Newfound rice gene shifts flowering by 1.5 hours to dodge heat damage

Rice plants at 8:30 AM: the plant with the regular EMF3 gene on the left shows no flowering, while the plant on the right, carrying the rare emf3-1D allele, has already started flowering. Credit: International Rice Research Institute

With El Niño-driven heat and prolonged dry spells threatening rice production, scientists from Japan's National Agriculture and Food Research Organization (NARO), other Japanese research institutions and the International Rice Research Institute (IRRI) have discovered a gene that helps rice "escape" heat during its most sensitive flowering stage. The gene, called EMF3 (Early Morning Flowering 3), shifts rice flowering to the early morning, when temperatures are cooler. By flowering earlier in the day, rice can avoid heat stress that would otherwise reduce grain formation and lower yields in tropical and subtropical regions. The research is published in the Plant Biotechnology Journal .

Rice normally flowers between 10 a.m. and noon, when temperatures reach their daily peak (33°C–35°C). Heat stress during this period, expected to intensify under global warming, can disrupt fertilization, leaving spikelets ("potential grains") sterile and therefore reducing yields. The EMF3 gene, particularly its variant emf3-1D, shifts flowering by 1.5 hours earlier, significantly improving grain fertility under high-temperature conditions.

For Dr. Tsutomu Ishimaru of NARO, Japan, the discovery represents a breakthrough. "It allows rice to 'escape the heat' at its most critical stage, protecting fertilization and ensuring farmers can harvest even under extreme temperatures," he said.

According to researchers, no other rice variety carries the emf3-1D allele. "It appears to be a rare variant and has the potential to work across many popular varieties, including indica and japonica types," said Dr. Sung-Ryul Kim, an IRRI scientist. "This trait could be advantageous for hybrid seed production , where adjusting flower opening time of both parental lines to the same time of day is an important consideration."

Researchers are already introducing emf3-1D into widely grown rice varieties such as IR64, Swarna (India), Pusa Basmati (India), TDK1 (Laos), Sahel 329 (West Africa), Caiapo (Brazil) and Toyomeki (Japan). These advanced lines act as prototypes that could maintain grain fertility even in hot conditions.

"The emf3-1D can be applied to diverse rice varieties worldwide through DNA marker selection, giving breeders a powerful tool to develop early-morning flowering rice," said Dr. Hideyuki Hirabayashi of NARO and Dr. Kazuhiro Sasaki of Japan International Research Center for Agricultural Sciences (JIRCAS).

This breakthrough, according to Dr. Inez Slamet-Loedin, head of IRRI's Rice Genetic Design & Validation Unit, opens the door for gene-editing approaches like prime editing to rapidly introduce the early-morning flowering (emf3-1D) trait into elite rice varieties, enhancing heat resilience across tropical and temperate rice ecosystems for both inbred and hybrid varieties.

Importantly, EMF3 affects only flower opening time and does not change overall plant growth or yield under normal temperature conditions, allowing rice to become heat resilient without losing other key traits.

Ishimaru further emphasized, "We can spend hot days in air-conditioned rooms, but rice plants must survive field heat. With EMF3, they 'wake up' early to avoid heat stress, showing that sometimes being an early riser is key, not just for birds but for crops too."

Publication details

Takuma Ishizaki et al, Rice EMF3 Alleles Adjust Flower Opening Time to Enhance the Seed Setting Rate Under High Temperature Stress, Plant Biotechnology Journal (2026). DOI: 10.1111/pbi.70653

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International Rice Research Institute

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