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Mapping microsatellite markers identified in porcine EST sequences.
G A Rohrer1, S C Fahrenkrug, D Nonneman
1US Meat Animal Research Center, USDA, ARS, Spur 18D, PO Box 166, Clay Center, NE 68933-0166, USA. rohrer@email.marc.usda.gov
Animal Genetics
|October 2, 2002
Summary
Researchers identified microsatellite markers in swine DNA, finding dinucleotide simple sequence repeats (SSRs) to be highly informative for genetic mapping. Higher-order repeats were less informative, suggesting dinucleotide SSRs are more valuable for porcine genetic studies.
Area of Science:
- Genomics
- Molecular Biology
- Animal Genetics
Background:
- Microsatellites, or simple sequence repeats (SSRs), are valuable genetic markers.
- Swine expressed sequence tags (ESTs) provide a resource for identifying SSRs in the porcine genome.
Purpose of the Study:
- To identify and characterize microsatellite repeat markers in swine.
- To compare the informativeness of different types of SSRs for genetic mapping in pigs.
Main Methods:
- Searched swine EST data in GenBank for microsatellite repeats.
- Designed primers for dinucleotide and higher-order nucleotide SSRs.
- Assessed marker informativeness and polymorphism in a reference population.
Main Results:
- Over 100 sequences containing SSRs were identified, with dinucleotide repeats being most common.
- Dinucleotide SSR markers were significantly more informative (72%) than higher-order repeats (7%).
- A high percentage of higher-order repeat markers were monomorphic (64%) compared to dinucleotide markers (14%).
Conclusions:
- Dinucleotide SSRs are more polymorphic and informative for genetic mapping in the porcine genome.
- Further investigation is needed to understand the low polymorphism of higher-order repeats in pigs.
- The identified SSR markers enhance the porcine genetic map and facilitate comparative genomics with the human genome.
