Summary Seedling emergence timing is crucial in competitive plant communities and so contributes to species fitness. To understand the mechanistic basis of variation in seedling emergence timing, we exploited the contrasting behaviour of two Arabidopsis thaliana ecotypes: Cape Verde Islands (Cvi) and Burren (Bur‐0). We used RNA‐Seq analysis of RNA from exhumed seeds and quantitative trait loci (QTL) analyses on a mapping population from crossing the Cvi and Bur‐0 ecotypes. We determined genome‐wide expression patterns over an annual dormancy cycle in both ecotypes, identifying nine major clusters based on the seasonal timing of gene expression, and variation in behaviour between them. QTL were identified for depth of seed dormancy and seedling emergence timing (SET). Both analyses showed a key role for DOG1 in determining depth of dormancy, but did not support a direct role for DOG1 in generating altered seasonal patterns of seedling emergence. The principle QTL determining SET (SET1: dormancy cycling) is physically close on chromosome 5, but is distinct from DOG1. We show that SET1 and two other SET QTLs each contain a candidate gene (AHG1, ANAC060, PDF1 respectively) closely associated with DOG1 and abscisic acid signalling and suggest a model for the control of SET in the field.

Environmental signals drive seed dormancy cycling in the soil to synchronize germination with the optimal time of year, a process essential for species' fitness and survival. Previous correlation of transcription profiles in exhumed seeds with annual environmental signals revealed the coordination of dormancy‐regulating mechanisms with the soil environment. Here, we developed a rapid and robust laboratory dormancy cycling simulation. The utility of this simulation was tested in two ways: firstly, using mutants in known dormancy‐related genes [DELAY OF GERMINATION 1 (DOG1), MOTHER OF FLOWERING TIME (MFT), CBL‐INTERACTING PROTEIN KINASE 23 (CIPK23) and PHYTOCHROME A (PHYA)] and secondly, using further mutants, we test the hypothesis that components of the circadian clock are involved in coordination of the annual seed dormancy cycle. The rate of dormancy induction and relief differed in all lines tested. In the mutants, dog1‐2 and mft2, dormancy induction was reduced but not absent. DOG1 is not absolutely required for dormancy. In cipk23 and phyA dormancy, induction was accelerated. Involvement of the clock in dormancy cycling was clear when mutants in the morning and evening loops of the clock were compared. Dormancy induction was faster when the morning loop was compromised and delayed when the evening loop was compromised.

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SUMMARYSeed crops of the variety Estima were grown in each of 2 years using two planting dates, two harvest dates, two plant densities and two irrigation regimes to produce seed tubers which had experienced different cultural and environmental conditions. The effects of these treatments on tuber characteristics, sprout production and stem development in the ware crop were then determined in subsequent experiments using storage regimes of 3 and 10 mC. Time of planting the seed crop affected numbers of eyes, sprouts and above ground stems in the subsequent ware crop because environmental conditions around the time of tuber initiation appeared to alter tuber shape. Cooler, wetter conditions in the 7 days after tuber initiation were associated with tubers which were longer, heavier and had more eyes, sprouts and above ground stems. In contrast, the time of harvesting the seed crop did not affect tuber shape or numbers of above ground stems and there was no interaction with tuber size. The density of the seed crop had no effect on any character measured and irrigation well after tuber initiation did not affect tuber shape, numbers of sprouts or numbers of stems. Seed production treatments, which resulted in earlier dormancy break, were associated with tubers that produced more sprouts and above ground stems, in contrast to the conventional understanding of apical dominance. Storage at 3 mC gave fewer sprouts, a lower proportion of eyes with sprouts and fewer stems than storage at 10 mC. The major effects on stem production appear to result from environmental conditions at the time of tuber initiation of the seed crop and sprouting temperature.

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