Evidence for rice Heading date 16 contribution to yield increase under low-nutrient conditions

Breeding new rice cultivars that are tolerant to low-nutrient condition is a solution to saving the usage of commercial fertilizer. We isolated Hitomebore EMS mutant, 520-6. Seedling growth of 520-6 is tolerant to low-nutrient supply, especially to low phosphorus (low P) supply and genetic mapping revealed the existence of nonsynonymous substitution within Os03g0793500 9th exon in 520-6. Os03g0793500 is reported as Heading date 16 (Hd16)/Early flowering1 (EL1), which is related with the rice flowering pathway. Hd16/EL1 encodes a casein kinase-I protein, and phosphorylates the floral repressor Ghd7 and the rice DELLA protein Slender rice 1 (SLR1). 520-6 carries the same nonfunctional Hd16 allele to that of Koshihikari, and the parental cultivar, Hitomebore, carries the functional Hd16 allele, as with Nipponbare. mRNA accumulation of GA-biosynthesis-related gene, OsGA2ox3 was enhanced in 520-6 compared with Hitomebore, indicating that Hd16 takes a part in feedback regulation of the GA biosynthetic gene. 520-6 and near-isogenic line (NIL) with nonfunctional Hd16 allele showed heavy straw weight and panicle weight in paddy fields with low nitrogen input and no fertilizer application in Kashimadai at Miyagi prefecture and Hikone at Shiga prefecture, respectively. In addition, plants with nonfunctional Hd16 allele showed late flowering phenotype in all tested fields. These results imply that disruption of Hd16 contributes to the improvement of rice growth by positively regulating GA signaling and late flowering, which resulted in increased rice yield under low-nutrient conditions.