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Summary  The alteration of photoperiod sensitivity has let breeders diversify flowering time in   O ryza sativa  (rice) and develop cultivars adjusted to a range of growing season periods. Map‐based cloning revealed that the rice flowering‐time quantitative trait locus ( QTL )   H eading date 16  (  H d16 ) encodes a casein kinase‐ I  protein. One non‐synonymous substitution in   H d16  resulted in decreased photoperiod sensitivity in rice, and this substitution occurred naturally in an old rice cultivar. By using near‐isogenic lines with functional or deficient alleles of several rice flowering‐time genes, we observed significant digenetic interactions between   H d16  and four other flowering‐time genes (  G hd7 ,   H d1 ,   DTH 8  and   H d2 ). In a near‐isogenic line with the weak‐photoperiod‐sensitivity allele of   H d16 , transcription levels of   E hd1 ,   H d3a , and   RFT 1  increased under long‐day conditions, and transcription levels of   H d3a  and   RFT 1  decreased under short‐day conditions. Expression analysis under continuous light and dark conditions showed that   H d16  was not likely to be associated with circadian clock regulation. Biochemical characterization indicated that the functional  H d16 recombinant protein specifically phosphorylated  G hd7. These results demonstrate that  H d16 acts as an inhibitor in the rice flowering pathway by enhancing the photoperiod response as a result of the phosphorylation of  G hd7.

H d16 , a gene for casein kinase I , is involved in the control of rice flowering time by modulating the day‐length response