 92:66–102Google Scholar
  27. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590PubMedPubMedCentralGoogle Scholar
  28. Nei M, Li WH (1979) Mathematical-model for studying genetic-variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 76:5269–5273PubMedCrossRefPubMedCentralGoogle Scholar
  29. Nei M, Tajima F (1983) Maximum likelihood estimation of the number of nucleotide substitutions from restriction sites data. Genetics 105:207–217PubMedPubMedCentralGoogle Scholar
  30. Ott J (1992) Strategies for characterizing highly polymorphic markers in human gene-mapping. Am J Hum Genet 51:283–290PubMedPubMedCentralGoogle Scholar
  31. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedPubMedCentralGoogle Scholar
  32. Repo-Carrasco R, Espinoza C, Jacobsen SE (2003) Nutritional value and use of the Andean crops quinoa (Chenopodium quinoa) and kañiwa (Chenopodium pallidicaule). Food Rev Int 19:179–189CrossRefGoogle Scholar
  33. Repo-Carrasco-Valencia R, de La Cruz AA, Alvarez JCI, Kallio H (2009) Chemical and functional characterization of kañiwa (Chenopodium pallidicaule) grain, extrudate and bran. Plant Foods Hum Nutr 64:94–101PubMedCrossRefGoogle Scholar
  34. Risi CJ, Galwey NW (1984) The Chenopodium grains of the Andes: Inca crops for modern agriculture. Adv Appl Biol 10:145–216Google Scholar
  35. Rist S (2000) Linking ethics and the market—Campesino economic strategies in the Bolivian Andes. Mt Res Dev 20:310–315CrossRefGoogle Scholar
  36. Rodríguez M (2007) Evaluación de las pérdidas de grano y grado de impurezas en cuatro métodos de cosecha de cañahua (Chenopodium pallidicaule Aellen) en la comunidad de Quipaquipani, Viacha. Universidad Mayor de San Andrés, La PazGoogle Scholar
  37. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar
  38. Thiel T, Michalek W, Varshney R, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422PubMedGoogle Scholar
  39. Todd JJ, Vodkin LO (1996) Duplications that suppress and deletions that restore expression from a chalcone synthase multigene family. Plant Cell 8:687–699PubMedCrossRefPubMedCentralGoogle Scholar
  40. Vaz ARD, Borba TCD, Brondani C, Rangel PHN, Camargo GSD, Telles MPD, Filho JAF, Brondani RPV (2009) Genetic analysis of a local population of Oryza glumaepatula using SSR markers: implications for management and conservation programs. Genetica 137:221–231CrossRefGoogle Scholar
  41. Weir B (1996) Genetic Data Analysis II: Methods for discrete population genetic data. Sinauer Assoc., Inc, SunderlandGoogle Scholar
  42. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population-structure. Evolution 38:1358–1370CrossRefGoogle Scholar
  43. Woods Páez A, Eyzaguirre P (2004) Cañahua deserves to come back. Leisa 20:11–13Google Scholar
  44. Wright S (1946) Isolation by distance under diverse systems of mating. Genetics 31:39–59PubMedCentralGoogle Scholar

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
  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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