Association mapping, trait variation, interaction and population structure analysis in cucumber (Cucumis sativus L.)

In several regions of the world, low productivity in this crop is attributed to several factors including poor understanding of the genomic complexity of important traits associated with fruit quality and yield. Therefore, genome wide association analysis was performed for important traits using simple sequence repeats (SSR) markers. Significant variation was recorded for all the studied traits in 78 cucumber genotypes under two environments (open field and net house) which indicated that the constituted association panel was suitable for association mapping. Genotyping was done using 60 highly polymorphic SSRs. By performing genome scanning out of 60 SSR markers, using mixed linear model (MLM) approach 4 and 6 markers explained an average of 23.93% and 17.37% of the trait variation under net house and open field condition, respectively. Based on MLM approach two markers on 3rd chromosome (UW084942) and 4th chromosome (UW062953) found to be associated with the average fruit weight (g) under both net house and open field condition. Population structure analysis revealed four distinct sub-populations that corroborated with the geographical origin as well as fruit quality and quantitative traits. The four sub-populations (A–D) had fixation index percentage equal to 24.35 29.48, 37.17 and 8.97 respectively, supporting the existence of moderate population structures. Therefore, the extensive phenotypic and genotypic characterization, population structure, and markers associated with important traits provided in this study will facilitate marker assisted improvement programs in cucumber.