Development and Use of Microsatellite Markers for Germplasm Characterization in Quinoa (Chenopodium quinoa Willd.)

Abstract

Quinoa (Chenopodium quinoa Willd.) is a widely consumed food crop and a primary protein source for many of the indigenous inhabitants of the Andean region of South America. The objective of this study was to develop a collection of reproducible and highly informative microsatellite markers for quinoa. A total of 1276 clones were sequenced from three microsatellite‐enriched (CA, ATT, ATG) libraries. Four hundred fifty‐seven (36%) of the clones contained unique microsatellites. The most common repeated motifs, other than CA, AAT, and ATG, were GA and CAA. Flanking primers were designed for 397 microsatellite loci and screened using a panel of diverse quinoa accessions and one accession of C. berlandieri Moq., a wild relative of quinoa. Two hundred eight (52%) of the microsatellite markers were polymorphic among the quinoa accessions. An additional 25 of the microsatellite markers (6%) were polymorphic when the C. berlandieri accession was included in the analysis. Only in rare instances (nine) did a microsatellite amplify in quinoa and not in C. berlandieri The number of observed alleles ranged from 2 to 13, with an average of four alleles detected per locus. Heterozygosity values ranged from 0.20 to 0.90 with a mean value of 0.57. Sixty‐seven markers (32%) were highly polymorphic (H ≥ 0.70). These microsatellites markers are an ideal resource for use in managing quinoa germplasm, trait mapping and marker‐assisted breeding strategies. The wide cross‐species transportability of these markers may extend their value to research involving other Chenopodium species.