Assessment of genetic diversity in the USDA and CIP-FAO international nursery collections of quinoa (Chenopodium quinoa Willd.) using microsatellite markers

Abstract Quinoa (Chenopodium quinoa Willd.) is a staple food crop for millions of impoverished ruralinhabitants of Andean South America where it has been cultivated for millennia. Interest inquinoa, due largely to its superior nutritional characteristics, is fuelling a growing export marketand has led to an increased focus on genetic research and the development of quinoa breedingprogrammesthroughoutSouthAmerica.Thesuccessofthesebreedingprogrammeswillrelyheav-ilyonthedevelopmentofcoregermplasmcollectionsandgermplasmconservation.Wereportthedevelopment ofa set of fluorescence-tagged microsatellite molecular markers thatcan be used tocharacterize genetic diversity within quinoa germplasm and we use this set of 36 microsatellitesmarkers to genetically characterize the diversity of 121 accessions of C. quinoa held in the USDAgermplasmbank,22accessionsfromtheCIP-FAOinternationalnurserycollectionandeightacces-sionsrepresentingparentsfromgeneticmappingpopulations.Atotalof420allelesweredetectedamong thequinoaaccessions withanaverageof11allelesdetectedper microsatellitelocus.Gen-eticheterogeneitywasobservedin32%ofthequinoaaccessionsatagivenlocusandsuggeststhatmany of these accessions represent heterogeneous seed lots or landraces. Both unweighted pair-group method with arithmetic averages (UPGMA) and principle components analysis (PCA) ana-lyses partitioned the quinoa accessions into two main clusters. The first major cluster consisted ofaccessionsfromtheAndeanhighlandsofPeru,Bolivia,Ecuador,Argentinaandextremenortheast-ernChile.TheothermainclustercontainedaccessionsfromboththelowlandsofChileandasetofUSDAaccessionswithnoknownpassportdata,collectedbyEmigdioBallo´n.Usingthepatternsofgenetic diversity detected within the C. quinoa accessions we discuss hypotheses regarding qui-noa’scentreofdiversity,includinghighlandandlowlandecotypeclusteringpatterns,originoflow-land varieties, origin of domestication, and diversity levels in the USDA and CIP-FAO collections.