Genetic diversity in the Ethiopian garden cress (Lepidium sativum L.) using microsatellite markers

Abstract

Diversity has not been exhaustively studied in the Ethiopian garden cress (Lepidium sativum L.). Therefore, the objective of the present study was to determine the genetic diversity among garden cress genotypes using microsatellite or simple sequence repeat (SSR) markers. One hundred twelve garden cress genotypes collected from diverse growing regions of Ethiopia were investigated using 12 SSR markers which were earlier developed for closely related Lepidium subulatum. A total of 1387 alleles were identified, with the average of 116 alleles per SSR marker. The average polymorphism information content (PIC), Shannon diversity index and Nei’s expected heterozygosity were 0.444, 0.750 and 0.443, respectively. High levels of Shannon diversity were noted within population (0.696) than between populations (0.304). Analysis of Molecular Variance (AMOVA) also confirmed that 79% and 21% of total variations were attributed to the within- and between-populations, respectively, indicating greater exchange of gene pool across regions of origin. The genetic distance between populations ranged from 0.044 to 0.396. Cluster analysis using un-weighted neighbor joining method revealed five clusters. The Principal Coordinate Analysis (PCoA) showed the distribution of genotypes in the scatter-plot was highly dispersed at 22% of the total variation, demonstrating complex genetic relationship among genotypes of different geographic origin. Genetic distance matrix among nine populations revealed three different groups to be used as divergent populations in the future breeding programs. Hence, these markers were effective in studying genetic diversity in the Ethiopian garden cress genotypes. Although the transferability of SSR markers from related species was found to be high, the efficiency of identifying more polymorphisms will be improved using garden cress specific markers. Keywords: Garden cress, Heterozygosity, Lepidium sativum, Microsatellites, Polymorphic information content, Shannon diversity index, SSR