Loss-of-Function Alleles of () Are Associated With Adaptation of Temperate Rice Plants to the Tropical Region.

Adaptation of temperate rice varieties to tropical regions is impeded by extremely early flowering probably due to photoperiod change from long to short. However, constant breeding efforts led to development of temperate varieties adapted to tropical/subtropical regions, but the genetic factor underlying this is still elusive. We analyzed the 45 diverse rice accessions and 12 tropical-adapted temperate lines for the allele types of seven major flowering genes , and and flowering time under three different field conditions in temperate and tropical locations. The accessions originated from the tropical/subtropical regions preferred the non-functional alleles of and not other flowering genes. The genetic effect analysis of each gene showed that only the functional caused early flowering in the tropical location. All 12 temperate breeding lines adapted to the tropics possessed the loss-of-function alleles of with no change of other flowering genes compared to common Korean temperate varieties. A phylogenetic analysis using 2,918 SNP data points revealed that the genome status of the 12 breeding lines were very similar to Korean temperate varieties. These results indicate that the functional alleles of temperate varieties induced extremely early flowering in the tropics and the non-functional alleles brought about the adaptation of temperate rice to tropical regions.