Natural variation in activation of KAI2/HTL pathway promotes germination in the dark in Arabidopsis

Elucidating direct roles of natural variation in biological processes has been challenging due to the difficulty in dissecting the causal role of a gene in traits displaying continuous variation. The decision of a seed to germinate is an easily quantifiable binary choice, which makes it an ideal phenotype to assess the contribution of natural variation in adaptation of plants to begin their lifecycle under optimal conditions. seeds must integrate a complex array of environmental signals to begin their lifecycle under optimal conditions. Light availability is a crucial environmental stimulus that promotes germination in many small seed plant species including Arabidopsis thaliana. Upon perception of light by photoreceptors, phytohormones act as internal signals to coordinate germination but the karrikin (KAR) signalling pathway through the HTL/KAI2 receptor is thought to play a rudimentary role in Arabidopsis germination (REF). Here we show that the AtHTL/KAI2 pathway is required and sufficient to promote germination under low light conditions. Activation of the AtHTL/KAI2 receptor by nanomolar Karrikin2 (KAR2) concentrations or inactivation of SMAX1 bypass the light requirement for germination. By performing a screen of A. thaliana accessions that can germinate under low light conditions, we identified an accession from Afghanistan (Ara-1) which misexpressed AtKAI2/HTL and had a nearly identical transcriptional signature to the activation of AtKAI2 upon addition of KAR2 in the reference accession. Our data suggest that AtKAI2 is a central regulator of germination in natural Arabidopsis populations in response to light availability, to optimize germination timing in their ecological niche. Examined the transcriptome profile of dark germinating (24h germination in dark after dark imbibition) Arabidopsis thaliana seeds from Ara-1 accession wild-type and AtKAI2 overexpression lines in Col-0 accession with different Karrikin2 (KAR2) treatment.