Cargando…
Systematic Profiling of Short Tandem Repeats in the Cattle Genome
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...
Autores principales: | , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381564/ https://www.ncbi.nlm.nih.gov/pubmed/28172841 http://dx.doi.org/10.1093/gbe/evw256 |
_version_ | 1782519956740505600 |
---|---|
author | Xu, Lingyang Haasl, Ryan J. Sun, Jiajie Zhou, Yang Bickhart, Derek M. Li, Junya Song, Jiuzhou Sonstegard, Tad S. Van Tassell, Curtis P. Lewin, Harris A. Liu, George E. |
author_facet | Xu, Lingyang Haasl, Ryan J. Sun, Jiajie Zhou, Yang Bickhart, Derek M. Li, Junya Song, Jiuzhou Sonstegard, Tad S. Van Tassell, Curtis P. Lewin, Harris A. Liu, George E. |
author_sort | Xu, Lingyang |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5381564 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-53815642017-04-10 Systematic Profiling of Short Tandem Repeats in the Cattle Genome Xu, Lingyang Haasl, Ryan J. Sun, Jiajie Zhou, Yang Bickhart, Derek M. Li, Junya Song, Jiuzhou Sonstegard, Tad S. Van Tassell, Curtis P. Lewin, Harris A. Liu, George E. Genome Biol Evol Research Article 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. Oxford University Press 2016-10-24 /pmc/articles/PMC5381564/ /pubmed/28172841 http://dx.doi.org/10.1093/gbe/evw256 Text en Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2016. This work is written by US Government employees and is in the public domain in the US. |
spellingShingle | Research Article Xu, Lingyang Haasl, Ryan J. Sun, Jiajie Zhou, Yang Bickhart, Derek M. Li, Junya Song, Jiuzhou Sonstegard, Tad S. Van Tassell, Curtis P. Lewin, Harris A. Liu, George E. Systematic Profiling of Short Tandem Repeats in the Cattle Genome |
title | Systematic Profiling of Short Tandem Repeats in the Cattle Genome |
title_full | Systematic Profiling of Short Tandem Repeats in the Cattle Genome |
title_fullStr | Systematic Profiling of Short Tandem Repeats in the Cattle Genome |
title_full_unstemmed | Systematic Profiling of Short Tandem Repeats in the Cattle Genome |
title_short | Systematic Profiling of Short Tandem Repeats in the Cattle Genome |
title_sort | systematic profiling of short tandem repeats in the cattle genome |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381564/ https://www.ncbi.nlm.nih.gov/pubmed/28172841 http://dx.doi.org/10.1093/gbe/evw256 |
work_keys_str_mv | AT xulingyang systematicprofilingofshorttandemrepeatsinthecattlegenome AT haaslryanj systematicprofilingofshorttandemrepeatsinthecattlegenome AT sunjiajie systematicprofilingofshorttandemrepeatsinthecattlegenome AT zhouyang systematicprofilingofshorttandemrepeatsinthecattlegenome AT bickhartderekm systematicprofilingofshorttandemrepeatsinthecattlegenome AT lijunya systematicprofilingofshorttandemrepeatsinthecattlegenome AT songjiuzhou systematicprofilingofshorttandemrepeatsinthecattlegenome AT sonstegardtads systematicprofilingofshorttandemrepeatsinthecattlegenome AT vantassellcurtisp systematicprofilingofshorttandemrepeatsinthecattlegenome AT lewinharrisa systematicprofilingofshorttandemrepeatsinthecattlegenome AT liugeorgee systematicprofilingofshorttandemrepeatsinthecattlegenome |