**6.6 EST (Expressed Sequence Tags )**

The use of functional molecular markers, such as those developed from EST allows direct access to the population diversity in genes of agronomic interest that they represent coding sequences, facilitating the association between genotype and phenotype. Nelson and Shoemaker (2006) identified approximately 45,000 potential gene sequences (pHaps) from EST sequences of Williams/Williams 82, an inbred genotype of soybean (*Glycine max* L. Merr.) using a redundancy criterion to identify reproducible sequence differences between related genes within gene families. Analysis of these sequences revealed single base substitutions and single base indels are the most frequently observed form of sequence variation between genes within families in the dataset. Genomic sequencing of selected loci indicates that intron-like intervening sequences are numerous and are approximately 220 bp in length. Functional annotation of gene sequences indicates functional classifications are not randomly distributed among gene families containing few or many genes. The identification of potential gene sequences (pHaps) from soybean allows the scientist to get a picture of the genomic history of the organism as well as to observe the evolutionary fates of gene copies in this highly duplicated genome.
