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Many years of domestication and breeding have given  rise to the wide range of chicken breeds that exist today; however, an  increasing number of local chicken breeds are under threat of extinction. A  comprehensive characterization of chicken markers (especially type I markers)  is needed to monitor and conserve genetic diversity in this species. The  explosion of genomics and functional genomics information in recent years has  opened new possibilities for the generation of molecular markers. We analyzed a  large number of expressed sequence tags (ESTs) to test the possibility of using  EST-derived microsatellite markers for investigating the Gallus gallus genome.  Chromosomal locations for the majority of these SSRs were predicted. Of the  31,576 unigenes assembled from the 544,150 redundant EST sequences, 1757 SSR  markers were discovered on 1544 ESTs, using the SSRLocator software, with an  average density of 28.7 kb per SSR. The dimer motifs were the most frequent  (46.38%), followed by trimeric (38.58%), tetrameric (10.19%), pentameric  (4.5%), and hexameric (&lt;1%) markers. Different from the case for cattle and  sheep, AT/TA was the most abundant dimeric repeat, accounting for 41.71% of all  dimeric repeats in the chicken ESTs. The EST-SSR distribution was not uniform  among the chromosomes; the majority of the EST-SSRs were located on chromosomes  GGA2 and GGA10. We found that most of the EST-SSRs are involved in positive  regulation of cellular and metabolic processes. This is the first time that EST  sequences have been mined to find chicken microsatellites. On average, 3.8% of  the G. gallus UniGene sequences could be exploited for development of  EST-SSRs, indicating a good source for molecular markers as well as for  functional genome analysis.

Application of functional genomic information to develop efficient EST-SSRs for the chicken (Gallus gallus)