Leaf shape in Populus tremula is a complex, omnigenic trait

Ecology and Evolution
Niklas MählerNathaniel R Street

Abstract

Leaf shape is a defining feature of how we recognize and classify plant species. Although there is extensive variation in leaf shape within many species, few studies have disentangled the underlying genetic architecture. We characterized the genetic architecture of leaf shape variation in Eurasian aspen (Populus tremula L.) by performing genome-wide association study (GWAS) for physiognomy traits. To ascertain the roles of identified GWAS candidate genes within the leaf development transcriptional program, we generated RNA-Seq data that we used to perform gene co-expression network analyses from a developmental series, which is publicly available within the PlantGenIE resource. We additionally used existing gene expression measurements across the population to analyze GWAS candidate genes in the context of a population-wide co-expression network and to identify genes that were differentially expressed between groups of individuals with contrasting leaf shapes. These data were integrated with expression GWAS (eQTL) results to define a set of candidate genes associated with leaf shape variation. Our results identified no clear adaptive link to leaf shape variation and indicate that leaf shape traits are genetically complex, likel...Continue Reading

Associated Datasets

Jul 31, 2020·Torgeir R. HvidstenNathaniel Street

References

Sep 27, 2001·Proceedings of the National Academy of Sciences of the United States of America·R E Cleland
Jul 1, 1997·The Plant Cell·S. E. Clark
Apr 12, 2005·The New Phytologist·Christopher TraiserVolker Mosbrugger
Aug 13, 2005·The International Journal of Developmental Biology·Hirokazu Tsukaya
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Jan 8, 2008·Nucleic Acids Research·Simon M LinWarren A Kibbe
Jan 25, 2008·Proceedings of the National Academy of Sciences of the United States of America·Martin Rosvall, Carl T Bergstrom
Jul 24, 2008·BMC Plant Biology·Max BylesjöNathaniel R Street
Dec 9, 2008·BMC Genomics·Nathaniel Robert StreetStefan Jansson
Sep 10, 2009·The Plant Journal : for Cell and Molecular Biology·Juan DuAndrew T Groover
Nov 19, 2009·Nucleic Acids Research·Robert D FinnAlex Bateman
Sep 28, 2010·Current Opinion in Plant Biology·Jihyun Moon, Sarah Hake
Mar 17, 2011·European Journal of Human Genetics : EJHG·Jian YangUNKNOWN GIANT Consortium
Jul 17, 2012·Nature Methods·Daniel MarbachGustavo Stolovitzky
Oct 17, 2012·Bioinformatics·Evguenia KopylovaHélène Touzet
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Feb 15, 2013·PLoS Genetics·Xiang ZhouMatthew Stephens
Apr 30, 2013·Molecular Biology and Evolution·Josephine T DaubLaurent Excoffier
May 24, 2013·Nature·Björn NystedtStefan Jansson
Nov 29, 2013·Plant Physiology·Daniel H ChitwoodNeelima R Sinha
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Jun 14, 2014·Proceedings of the National Academy of Sciences of the United States of America·Yasunori IchihashiNeelima R Sinha
Sep 28, 2014·Bioinformatics·Simon AndersWolfgang Huber
Nov 5, 2014·American Journal of Botany·Roger D Meicenheimer
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
May 25, 2015·Trends in Genetics : TIG·Aaron Sluis, Sarah Hake
Jul 1, 2015·BMC Plant Biology·Derek R DrostMatias Kirst
Jul 21, 2015·The New Phytologist·David SundellNathaniel R Street
Aug 5, 2015·Cold Spring Harbor Perspectives in Biology·Hjördis Czesnick, Michael Lenhard

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Datasets Mentioned

BETA
ERP014886
PRJEB31491

Methods Mentioned

BETA
transcription profiling
Illumina sequencing
transgenic

Software Mentioned

ape package
R
ANGUSTIFOLIA
LeafDev
Tigress
GENIE3
DESeq2
Gephi
ROTUNDIFOLIA
qvalue R package

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