Comparative genetic analysis of highland maize inbred lines using AFLP and SSR markers

Abstract

The objectives of the study were (1) to compare the informativeness of SSR and AFLP markers in genetic diversity analysis of highland maize inbred lines, and (2) to compare their effectiveness in classifying the inbred lines into heterotic groups. Thirty-two inbred lines were assayed for polymorphism using 29 microsatellite (SSR) loci and eight Amplified Fragment Length Polymorphism (AFLP) primer pair combinations. SSR markers revealed the greater amount of polymorphism among the inbred lines as determined by high polymorphic information content (0.50) of the loci involved in the study. Conversely, AFLP markers generated a considerably higher marker index ratio (18.55). Mean genetic distance (GD) values determined for each marker system, and based on combined data analyses did not show marked differences. Nevertheless, correlation of GDs between the two markers was moderate (0.50), but highly significant. Cluster analysis of AFLP and SSR data corresponded well when classifying the inbred lines into putative heterotic groups. Based on available pedigree records, AFLPs were moreprudent in this respect than SSR markers; however, DNA resolution using SSR loci is less complex and more sensitive to detect polymorphism, which is in line with previous reports that suggested the uniqueness of SSR allelic diversity.