Natural variation for anthocyanin accumulation under high‐light and low‐temperature stress is attributable to the ENHANCER OF AG ‐4 2 ( HUA 2 ) locus in combination with PRODUCTION OF ANTHOCYANIN PIGMENT 1 ( PAP 1 ) and PAP 2

Summary Growing conditions combining high light intensities and low temperatures lead to anthocyanin accumulation in plants. This response was contrasted between two A rabidopsis thaliana accessions, which were used to decipher the genetic and molecular bases underlying the variation of this response. Quantitative trait loci ( QTL s) for flowering time ( FT ) and anthocyanin accumulation under a high‐light and low‐temperature scenario versus a control environment were mapped. Major QTL s were confirmed using near‐isogenic lines. Candidate genes were examined using mutants and gene expression studies as well as transgenic complementation. Several QTL s were found for FT and for anthocyanin content, of which one QTL co‐located at the ENHANCER OF AG ‐4 2 ( HUA 2 ) locus. That HUA 2 is a regulator of both pathways was confirmed by the analysis of loss‐of‐function mutants. For a strong expression of anthocyanin, additional allelic variation was detected for the PRODUCTION OF ANTHOCYANIN PIGMENT 1 ( PAP 1 ) and PAP 2 genes which control the anthocyanin pathway. The genetic control of variation for anthocyanin content was dissected in A . thaliana and shown to be affected by a common regulator of flowering and anthocyanin biosynthesis together with anthocyanin‐specific regulators.