Phenotypic and genotypic resources for the USDA quinoa (Chenopodium quinoa) genebank accessions

Quinoa (Chenopodium quinoa) is a nutritious grain, with balanced composition of amino acids, and a facultative halophyte. Under greenhouse conditions, we assessed 148 quinoa accessions from the USDA genebank for grain weight, phenological, and morphological characteristics. For all traits, the analysis of variance revealed a significant difference among accessions. The accessions matured as late as 146 days after planting and produced grain weight up to 19.6 g/plant. Days to maturity showed negative correlation with grain weight per plant, whereas the number of branches was positively correlated with grain weight per plant. By adopting the NsiI/BfaI combination to enhance the genotyping-by-sequencing technique, we were able to generate 59,248 filtered single nucleotide polymorphism markers by mapping to the reference genome. Molecular markers showed an average heterozygosity of 11.76% across the accessions with a range of 4.9%-21.9%. The first two principal component analyses (PCAs) explained nearly 50% of molecular markers. The genetic diversity analysis using PCA revealed the presence of four main groups. Groups A and B consisted of mainly Bolivian and Peruvian accessions with relatively slower maturity and taller plant stature. In contrast, groups C and D were mainly accessions registered from USA and Chile with relatively faster maturity and shorter plant stature. Groups C and D together have shown far more private single nucleotide polymorphisms than accessions in A and B groups, indicating the higher levels of diversity within these groups and more levels of similarities among individuals of A and B groups. Marker-trait association revealed significant markers for grain weight per plant and days to flowering. We only analyzed linkage disequilibrium on the scaffolds that harbor these marker-trait associations. LD expressed in r(2) persisted as high as 0.2 in ranges greater than 600 kb for scaffold 1992 but dropped more quickly for scaffold 1843. These phenotypic and genotypic resources will serve as a reference for the cataloging and conservation of germplasm and, for the selection of a core collection for the improvement of quinoa to address food security.