Preponderant alleles at Hd1 and Ehd1 lead to photoperiod insensitivity in japonica rice varieties

Adaptation of photoperiod-sensitive japonica rice varieties from long-day (LD) to short-day (SD) conditions is impeded by their extremely early flowering in response to photoperiod change, but the genetic factor underly-ing this is still elusive. We detected mutations in Hd1 in Zhenjing2400 through gene mapping and sequencing analysis. Genome resequencing of the varieties Zhenjing2400 and Jiahe218 identified single nucleotide polymorphisms (SNPs) in the other flowering-related genes Ehd1, SDG725, OsCOL15, DTH2, and DTH7. We constructed recombinant inbred lines (RILs) derived from a cross between Zhenjing2400 and Jiahe218, and selected homozygous lines with these six genes. We established that photoperiod insensitivity is caused by a defective Hd1 gene. In addition, the effect of Hd1 and Ehd1 on heading date was stronger than that of the other four genes. Measurements of agronomic traits and quality traits in homozygous lines demonstrated the superiority of the hd1 ehd1 genotype for eating quality and photoperiod-insensitive high yield.