ARS | Publication request: IDENTIFICATION AND MAPPING OF MICROSATELLITES IN RAINBOW TROUT EST SEQUENCES

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: January 10, 2003
Publication Date: January 10, 2003
Citation: Rexroad III, C.E., Keele, J.W., Hostuttler, M.A., Palti, Y. 2003. Identification and mapping of microsatellites in rainbow trout est sequences. Plant and Animal Genome XI Book of Abstracts. p.242.

Technical Abstract: The NCCCWA is developing a selective breeding program implementing molecular genetic tools for improving rainbow trout aquaculture production efficiency. This involves characterizing three strains of germplasm with respect to phenotypes associated with growth, disease resistance, reproduction, and stress. In addition to characterizing such phenotypes, we are progressing toward chromosomal localization of genetic variation affecting these traits by generating microsatellite markers for use in identifying quantitative trait loci. Our laboratory has identified candidate microsatellite sequences for marker development from three sources: 1) repeat-enriched libraries, 2) sub-clones from bacterial artificial chromosomes, and 3) expressed sequence tags. This poster outlines our efforts to generate microsatellite markers from rainbow trout EST sequences to produce polymorphic genetic markers linked to Type I loci, allowing for exploitation of comparative genome information. High-density filters from a rainbow trout normalized cDNA library were probed with (GA)11 and (GT)11 radiolabeled oligonucleotides. Positive clones were sequenced and unique sequences submitted to GenBank for BLAST analyses. PCR primers were designed and used to amplify rainbow trout DNA including reference family parents provided by Dr. Roy Danzmann, University of Guelph, and a panel of other salmonids. Markers for which the parental genotypes were informative were genotyped on reference family offspring for linkage analysis. Overall, 92 microsatellite markers were developed from EST sequences, 84 which were polymorphic and 47 which were informative in a mapping reference family. Mapping of these loci will aid in the identification of QTL and the development of comparative maps between rainbow trout and other species.