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- Title
Systematic Profiling of Short Tandem Repeats in the Cattle Genome.
- Authors
Lingyang Xu; Haasl, Ryan J.; Jiajie Sun; Yang Zhou; Bickhart, Derek M.; Junya Li; Jiuzhou Song; Sonstegard, Tad S.; Van Tassell, Curtis P.; Lewin, Harris A.; Liu, George E.
- Abstract
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.
- Subjects
SHORT tandem repeat analysis; TANDEM repeats; GENETIC polymorphisms; MICROSATELLITE repeats; DINUCLEOTIDES; CATTLE
- Publication
Genome Biology & Evolution, 2017, Vol 9, Issue 1, p20
- ISSN
1759-6653
- Publication type
Article
- DOI
10.1093/gbe/evw256