Pool-seq data from artificial selection experiment in Arabidopsis thaliana

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 is shoot branching in the model plant Arabidopsis, and its plasticity in response to nitrate supply. There is substantial natural variation in these traits, associated with alternative life history strategies for coping with nutrient limitation. Association mapping failed to recover much of their heritability. Here we use artificial selection under contrasting nitrate supplies to dissect their genetic architecture. We found a consistent response to selection for high branching, with the correlated traits of plasticity and flowering time co-selected. Genome-wide scans identified several candidate 'selective-sweep-QTL' with little QTL overlap between replicate populations, and evidence of strong allele specific effects. Thus the regulatory network controlling shoot branching, its plasticity and its association with flowering time can be tuned in many different ways to give remarkably similar behaviours.