Breeding for delayed bolting decelerated the circadian clock in cultivated lettuce

Abstract

Circadian clocks pace biological events and influence developmental traits, but their role in leafy crop domestication has remained unexplored. We investigated whether selection for delayed bolting during lettuce domestication targeted clock components. We phenotyped circadian rhythms and developmental timing across 234 cultivated and wild lettuce accessions. Using high-throughput leaf movement tracking, genome-wide association studies (GWAS) and haplotype analyses, we identified genetic variants controlling both the clock period and bolting time. Cultivated lettuce exhibits a significantly longer circadian period than its wild relatives, associated with a truncating mutation in PHYTOCHROME C (PHYC). This allele is not only associated with a decelerated clock but also with delayed bolting and flowering time in multiple field experiments. The truncating PHYC allele (H02) is enriched in modern cultivars and phylogenetically close to the wild ancestor (Lactuca serriola) alleles, indicating an early selection during lettuce domestication. Our study directly links for the first time circadian clock deceleration to domestication and breeding in a leafy crop. PHYC emerges as a pleiotropic regulator of the clock and developmental timing shaped by selecting delayed bolting during lettuce domestication and breeding. We demonstrate that circadian phenotyping is a powerful, scalable tool to predict developmental timing and uncover targets for crop improvement.