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Background  Rice is considered a short day plant. Originally from tropical regions rice has been progressively adapted to temperate climates and long day conditions in part by modulating its sensitivity to day length.  Heading date 3a  ( Hd3a ) and  RICE FLOWERING LOCUS T 1  ( RFT1 ) that code for florigens, are known as major regulatory genes of floral transition in rice. Both  Hd3a  and  RFT1  are regulated by  Early heading date 1  ( Ehd1)  and  Days to heading on chromosome 2  ( DTH2 ) while  Heading date 1  ( Hd1 ) also governs  Hd3a  expression. To investigate the mechanism of rice adaptation to temperate climates we have analyzed the natural variation of these five genes in a collection of  japonica  rice representing the genetic diversity of long day cultivated rice.    Results  We have investigated polymorphisms of  Hd3a ,  RFT1 ,  Ehd1, Hd1  and  DTH2  in a collection of 57  japonica  varieties.  Hd3a  and  RFT1  were highly conserved, displaying one major allele. Expression analysis suggested that  RFT1  rather than  Hd3a  could be the pivotal gene controlling flowering under long day conditions. While few alleles were found in the  Ehd1  promoter and  DTH2  coding region, a high degree of variation in  Hd1 , including non-functional alleles, was observed. Correlation analysis between gene expression levels and flowering periods suggested the occurrence of other factors, additionally to  Ehd1,  affecting  RFT1  regulation in long day adapted cultivars.    Conclusions  During domestication, rice expansion was accompanied by changes in the regulatory mechanism of flowering. The existence of non-functional  Hd1  alleles and the lack of correlation of their presence with flowering times in plants grown under long day conditions, indicate a minor role of this branch in this process and the existence of an alternative regulatory pathway in northern latitudes. Expression analysis data and a high degree of conservation of  RFT1  suggested that this gene could be the main factor regulating flowering among  japonica  cultivars adapted to northern areas. In the absence of inhibition exerted by  Hd1  through repression of  Hd3a  expression, the role of  Ehd1  as a regulator of  RFT1  and  Hd3a  appears to be reinforced. Data also indicated the occurrence of additional regulatory factors controlling flowering.

Diversity of floral regulatory genes of japonica rice cultivated at northern latitudes