Association analysis of grain yield and yield components in Quinoa (Chenopodium quinoa Willd.) using SSR markers

Abstract

Abstract Quinoa is a pseudocereal crop that is considered as a valuable crop to provide food and nutrition security worldwide due to its high nutritional value and resistance to environmental stresses. However, no considerable genetic and especially molecular researches has been done on this plant and the genetic basis of many traits is unknown. 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 mapping. 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 results of association mapping using general linear model (GLM) identified 39 significant marker-trait associations (MTAs), while 36 significant MTAs were observed in multiple linear model (MLM). The five markers KAAT030, KCAA022, KGA003, KCAA107, and KAAT023 were significantly associated with more than one trait using both the GLM and MLM models and can therefore be suggested for mapping studies in quinoa populations. The findings of the present study provide useful information about the genetic basis of the studied traits and can be used to breed quinoa populations.