ARS | Publication request: MAPPING MICROSATELLITE MARKERS IDENTIFIED IN PORCINE EST SEQUENCES

Submitted to: Journal of Animal Science Supplement
Publication Type: Abstract Only
Publication Acceptance Date: February 5, 2001
Publication Date: N/A

Technical Abstract: A recent focus of swine genomics research has been to sequence a significant number of the genes which are expressed in the pig. Single-pass sequence data from cDNA clones between 400 and 600 bases in length, are called expressed sequence tags (EST). A sequence search of these data in GenBank and the MARC swine EST data identified over 100 sequence files which contained a microsatellite repeat. Most repeat motifs detected were dinucleotide (CA/GT) repeats; however, a number of tri-, tetra-, penta- and hexa-nucleotide repeats were also detected. Fifty-eight pair of primers were ordered representing 44 di-, 7 tri-, 1 tetra-, 1 penta-, and 4 hexa-nucleotide repeats, as well as 1 compound (contained a di-, tri- and tetra-nucleotide repeat) repeat motif. Thirty-four markers were polymorphic, 13 markers were uninformative and 11 primer pairs failed to satisfactorily amplify genomic DNA. A comparison of di-nucleotide repeat versus markers with repeat motifs of 3-6 bases determined that 73% of the di-nucleotide markers were useful relative to only 8% for the other repeat motifs. The difference was due to a much higher percentage of monomorphic markers in the 3-6 base repeat motif markers than in the di-nucleotide markers (69% vs 9%). Either the higher order repeat motifs are less polymorphic in the porcine genome or our selection criteria was too low. The mapped markers not only add useful microsatellites to the porcine genetic map but they also provide valuable links between the porcine and human genome.