Genome-wide association mapping of growth dynamics detects time-specific and general quantitative trait loci.
Growth is a complex trait determined by the interplay between many genes, some of which play a role at a specific moment during development whereas others play a more general role. To identify the genetic basis of growth, natural variation in Arabidopsis rosette growth was followed in 324 accessions by a combination of top-view imaging, high-throughput image analysis, modelling of growth dynamics, and end-point fresh weight determination. Genome-wide association (GWA) mapping of the temporal growth data resulted in the detection of time-specific quantitative trait loci (QTLs), whereas mapping of model parameters resulted in another set of QTLs related to the whole growth curve. The positive correlation between projected leaf area (PLA) at different time points during the course of the experiment suggested the existence of general growth factors with a function in multiple developmental stages or with prolonged downstream effects. Many QTLs could not be identified when growth was evaluated only at a single time point. Eleven candidate genes were identified, which were annotated to be involved in the determination of cell number and size, seed germination, embryo development, developmental phase transition, or senescence. For eight of these, a mutant or overexpression phenotype related to growth has been reported, supporting the identification of true positives. In addition, the detection of QTLs without obvious candidate genes implies the annotation of novel functions for underlying genes.
Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
Johanna A
JA
Bac-Molenaar
Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
Dick
D
Vreugdenhil
Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, UMR 759, Institut National de la Recherche Agronomique/Ecole Nationale Supérieure d'Agronomie, Place Viala, F-34060 Montpellier, Cedex 1, France.
Christine
C
Granier
Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands joost.keurentjes@wur.nl.
Joost J B
JJ
Keurentjes
D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development*; D055106:Genome-Wide Association Study; D007091:Image Processing, Computer-Assisted; D010641:Phenotype; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development; D040641:Quantitative Trait Loci
Arabidopsis thaliana; GWAS; PLA; genome-wide association mapping; growth dynamics; natural variation; plant phenotyping; projected leaf area; rosette growth.