Cañahua (Chenopodium pallidicaule Aellen) is a poorly studied, annual subsistence crop of the high Andes of South America. Its nutritionally value (high in protein and mineral content) and ability to thrive in harsh climates (drought, extreme elevations, etc.) 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 (C. quinoa and C. petiolare) were evaluated for polymorphism using 192 microsatellite markers derived from random genomic sequences produced by 454 pyro-sequencing of cañahua genomic DNA. In addition, another and 424 C. quinoa based microsatellite markers were evaluate as potential cross-species marker loci. A total of 48 polymorphic microsatellite marker loci were identified which detected a total of 168 alleles with an average of 3.5 alleles per marker locus and an average heterozygosity value of 0.47. A cluster analysis, based on Nei genetic distance, grouped the cultivated cañahua into a single dominant branch clearly separated from wild cañahua genotypes and the outgroup species. Within the cultivated genotypes, two dominant subclades were present that were further partitioned by AMOVA analysis into five model-based clusters. Significant correlations were found between genetic distance and morphological traits. 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.



College and Department

Life Sciences; Plant and Wildlife Sciences



Date Submitted


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Genetic diversity, cañahua, microsatellite markers, population structure