Genetic diversity analysis of maize lines using AFLP and TE-based molecular marker systems

Maize has been domesticated in diverse environments ranging from low latitudes in tropical countries to high latitudes in Canada. Because maize breeding programs primarily focus on hybrid vigor by selectively crossing inbred lines to maximize recombination, we collected a diverse array of commercial hybrid and inbred lines from southern Asia, China, and Canada and analyzed them by amplified length fragment polymorphism (AFLP), sequence-specific amplified polymorphism (SSAP), and CACTA-transposon display (TD) analyses. Cluster analyses using these molecular marker systems clearly differentiated these maize lines into three groups: southern Asian lines, northern Asian lines, and Canadian lines. However, principal coordinate analysis (PCoA) based on Nei's distances grouped them into two groups: Asian and Canadian lines. Thus, groupings by cluster dendrograms and PCoA showed that geographic origin was a more dominant factor than growing seasonal differences resulting from different latitudes. The overall genetic diversity (Ht) was found to be high (more than 80 % molecular variations) among the maize lines by all three of the marker systems.