**1. Introduction**

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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).

There are advantages and limitations for all molecular marker detection methods. In partic‐ ular, RFLP probes can be shared in related species so RFLP is advantageous over other mo‐ lecular markers in comparative genomics. However, the detection procedure in RFLP is complicated and costly. Additionally, RFLP is not easily automated to analyze thousands of individuals for marker assisted selection. AFLP is a commonly used molecular marker sys‐ tem since it can detect multiple genetic loci in a genome. On the other hand, there are many steps in the AFLP detection procedure, which limits its application in marker assisted selec‐ tion when thousands of individual DNA samples need to be analyzed in a short time. SSRs often have a high level of polymorphism in plant genomes and are commonly used in most genomic applications. Since SSR technology only detects sequence repeats, the number of SSRs in a genome is relatively limited compared with numerous SNPs. RAPD is easily per‐

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formed in one round of PCR, however, a low level of reproducibility of RAPD amplification limits its wide use in genomic analysis.

As next generation sequencing (NGS) technologies dramatically increase capacity and throughput of DNA sequencing, whole genome sequencing of many plant species has been accomplished and most economically important crop species such as rice, maize, soybean, sorghum, potato, tomato and Chinese cabbage have been fully sequenced. Although it is still challenging to use NGS for assembling a whole complex genome such as barley and wheat, there are thousands of SNPs identified in NGS that can be used to develop molecular markers in species with complex genomes. Furthermore, NGS is directly used in SNP dis‐ covery and a few dozen genotypes can be sequenced simultaneously to assemble ultradense genetic maps. Additionally, different strategies are used to produce partial genomes that can be used to directly sequence SNPs using next generation technologies.
