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The capacity of organisms to tune their development in response to environmental cues is pervasive in nature. This phenotypic plasticity is particularly striking in plants, enabled by their modular and continuous development. A good example is the activation of lateral shoot branches in Arabidopsis, which develop from axillary meristems at the base of leaves. The activity and elongation of lateral shoots depends on the integration of many signals both external (e.g. light, nutrient supply) and internal (e.g. the phytohormones auxin, strigolactone and cytokinin). Here, we characterise natural variation in plasticity of shoot branching in response to nitrate supply using two diverse panels of Arabidopsis lines. We find extensive variation in nitrate sensitivity across these lines, suggesting a genetic basis for variation in branching plasticity. High plasticity is associated with extreme branching phenotypes such that lines with the most branches on high nitrate have the fewest under nitrate deficient conditions. Conversely, low plasticity is associated with a constitutively moderate level of branching. Furthermore, variation in plasticity is associated with alternative life histories with the low plasticity lines flowering significantly earlier than high plasticity lines. In Arabidopsis, branching is highly correlated with fruit yield, and thus low plasticity lines produce more fruit than high plasticity lines under nitrate deficient conditions, whereas highly plastic lines produce more fruit under high nitrate conditions. Low and high plasticity, associated with early and late flowering respectively, can therefore be interpreted alternative escape vs mitigate strategies to low N environments. The genetic architecture of these traits appears to be highly complex, with only a small proportion of the estimated genetic variance detected in association mapping., Competing Interests: The authors have declared that no competing interests exist.

Quantitative traits may be controlled by many loci, many alleles at each locus, and subject to genotype-by-environment interactions, making them difficult to map. One example of such a complex trait is shoot branching in the model plant Arabidopsis, and its plasticity in response to nitrate. Here, we use artificial selection under contrasting nitrate supplies to dissect the genetic architecture of this complex trait, where loci identified by association mapping failed to explain heritability estimates. We found a consistent response to selection for high branching, with correlated responses in other traits such as plasticity and flowering time. Genome-wide scans for selection and simulations suggest that at least tens of loci control this trait, with a distinct genetic architecture between low and high nitrate treatments. While signals of selection could be detected in the populations selected for high branching on low nitrate, there was very little overlap in the regions selected in three independent populations. Thus the regulatory network controlling shoot branching can be tuned in different ways to give similar phenotypes. Author summary: Unlike in animals, plant development happens continuously throughout an individual's lifespan and strongly interacts with the external environment. An example is the regulation of shoot branching, which depends on the regulated activity of buds in the axils of leaves. The switch between dormancy and activity in buds involves the integration of both internal (hormonal) and external (environmental) signals. We have previously shown that shoot branching in Arabidopsis is a highly plastic trait in response to nitrate in the soil. This plasticity is genetically variable, however previous studies have failed to elucidate fully its genetic architecture (number, location and effect of the underlying loci). Here, we use an artificial selection approach, combined with genome sequencing and simulations, to tackle this challenge. Our results suggest that this trait is controlled by at least tens of loci of small effect. We show that different populations achieve a similar average number of branches, despite selection for different loci, suggesting some genetic redundancy, such that multiple genetic makeups can result in similar phenotypes. Also, the genetic architecture differed between populations selected with high vs low nitrate concentrations in the soil, suggesting that different regulatory pathways may be involved in the activation of dormant buds depending on the nutrient levels available to the plant. Our study thus clarifies the complex interactions between the environment and genetics for shoot branching regulation in plants. [ABSTRACT FROM AUTHOR]