Quinoa (Chenopodium quinoa Willd.) is a staple grain for the indigenous people of the Andean region of South America with excellent nutritional qualities, including protein content. The objective of this study is to report on the development of fluorescence-tagged simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) to (1) genetically characterize the inherent diversity of 152 accessions of C. quinoa; (2) determine to what degree the CIP-FAO collection represents the range of genetic diversity in quinoa; and (3) test four hypotheses regarding quinoa?s center of diversity, Highland and Lowland clustering patterns, origin of Lowland varieties, and the origin of domestication. Thirty-five SSR loci comprising 432 alleles ranging from 5 (QAAT10) to 28 (QAAT50) alleles per locus (mean=13) were used to survey the 152 accessions of quinoa from the USDA and CIP-FAO collections. Heterozygosity was detected in 14.25% of the accessions for SNP loci and in at least one locus for 51% of the accessions. Both UPGMA and PCA analyses partitioned the quinoa accessions into two main clusters. The first major cluster consisted of accessions from the Andean highlands of Peru, Bolivia, Ecuador, Argentina, and extreme northeastern Chile. The other main cluster contained accessions from both the Lowlands of Chile and those collected by Emigdio Ballón The CIP-FAO collection appears to give a good representation of quinoa's genetic diversity within these two main clusters. The significance of patterns of genetic diversity within C. quinoa is discussed.



College and Department

Life Sciences; Plant and Wildlife Sciences



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Chenopodium quinoa, genetic diversity, SSR, SNP