High-density mapping of QTL controlling agronomically important traits in quinoa (Chenopodium quinoa Willd.)

Abstract Quinoa is a pseudocereal originating from the Andean regions. In spite of quinoa’s long cultivation history, genetic analysis of this crop is still in its infancy. We aimed to localize QTL contributing to the phenotypic variation of agronomically important traits. We crossed the Chilean accession PI-614889 and the Peruvian accession CHEN-109, which depicted significant differences in days to flowering, days to maturity, plant height, panicle length, thousand kernel weight (TKW), saponin content, and mildew susceptibility. We observed sizeable phenotypic variation across F 2 plants and F 3 families grown in the greenhouse and in the field, respectively. We used Skim-seq to genotype the F 2 population and constructed a high-density genetic map with 133,923 SNPs. Fifteen QTL were found for ten traits. Two significant QTL, common in F 2 and F 3 generations, depicted pleiotropy for days to flowering, plant height, and TKW. The pleiotropic QTL harbored several putative candidate genes involved in photoperiod response and flowering time regulation. This study presents the first high-density genetic map of quinoa that incorporates QTL for several important agronomical traits. The pleiotropic loci can facilitate marker assisted selection in quinoa breeding programs. Key message Skim-sequencing enabled the construction a high-density genetic map (133,923 SNPs) and fifteen QTL were detected for ten agronomically important traits.