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United States Department of Agriculture

Agricultural Research Service

Title: Mapping Microsatellite Markers Identified in Porcine Est Sequences

Authors
item Rohrer, Gary
item Fahrenkrug, Scott - UNIV. MINNESOTA
item Nonneman, Danny
item Tao, N - MONSANTO, CHESTERFIELD MO
item Warren, Wes - INCYTE GENOMICS ST. LOUIS

Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 11, 2002
Publication Date: October 1, 2002
Citation: ROHRER, G.A., FAHRENKRUG, S.C., NONNEMAN, D.J., TAO, N., WARREN, W.C. MAPPING MICROSATELLITE MARKERS IDENTIFIED IN PORCINE EST SEQUENCES. ANIMAL GENETICS. 2002. v. 33. p. 372-376.

Interpretive Summary: In an effort to increase the number of links between the human and pig genetic maps, we attempted to map 72 genes in the pig genome. Markers for genes were identified by scanning the public DNA sequence databases for simple sequence repeats (microsatellites). Seventy-two pig gene sequences, or expressed sequence tags (EST), which contained microsatellites were selected for marker development. Overall, 43 markers (60%) were placed on the pig genetic map. The remaining markers were either unable to amplify or were not informative in our reference population. These new markers are useful for mapping economically important loci as well as provide reference points between the pig and human genomes.

Technical Abstract: A sequence search of swine EST data in GenBank 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. An initial assessment of 7 dinucleotide and 14 higher-order repeat markers indicated that only dinucleotide markers yielded a sufficient number of informative markers (100% vs 14% for dinucleotide and higher order repeats, respectively). Primers were designed for an additional 50 di- and 1 tri-nucleotide SSRs. Overall, forty-three markers were polymorphic in the MARC reference population, 17markers were uninformative and 12 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 72% of dinucleotide markers were useful relative to only 7% of 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 dinucleotide markers (64% vs 14%). Either higher order repeat motifs are less polymorphic in the porcine genome or our selection criteria for repeat length was too low. The mapped microsatellites add useful markers to the porcine genetic map and provide valuable links between the porcine and human genome.

Last Modified: 12/28/2014
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