Arabidopsis thaliana exhibits wide within-species variation in tolerance to boron limitation and root and shoot trait resilience associate with a pleiotropic locus.

To improve plant tolerance to suboptimal availability of the micronutrient boron (B), it is crucial to understand the mechanisms plants have evolved to tolerate B-limited conditions. We assessed temporal physiological, ionomic and molecular responses to B deficiency across 185 Arabidopsis thaliana accessions grown in soil-substrate in an automated phenotyping system and on agar plates. Whilst profound shoot- and root-growth inhibition was observed in most accessions under B limitation, seven highly B-deficiency tolerant accessions with < 20% reduced fresh and digital biomass accumulation were identified. Boron-efficient accessions were characterised by sustaining lateral more than primary root growth under B limitation. Whilst expression of B transporters increased under B limitation, no correlations between expression and B uptake or B efficiency were observed, suggesting increased B-use efficiency in B-efficient accessions. Phylogenetic analysis suggests B efficiency evolved independently multiple times in response to local environmental needs. Genome-wide association analyses identified a QTL on chromosome 4 that is associated with both root and shoot resilience to B limitation. Our results suggest that an optimised root system contributes to maintaining shoot productivity in B-limited conditions. Further dissection of the identified QTL and candidate genes will form an important strategy for elucidating the molecular control of B efficiency.