ARS | Publication request: CHARACTERIZATION AND COMPARISON OF MICROSATELLITES DERIVED FROM REPEAT-ENRICHED LIBRARIES AND EXPRESSED SEQUENCE TAGS

Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 9, 2005
Publication Date: March 9, 2005
Citation: Coulibaly, I., Gharbi, K., Danzmann, R., Yao, J., Rexroad III, C.E. 2005. Characterization and comparison of microsatellites derived from repeat-enriched libraries and expressed sequence tags. Animal Genetics 36, 309-315.

Interpretive Summary: The genetic improvement of agriculturally important species is enhanced by the use of DNA marker technologies such as genetic mapping. The development of genetic maps for rainbow trout is facilitating the identification of genes affecting traits important to aquaculture production. We report the development and characterization of DNA markers for rainbow trout created from gene sequences. We compared these markers to others generated from non-gene sequences with respect to polymorphism, heterozygosity, and ability to classify salmonid species in terms of evolutionary divergence. This information will increase the marker densities on salmonid genetic maps and facilitate extraction of comparative information from genomes of other species. This information will ultimately aid scientists in the identification of genes affecting aquaculture production traits.

Technical Abstract: We performed a comparison of allelic variation between rainbow trout (Oncorhynchus mykiss) microsatellite markers developed from expressed sequence tag (EST) data and anonymous markers identified from repeat-enriched libraries constructed from genomic DNA. A subset of 70 markers (37 and 33, respectively) was characterized with respect to polymorphism information content (PIC), number of alleles, repeat number, locus duplication within the genome and ability to amplify in other salmonid species. Higher polymorphism information content (PIC) was detected in dinucleotide microsatellites derived from ESTs than anonymous markers (72.7% vs. 54.0%). In contrast, dinucleotide repeat numbers were higher for anonymous microsatellites than for EST derived microsatellites (27.4 vs. 18.1). A higher rate of cross-species amplification was observed for EST microsatellites. Approximately half of each marker type was duplicated within the genome. Unlike single-copy markers, amplification of duplicated microsatellites in other salmonids was not correlated to phylogenetic distance. Genomic microsatellites proved more useful than EST derived microsatellites in discriminating among the salmonids.