ArticleGenome biology and evolution2017
Systematic Profiling of Short Tandem Repeats in the Cattle Genome.
Article in Genome biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 35 citations in OpenAlex.
- Causal variants in animal genomes: approaches to identification, phenotypic impact, and implications for selective breeding.BMC genomics · 2026Review
- Detection of short tandem repeats in the cattle genome: a comparison of bioinformatic tools.BMC genomics · 2026Article
- Statistical Genomics Analysis of Simple Sequence Repeats from the Paphiopedilum Malipoense Transcriptome Reveals Control Knob Motifs Modulating Gene Expression.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue.Genetics · 2023Article
- Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species.Journal of evolutionary biology · 2023Review
- A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.Genetics, selection, evolution : GSE · 2021Article
- Discovery of Genomic Characteristics and Selection Signatures in Southern Chinese Local Cattle.Frontiers in genetics · 2020Article
- QTL-mapping and genomic prediction for bovine respiratory disease in U.S. Holsteins using sequence imputation and feature selection.BMC genomics · 2019Article
- Genome-Wide Scan Identifies Selection Signatures in Chinese Wagyu Cattle Using a High-Density SNP Array.Animals : an open access journal from MDPI · 2019Article
- Tandem Repeats Contribute to Coding Sequence Variation in Bumblebees (Hymenoptera: Apidae).Genome biology and evolution · 2018Article
- Identification and characterization of short tandem repeats in the Tibetan macaque genome based on resequencing data.Zoological research · 2018Article
- Characterization of Duck (Frontiers in genetics · 2018Article
Corrections and comments
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Authors and funding
11 authors at 7 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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