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

Abstract

Abstract 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. In this study, we characterized a photoperiod-insensitive variety of rice (Oryza sativa L.), named Zhenjing2400. We mapped the causal gene of the photoperiod insensitive to a 4.1-Mb interval on chromosome 6 that contained the major flowering gene Hd1. Sequencing analysis detected two single nucleotide polymorphisms (SNPs) and a 123-bp insertion in Hd1 in Zhenjing2400, leading to the early termination of translation. Genome resequencing of the varieties Zhenjing2400 and Jiahe218 also identified SNPs in the other flowering-related genes Ehd1, SDG725, OsCOL15, DTH2, and DTH7. To dissect the individual contribution of these six genes, we constructed recombinant inbred lines (RILs) derived from a cross between Zhenjing2400 and Jiahe218, and selected homozygous lines with different genotype combinations of 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 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.