Genetic variations in some Egyptian Zea mexicana genotypes based on RAPD and AFLP markers

Maize-Teosinte hybrids are of significant interest to maize breeders as a resource of genetic diversity during the maize domestication process as a genetic pool for maize improvement. This study examines the genetic diversity and population structure of 16 Zea mexicana populations which are currently active in Zea breeding programs in Egypt using Random Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP) markers. RAPD analysis (14 primers) produced 141 bands; out of which, 102 (72.3%) were polymorphic. On the other hand, AFLP (5 primer combinations) yielded 276 peaks including 267 (96.7%) polymorphic ones with an average of 53.4 peaks per primer combination. A total of 11 unique RAPD markers were created by 6 primers and identified 8 genotypes. The five primer combinations generated 56 unique amplicons that successfully distinguished 12 out of the 16 genotypes tested. Furthermore, the number of observed alleles (Na), effective multiplex ratio (EMR), and polymorphic information content (PIC) indices showed higher values for AFLP (2.00, 53.4, and 0.21) than for RAPD (1.67, 7.3, and 0.15). Cluster analysis based on Nei and Li genetic distance and an Unweighted Pair Group Method with Arithmetic Mean (UPGMA) revealed 5 main clusters representing the 16 Zea mexicana confirming the population structure analysis obtained. High variability of the studied teosinte genotypes using RAPD and AFLP markers will provide valuable tools for Zea mexicana breeding programs in Egypt.