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Lots of traits in cereals are quantitatively inherited and controlled by multiple genes. In general, these kinds of traits have wide natural variations. Linkage analysis and Linkage Disequilibrium (LD) analysis are the main approaches to discover and locate target genes underlying the traits. Several kinds of molecular markers such as restriction fragment length polymorphism and simple sequence repeats have been used for genetic mapping. But these markers are not suitable for developing a high-density genetic map. Due to its abundance and uniform distribution throughout a genome, and single nucleotide polymorphisms (SNPs) are considered to be the most desirable molecular markers and have been demonstrated to be efficient markers for developing high-density genome scan [1,2]. Wholegenome sequencing and oligonucleotide microarray are the two main strategies used to create SNP markers. Because of its economic cost, SNP array, a high-throughput genome scan, is an important tool for genetic studies and breeding applications. A SNP array designed with a very huge number of SNPs evenly spaced genetically across genomes has been developed in maize, rice and wheat [3-5]. But currently, they are not widely used for genetic analysis. The most important factor limited the application of SNP array is its comparative high cost to researchers. Meanwhile, the researchers also focus on how many SNPs are positioned on the array and when low-, medium- or high-density SNP arrays are used.
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