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 …

Background-dependent effects of polyglutamine variation in the Arabidopsis thaliana gene ELF3

SF Undurraga, MO Press, M Legendre… - Proceedings of the …, 2012 - National Acad Sciences
Tandem repeats (TRs) have extremely high mutation rates and are often considered to be
neutrally evolving DNA. However, in coding regions, TR copy number mutations can …

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 …

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 …

Genetic architecture of regulatory variation in Arabidopsis thaliana

X Zhang, AJ Cal, JO Borevitz - Genome research, 2011 - genome.cshlp.org
Studying the genetic regulation of expression variation is a key method to dissect complex
phenotypic traits. To examine the genetic architecture of regulatory variation in Arabidopsis …

Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana

CM Alexandre, JR Urton, K Jean-Baptiste… - Molecular Biology …, 2018 - academic.oup.com
Variation in regulatory DNA is thought to drive phenotypic variation, evolution, and disease.
Prior studies of regulatory DNA and transcription factors across animal species highlighted a …

Inheritance Beyond Plain Heritability: Variance-Controlling Genes in Arabidopsis thaliana

X Shen, M Pettersson, L Rönnegård, Ö Carlborg - 2012 - journals.plos.org
The phenotypic effect of a gene is normally described by the mean-difference between
alternative genotypes. A gene may, however, also influence the phenotype by causing a …

A Polynucleotide Repeat Expansion Causing Temperature-Sensitivity Persists in Wild Irish Accessions of Arabidopsis thaliana

A Tabib, S Vishwanathan, A Seleznev… - Frontiers in Plant …, 2016 - frontiersin.org
Triplet repeat expansions underlie several human genetic diseases such as Huntington's
disease and Friedreich's ataxia. Although such mutations are primarily known from humans …

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 …

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 …