title: Visualizing the genetic landscape of Arabidopsis seed performance.
abstract: Perfect timing of germination is required to encounter optimal conditions for plant survival and is the result of a complex interaction between molecular processes, seed characteristics, and environmental cues. To detangle these processes, we made use of natural genetic variation present in an Arabidopsis (Arabidopsis thaliana) Bayreuth × Shahdara recombinant inbred line population. For a detailed analysis of the germination response, we characterized rate, uniformity, and maximum germination and discuss the added value of such precise measurements. The effects of after-ripening, stratification, and controlled deterioration as well as the effects of salt, mannitol, heat, cold, and abscisic acid (ABA) with and without cold stratification were analyzed for these germination characteristics. Seed morphology (size and length) of both dry and imbibed seeds was quantified by using image analysis. For the overwhelming amount of data produced in this study, we developed new approaches to perform and visualize high-throughput quantitative trait locus (QTL) analysis. We show correlation of trait data, (shared) QTL positions, and epistatic interactions. The detection of similar loci for different stresses indicates that, often, the molecular processes regulating environmental responses converge into similar pathways. Seven major QTL hotspots were confirmed using a heterogeneous inbred family approach. QTLs colocating with previously reported QTLs and well-characterized mutants are discussed. A new connection between dormancy, ABA, and a cripple mucilage formation due to a naturally occurring mutation in the MUCILAGE-MODIFIED2 gene is proposed, and this is an interesting lead for further research on the regulatory role of ABA in mucilage production and its multiple effects on germination parameters.
authors.affiliation: Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands.
authors.forename: Ronny Viktor Louis
authors.initials: RV
authors.lastname: Joosen
authors.forename: Danny
authors.initials: D
authors.lastname: Arends
authors.forename: Leo Albert Jan
authors.initials: LA
authors.lastname: Willems
authors.forename: Wilco
authors.initials: W
authors.lastname: Ligterink
authors.forename: Ritsert C
authors.initials: RC
authors.lastname: Jansen
authors.forename: Henk W M
authors.initials: HW
authors.lastname: Hilhorst
mesh_terms: D017360:Arabidopsis / Q000196:embryology* / Q000235:genetics; D004843:Epistasis, Genetic; D017343:Genes, Plant; D018525:Germination; D040641:Quantitative Trait Loci; D012639:Seeds / Q000502:physiology*