EST-based marker discovery and SNP genotyping in plants genome

In conventional plant breeding, genetic variation is usually identified by visual selection. Currently, with the development of molecular markers in many crop species, it can be identified at the molecular level based on changes in the DNA and its effect on the phenotype. DNA-based molecular markers are the most powerful diagnostic tools to detect DNA polymorphism both at the level of specific loci and at the whole genome level. In the past, such markers were developed either from genomic DNA libraries (RFLPs and SSRs) or from random PCR amplification of genomic DNA (RAPDs) or both (AFLP). Recently, the availability of genomic DNA and cDNA sequences (ESTs) in the public databases has made marker development more direct and even cost effective. The common applications of those markers in agriculture sector are molecular characterization of germplasm, mapping of genes/QTLs and marker assisted selection (MAS). Advances in the area of marker discovery and SNP genotyping using EST-based marker assays are discussed in this review.