Molecular characterization and genetic diversity analysis of selected maize inbreds using SSR markers

Abstract

Aim: The aim of the current study was to analyze the molecular diversity and genetic relationship among selected maize inbreds using SSR markers. Methodology: Genomic DNA of individual inbreds was isolated by using the standard CTAB procedure (Doyle and Doyle, 1987) with some modifications. Thermal cycler was used to perform the polymerase chain reactions. 50ng of genomic DNA was used in 10 ?l total volume with a final concentration of 10X Taq buffer, MgCl2 (50 ?M), each primers (10 ?M), nucleotides (2.5 mM) and 1 U Red Taq DNA polymerase. Amplified PCR products were resolved by electrophoresis on horizontal gel (3.0% Agarose gel) system using 1x TBE Buffer. The gels were photographed with CCD camera attached to a gel documentation system. Co Results: In total, 191 alleles were detected which showed a range of 2 to 6 alleles per marker and an average value of 3.82 alleles per locus. Polymorphic information content (PIC) value showed a range of 0.050 (umc1069) to 0.817 (bnlg1823) with an average value of 0.585 indicating the efficiency of markers to study the level of polymorphism available in the maize inbred lines. The value of genetic similarity coefficients for the twenty maize inbreds based on 50 SSR markers ranged from 0.51 to 0.74. The maximum value of similarity coefficient was observed between CIM-127 vs CIM-130, whereas the minimum value of it was between TSK-7 vs TSK-2, TSK-41 vs TSK-2. Cluster analyses, done using matrices of similarity in the NTSYS-pc software, classified studied inbred lines into four distinct clusters, Cluster A, B, C and D comprising of 5, 5, 5 and 5 maize inbred lines, respectively. Interpretation: In this study, PIC values indicated a good efficiency of markers for studying the polymorphism level available in studied inbred lines. High level of diversity among the inbreds detected with SSR markers indicated their suitability for further breeding programs.