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Genome Biol Evol. 2017 Jan 1;9(1):20-31. doi: 10.1093/gbe/evw256.

Systematic Profiling of Short Tandem Repeats in the Cattle Genome.

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Animal Genomics and Improvement Laboratory, Agricultural Research Service, Beltsville, MD.
Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
Department of Animal and Avian Sciences, University of Maryland, College Park, MD.
Department of Biology, University of Wisconsin - Platteville, WI.
College of Animal Science, South China Agricultural University, Guangzhou, China.
College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shannxi, China
Department of Evolution and Ecology, University of California, Davis, CA.


Short tandem repeats (STRs), or microsatellites, are genetic variants with repetitive 2–6 base pair motifs in many mammalian genomes. Using high-throughput sequencing and experimental validations, we systematically profiled STRs in five Holsteins. We identified a total of 60,106 microsatellites and generated the first high-resolution STR map, representing a substantial pool of polymorphism in dairy cattle. We observed significant STRs overlap with functional genes and quantitative trait loci (QTL). We performed evolutionary and population genetic analyses using over 20,000 common dinucleotide STRs. Besides corroborating the well-established positive correlation between allele size and variance in allele size, these analyses also identified dozens of outlier STRs based on two anomalous relationships that counter expected characteristics of neutral evolution. And one STR locus overlaps with a significant region of a summary statistic designed to detect STR-related selection. Additionally, our results showed that only 57.1% of STRs located within SNP-based linkage disequilibrium (LD) blocks whereas the other 42.9% were out of blocks. Therefore, a substantial number of STRs are not tagged by SNPs in the cattle genome, likely due to STR's distinct mutation mechanism and elevated polymorphism. This study provides the foundation for future STR-based studies of cattle genome evolution and selection.

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