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.
Highlights
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
We used a recombinant inbred line (RIL) population derived from two Arabidopsis (Arabidopsis thaliana) ecotypes: Bayreuth (Bay-0), which originates from a fallow land habitat in Germany, and Shahdara (Sha), which grows at high altitude in the Pamiro-Alay mountains in Tadjikistan (Loudet et al, 2002)
The Bay-0 3 Sha RIL population has been used in many previous studies to map quantitative trait locus (QTL) positions for root morphology (Loudet et al, 2005; Reymond et al, 2006), anion content (Loudet et al, 2003a), nitrogen use efficiency (Loudet et al, 2003b), cell wall digestibility (Barriere et al, 2005), carbohydrate content (Calenge et al, 2006), sulfate content (Loudet et al, 2007), leaf senescence (Diaz et al, 2006), morningspecific growth (Loudet et al, 2008), and cold-dark germination (Meng et al, 2008)
Summary
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 3 Shahdara recombinant inbred line population. We determined germination sensu stricto for primary dormancy in freshly harvested seeds, germination of fully after-ripened seeds with and without a preceding cold stratification period (for conditions, see “Materials and Methods”), and germination under various stress conditions (low/high temperature, salt/osmotic stress, and ABA) to assess natural variation in the Bay-0 3 Sha RIL population. Evaluation of these high numbers of phenotypes demanded methods of QTL analysis that extended beyond mapping of individual traits and that allowed comprehensive and comprehensible visualization
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