Association study of morpho-phenological traits in quinoa (Chenopodium quinoa Willd.) using SSR markers

In this study, the genetic and molecular diversity of 60 quinoa accessions was assessed using agronomically important traits related to grain yield as well as microsatellite (SSR) markers, and informative markers linked to the studied traits were identified using association study. The results showed that most of the studied traits had a relatively high diversity, but grain saponin and protein content showed the highest diversity. High diversity was also observed in all SSR markers, but KAAT023, KAAT027, KAAT036, and KCAA014 showed the highest values for most of the diversity indices and can be introduced as the informative markers to assess genetic diversity in quinoa. Population structure analysis showed that the studied population probably includes two subclusters, so that out of 60 quinoa accessions, 29 (48%) and 23 (38%) accessions were assigned to the first and second subclusters, respectively, and eight (13%) accessions were considered as the mixed genotypes. The study of the population structure using Structure software showed two possible subgroups (K = 2) in the studied population and the results of the bar plot confirmed it. Association study using the general linear model (GLM) and mixed linear model (MLM) identified the number of 35 and 32 significant marker-trait associations (MTAs) for the first year (2019) and 37 and 35 significant MTAs for the second year (2020), respectively. Among the significant MTAs identified for different traits, the highest number of significant MTAs were obtained for grain yield and 1000-grain weight with six and five MTAs, respectively.