NARO and partners discover gene that controls rice flowering time

A research group including Senior Researcher Tsutomu Ishimaru of the Department of Large-scale Lowland Crop Rotation Research, Central Region Agricultural Research Center, National Agriculture and Food Research Organization (NARO), and Principal Researcher Kazuhiro Sasaki of the Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), in collaboration with Takasaki University of Health and Welfare, Kibi International University, and the International Rice Research Institute (IRRI) in the Philippines, announced on June 12 the discovery of "EMF3," a novel gene that regulates the flowering time of rice. The group demonstrated that rice strains possessing a specific single-nucleotide polymorphism in this gene begin flowering approximately two hours earlier than usual. These early-flowering plants showed significantly improved fertility compared to conventional rice that blooms during peak daytime temperatures. Because this heat-escape trait can be introduced into a wide array of global cultivars, it is highly anticipated to contribute to the stabilization of global rice yields. The findings were published in the Plant Biotechnology Journal.

While rice is relatively heat-tolerant, high temperatures during the ripening stage cause chalky grains, reducing its market value. Furthermore, there are growing concerns that future temperature increases will expose rice to extreme heat precisely during its flowering period, leading to sterility where grains fail to form. Since rice serves as the staple food for roughly half of the world's population, this issue is considered a global challenge.

A rice flower physically opens its husk when water flows into the lodicules, which correspond to petals. The enclosed anthers then dehisce (split open), allowing pollen to fall onto the stigma for pollination. If ambient temperatures are excessively high at the time of flowering, anther dehiscence fails, leading to unsuccessful pollination and subsequent sterility.

The flowering window for rice is fixed between 10:00 AM and noon depending on the variety. Each flower opens and closes within about an hour, making it a daily flower that is most vulnerable to heat at the exact moment of blooming. A temperature of 35℃ is generally considered the threshold for heat-induced sterility. Conversely, the impact of high temperatures is relatively low once pollination and fertilization are complete.

In 2015, the research group successfully bred an early-morning flowering rice line by utilizing a wild rice species (O. officinalis) that possesses an early-blooming trait, advancing the flowering time by approximately two hours. This work indicated that a gene associated with early-morning flowering likely resided on chromosome 3. However, the specific gene had yet to be identified.

In the present study, the research group aimed to isolate the gene responsible for early-morning flowering and pinpoint the exact nucleotide sequence mutation.

By comparing the early-morning flowering lines with conventional rice, they discovered a single-nucleotide difference within a gene located on chromosome 3 and named it EMF3 (Early Morning Flowering 3). In the early-morning flowering rice, the 181st nucleotide of this gene was substituted from cytosine (C) to thymine (T). This mutation altered the 61st amino acid of the encoded protein from leucine (L) to phenylalanine (F).

While conventional rice carrying leucine at position 61 flowers between 10:00 AM and noon, knocking out the function of this gene caused the plants to flower sporadically across a broad timeframe from early morning until evening.

Furthermore, when checking flowering times using a mutant line population of the Japanese cultivar "Toyomeki" that carries variations in the EMF3 gene, the team discovered that a line whose 563rd amino acid was substituted from threonine (T) to isoleucine (I) also exhibited the early-morning flowering trait.

Next, the team evaluated the fertility of the early-morning flowering rice under high-temperature conditions.

Using a temperature-elevated chamber, they established a heat-stress environment where the temperature started at 28℃ at 6:00 AM and gradually rose to 38℃ by noon to compare conventional rice with the early-morning flowering lines.

The results showed that while conventional rice suffered a severe drop in fertility under these high temperatures, the early-morning flowering rice successfully averted sterility because it bloomed before the temperature reached 35℃.

The team also confirmed that no existing standard rice cultivars worldwide possess these specific amino acid changes at position 61 or 563 seen in the early-morning flowering lines. In collaboration with IRRI, they introduced the mutation via cross-breeding into various cultivars grown across Southeast Asia, South Asia, and West Africa. Every single variety demonstrated an advancement in flowering time by an hour or more, indicating that this method is applicable to diverse global rice strains.

To investigate the underlying mechanism, the researchers analyzed the organs where the EMF3 gene is expressed and confirmed expression in the anthers and pollen. While it was previously believed that the lodicules primarily controlled flowering time, these findings suggest that the anthers play a crucial role in the process.

Ishimaru commented: "Moving forward, we anticipate that the utilization of this 'single-nucleotide change' will accelerate the development of highly accurate DNA markers both domestically and internationally, speeding up the breeding of early-morning flowering rice cultivars. We believe this study provides a vital clue to scientifically unraveling the entire regulatory mechanism of flowering time mediated by the EMF3 gene expressed in the anthers."

Journal Information
Publication: Plant Biotechnology Journal
Title: Rice EMF3 Alleles Adjust Flower Opening Time to Enhance the Seed Setting Rate Under High Temperature Stress
DOI: 10.1111/pbi.70653