Genetic Regulation of Transcriptional Variation in Natural Arabidopsis thaliana Accessions

G3 : Genes - Genomes - Genetics
Yanjun ZanÖrjan Carlborg

Abstract

An increased knowledge of the genetic regulation of expression in Arabidopsis thaliana is likely to provide important insights about the basis of the plant's extensive phenotypic variation. Here, we reanalyzed two publicly available datasets with genome-wide data on genetic and transcript variation in large collections of natural A. thaliana accessions. Transcripts from more than half of all genes were detected in the leaves of all accessions, and from nearly all annotated genes in at least one accession. Thousands of genes had high transcript levels in some accessions, but no transcripts at all in others, and this pattern was correlated with the genome-wide genotype. In total, 2669 eQTL were mapped in the largest population, and 717 of them were replicated in the other population. A total of 646 cis-eQTL-regulated genes that lacked detectable transcripts in some accessions was found, and for 159 of these we identified one, or several, common structural variants in the populations that were shown to be likely contributors to the lack of detectable RNA transcripts for these genes. This study thus provides new insights into the overall genetic regulation of global gene expression diversity in the leaf of natural A. thaliana acces...Continue Reading

References

Mar 30, 2002·Science·Rachel B BremLeonid Kruglyak
Mar 21, 2003·Nature·Eric E SchadtStephen H Friend
Aug 9, 2003·Proceedings of the National Academy of Sciences of the United States of America·Scott D MichaelsRichard M Amasino
Sep 25, 2003·Proceedings of the National Academy of Sciences of the United States of America·Juergen KroymannThomas Mitchell-Olds
Jul 23, 2004·Nature·Michael MorleyVivian G Cheung
Oct 27, 2004·Proceedings of the National Academy of Sciences of the United States of America·M E NasrallahJ B Nasrallah
Feb 8, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jonathan D WernerDetlef Weigel
May 24, 2005·PLoS Biology·Magnus NordborgJoy Bergelson
Oct 6, 2005·Genetics·Daniel J KliebensteinDina A St Clair
Oct 24, 2006·PLoS Genetics·Enrico PetrettoTimothy J Aitman
Jan 24, 2007·Proceedings of the National Academy of Sciences of the United States of America·Joost J B KeurentjesRitsert C Jansen
Mar 27, 2007·Bioinformatics·Yurii S AulchenkoCornelia M van Duijn
Aug 7, 2007·Nature Genetics·Sung KimMagnus Nordborg
Oct 19, 2007·PLoS Genetics·Adam M WentzellDaniel J Kliebenstein
Apr 18, 2008·PLoS Biology·Erin N Smith, Leonid Kruglyak
Feb 20, 2009·Molecular Systems Biology·Stephanie PlantegenetChristian S Hardtke
Jun 13, 2009·Genome Biology·Detlef Weigel, Richard Mott
Mar 12, 2010·Nature·Stephen B MontgomeryEmmanouil T Dermitzakis
Mar 12, 2010·Nature·Joseph K PickrellJonathan K Pritchard
May 19, 2010·Proceedings of the National Academy of Sciences of the United States of America·Adnane NemriJonathan D G Jones
Apr 7, 2011·Genome Research·Xu ZhangJustin O Borevitz
Aug 30, 2011·Nature Genetics·Jun CaoDetlef Weigel
Apr 26, 2012·PLoS Genetics·Christina L RichardsMichael D Purugganan
Jul 26, 2012·The Plant Journal : for Cell and Molecular Biology·Catharine LieXuelin Wu
Mar 8, 2013·Nature·Robert J SchmitzJoseph R Ecker

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Citations

Aug 7, 2018·The Plant Journal : for Cell and Molecular Biology·Elise AlbertMathilde Causse
Jan 11, 2019·Frontiers in Plant Science·Jennifer R OlinsSamuel P Hazen

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Datasets Mentioned

BETA
GSE43858
GSE54680

Methods Mentioned

BETA
RNA-seq

Software Mentioned

Bioscope
PALMapper aligner
cgmisc R - package
GenABEL
Cufflinks

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