Molecular markers are commonly used in genetic diversity analysis, genetic map construc‐ tion, gene mapping and cloning, and marker assisted selection in plant breeding. Based on detection procedure, most molecular marker technologies can be classified into hybridiza‐ tion-based or PCR-based systems. Restriction fragment length polymorphism (RFLP) is the first hybridization-based molecular marker system that was intensively used at the begin‐ ning of the molecular biology era in life science while hybridization-based marker methods such as microarrays and diversity array technology (DArT) are used currently to detect sin‐ gle nucleotide polymorphisms (SNP). In contrast, many PCR-based molecular marker detec‐ tion methods have been developed. For example, amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), simple sequence repeats (SSR) and sequence related amplified polymorphism (SRAP), inter-simple sequence repeat (ISSR), se‐ quence tagged site (STS), and sequence characterized amplification region (SCAR), are com‐ monly used in genomic analysis (Jones et al., 2009).