Genetic effect of a new allele for the flowering time locus Ghd7 in rice

The optimization of flowering time is a key aspect in maximizing grain productivity in rice. Allelic variations in genes for flowering time are major drivers in the wide adaptability of cultivated rice around the world. Here, we identified a novel allele of flowering time gene Grain number, plant height and heading date 7 (Ghd7). Loss-of-function ghd7, Ghd7-0a, is important for extremely early flowering time for adaptability to cultivation in Hokkaido, Japan. However, the rice variety Sorachi lacks a key functional nucleotide polymorphism of Ghd7, which results in a loss of function of the gene. Based on the sequence of Ghd7 allele in Sorachi, we identified the insertion of a transposon-like sequence at an upstream site of Ghd7. Segregation analysis using an F(2) population derived from the cross between Hoshinoyume and Sorachi demonstrated that the Ghd7 locus contributed to extremely early flowering time in Sorachi. This Ghd7 allele in Sorachi showed a weak function in terms of delay of flowering time, compared with loss-of-function allele, and a distinct distribution in northern Japan.