Loss-of-Function Alleles of Heading date 1 (Hd1) Are Associated With Adaptation of Temperate Japonica Rice Plants to the Tropical Region

Abstract

Adaptation of temperate <i>japonica</i> 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 <i>japonica</i> 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 <i>japonica</i> lines for the allele types of seven major flowering genes <i>Hd1, OsPPR37, DTH8, Ghd7, Ehd1, RFT1</i>, and <i>Hd3a</i> 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 <i>Hd1</i> and not other flowering genes. The genetic effect analysis of each gene showed that only the functional <i>Hd1</i> caused early flowering in the tropical location. All 12 temperate <i>japonica</i> breeding lines adapted to the tropics possessed the loss-of-function alleles of <i>Hd1</i> with no change of other flowering genes compared to common Korean temperate <i>japonica</i> 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 <i>japonica</i> varieties. These results indicate that the functional <i>Hd1</i> alleles of temperate <i>japonica</i> varieties induced extremely early flowering in the tropics and the non-functional <i>hd1</i> alleles brought about the adaptation of temperate <i>japonica</i> rice to tropical regions.