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Significance Internal timekeepers, called circadian clocks, are prevalent in all domains of life. Variation in circadian rhythms allows fine-tuning of an organism to its specific environment. Here we show that a mutation inLNK2 , in addition to the already described mutation inEID1 , was responsible for the deceleration of circadian rhythms in cultivated tomatoes. We show that the mutant alleles of both genes arose in the earliest cultivated types and were selected during the domestication process. Notably, both mutant alleles specifically affect light input to the clock, leading to a light-conditional clock deceleration. Such light-conditionality may be a widespread means to enhance resonance with changed day–night cycles at higher latitudes, despite the fixed 24-h period of the Earth.

Mutations in EID1 and LNK2 caused light-conditional clock deceleration during tomato domestication