Length variation in short tandem repeats affects gene expression in natural populations of Arabidopsis thaliana

WB Reinar, VO Lalun, T Reitan, KS Jakobsen… - The Plant …, 2021 - academic.oup.com
The genetic basis for the fine-tuned regulation of gene expression is complex and ultimately
influences the phenotype and thus the local adaptation of natural populations. Short tandem …

Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana

MO Press, RC McCoy, AN Hall, JM Akey… - Genome …, 2018 - genome.cshlp.org
Short tandem repeat (STR) mutations may comprise more than half of the mutations in
eukaryotic coding DNA, yet STR variation is rarely examined as a contributor to complex …

Variability in a Short Tandem Repeat Mediates Complex Epistatic Interactions in Arabidopsis thaliana

MO Press, C Queitsch - Genetics, 2017 - academic.oup.com
Short tandem repeats (STRs) are hypervariable genetic elements that occur frequently in
coding regions. Their high mutation rate readily generates genetic variation, contributing to …

Plant simple sequence repeats: distribution, variation, and effects on gene expression

N Sharopova - Genome, 2008 - cdnsciencepub.com
Genome-wide simple sequence repeat (SSR) information was analyzed together with
functional annotations of Arabidopsis genes and public gene expression data for …

[HTML][HTML] Intergenic and genic sequence lengths have opposite relationships with respect to gene expression

J Colinas, SC Schmidler, G Bohrer, B Iordanov… - PLoS …, 2008 - journals.plos.org
Eukaryotic genomes are mostly composed of noncoding DNA whose role is still poorly
understood. Studies in several organisms have shown correlations between the length of …

Widespread inter‐individual gene expression variability in Arabidopsis thaliana

S Cortijo, Z Aydin, S Ahnert… - Molecular systems biology, 2019 - embopress.org
A fundamental question in biology is how gene expression is regulated to give rise to a
phenotype. However, transcriptional variability is rarely considered although it could …

Polymorphism revealed by simple sequence repeats

W Powell, GC Machray, J Provan - Trends in plant science, 1996 - cell.com
Simple sequence repeats (SSRs) are a group of repetitive DNA sequences that represent a
significant portion of higher eukaryote genomes. They can serve as highly informative …

[HTML][HTML] Distinct patterns of SSR distribution in the Arabidopsis thalianaand rice genomes

MJ Lawson, L Zhang - Genome biology, 2006 - Springer
Abstract Background Simple sequence repeats (SSRs) in DNA have been traditionally
thought of as functionally unimportant and have been studied mainly as genetic markers. A …

Inferring short tandem repeat variation from paired-end short reads

MD Cao, E Tasker, K Willadsen, M Imelfort… - Nucleic acids …, 2014 - academic.oup.com
The advances of high-throughput sequencing offer an unprecedented opportunity to study
genetic variation. This is challenged by the difficulty of resolving variant calls in repetitive …

[HTML][HTML] A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in Arabidopsis thaliana

J Lachowiec, X Shen, C Queitsch, Ö Carlborg - PLoS genetics, 2015 - journals.plos.org
Efforts to identify loci underlying complex traits generally assume that most genetic variance
is additive. Here, we examined the genetics of Arabidopsis thaliana root length and found …