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Mapping microsatellite markers identified in porcine EST sequences 1
Author(s) -
Rohrer G. A.,
Fahrenkrug S. C.,
neman D.,
Tao N.,
Warren W. C.
Publication year - 2002
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1046/j.1365-2052.2002.00880.x
Subject(s) - dinucleotide repeat , biology , microsatellite , genetics , genetic marker , genbank , genome , primer (cosmetics) , population , repeated sequence , gene , allele , chemistry , demography , organic chemistry , sociology
A sequence search of swine expressed sequence tags (EST) data in GenBank identified over 100 sequence files which contained a microsatellite repeat or simple sequence repeat (SSR). Most of these repeat motifs were dinucleotide (CA/GT) repeats; however, a number of tri‐, tetra‐, penta‐ and hexa‐nucleotide repeats were also detected. An initial assessment of six 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 one tri‐nucleotide SSRs. Overall, 42 markers were polymorphic in the US Meat Animal Research Center (MARC) reference population, 17 markers were uninformative and 12 primer pairs failed to satisfactorily amplify genomic DNA. A comparison of di‐nucleotide repeat vs. markers with repeat motifs of three to six bases demonstrated that 72% of dinucleotide markers were informative relative to only 7% of other repeat motifs. The difference was the result of a much higher percentage of monomorphic markers in the three to six 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 of more than 17 contiguous bases was too low. The mapped microsatellite markers add to the porcine genetic map and provide valuable links between the porcine and human genome.