(Image provided by the Research Institute of Rice Production & Technology Co., Ltd.)
On an otherwise unremarkable day in late autumn, I noticed during my lunch break that a line was forming in the courtyard in front of Toyoda Auditorium. It turned out to be an annual event where an unusual variety of rice developed and grown on university-affiliated fields is sold on campus. The organizers told me that they sell out quickly every year, so they limit purchases to one 3-kilogram bag per person. Realizing the urgency of the situation, I joined the line and waited to buy a bag before the stock was gone. When I tried cooking it myself at home, the large rice grains had a wonderfully chewy texture. Intrigued by the taste, I went out to investigate the secret behind its deliciousness!
Shoppers gather at Toyoda Auditorium to purchase rice from a university-affiliated field.
A New Rice Variety Developed by Nagoya University
Researchers from Nagoya University were involved in the development of a new variety of rice called "Hybrid Tōgō No. 3" (hereafter referred to as Tōgō 3). Joint research between Nagoya University and private industry began in 2000, leading to repeated crossbreeding, selection, and seed collection at the Tōgō Field in the town of Tōgō, Aichi Prefecture. The variety that this partnership produced was officially registered in 2014.
What distinguishes Tōgō 3 from conventional varieties is its breeding method: a technique known as "DNA marker-assisted breeding." In this process, researchers first analyze rice genes for specific DNA sequences called "markers." They then use these markers to select and crossbreed plants that have desirable traits such as good taste, high yield, or disease resistance, resulting in the creation of a superior variety of rice.
Illustration of rice breeding using DNA markers. The colored boxes indicate different traits such as disease resistance and growth speed, which are used to create varieties of rice that are adapted to the local climate. (Provided by the Research Institute of Rice Production & Technology Co., Ltd.)
As a staple part of the Japanese diet, rice has long been at the forefront of genetic research and its entire DNA sequence (genome) was decoded by 2004. Based on this genome information, a wide array of DNA markers and their functions have been identified that can now be used in breeding efforts, including the creation of Tōgō 3.
Picking Out the Best Traits with Marker-Assisted Selection
Traditional breeding methods rely on visual observation of plant characteristics (phenotypes) to select superior individuals. The selected parent plants are crossbred, and their offspring are grown to evaluate growth, yield, and flavor through taste testing. In addition to being labor and time intensive, this process has the drawback of being easily affected by environmental factors during cultivation.
In contrast, marker-assisted selection enables screening at the seedling stage, significantly reducing the time, effort, and cultivation space required for selection. Moreover, it minimizes environmental influence, allowing for more accurate assessment of the breeding outcome. By using genetic data to guide the selection of traits, researchers can develop rice varieties that combine multiple strengths, such as strong disease resistance, high yields, and great flavor.
Evaluation comparing Tōgō varieties (orange) and the well-known "Koshihikari" variety (blue) in terms of appearance, scent, flavor, stickiness, and tenderness (clockwise from top) when prepared for consumption. (Provided by the Research Institute of Rice Production & Technology Co., Ltd.)
Visiting the Tōgō 3 Breeding Site
I visited the Research Institute of Rice Production & Technology Co., Ltd., the venture company that took over the breeding of Tōgō 3 after the initial development, to learn more about this innovative technique. Located in Toyoake, Aichi Prefecture, the Research Institute works on developing new rice varieties, supplying seeds, and supporting rice producers.
"Wait, where is the rice field?" I wondered as I arrived at a warehouse tucked away in a residential neighborhood. One of the rooms contained a small greenhouse made of pipes and transparent vinyl, where yet-unnamed varieties of rice plants were being grown. "Marker-assisted selection requires only a small amount of rice plants depending on the target traits," President Kenji Jinushi said, "so there is no need for sprawling fields."
President Kenji Jinushi demonstrating crossbreeding work (top left), along with some scenes from inside the Research Institute.
In a separate room, researchers were immersed in analyzing DNA markers. Using a polymerase chain reaction (PCR) test, the same method used to detect COVID-19, they injected liquefied rice grain samples into specialized measuring instruments to visualize the markers.
DNA marker identification using PCR testing.
A Combination of Traits Loved by Consumers and Producers Alike
Tōgō 3 is derived from the well-known "Koshihikari" rice variety and carries genes for high yield (gn1a), lodging resistance (sd1), improved seed production efficiency (CR1), semi-glutinous texture (Wx-mq), and disease resistance (Pb1). Its taste, popular among consumers, is characterized by a chewy texture and delicious flavor even when cold. On the production side, the variety boasts high yield, resistance to lodging, and resistance to rice blast disease, living up to its reputation as a "chosen" variety.
According to the Research Institute, the variety's yield is 30-40% higher than typical rice plants. The rice contains 15-16% amylose, a type of starch component, compared to about 18% in regular non-glutinous rice. This gives the rice a stickier, chewier texture. "I do not think there are any other varieties of rice that combine these distinct traits in a single strain," explained President Jinushi.
As the name suggests, Tōgō 3 is one of four varieties of rice that make up the Tōgō series. The Research Institute distributes these varieties in a made-to-order format, customized based on the climate of the cultivation region and the needs of producers. For example, Tōgō 2 and Tōgō 4 carry genes for early ripening (hd1) to allow for faster harvest, while Tōgō 1 and Tōgō 2 have the gene for semi-glutinous texture (Wx-mq) removed reduce the stickiness of the rice.
Seeds are supplied to meet diverse needs such as harvest timing and rice stickiness. Tōgō 1 (blue), Tōgō 2 (orange), Tōgō 3 (green), and Tōgō 4 (red) all contain different combinations of traits. (Provided by the Research Institute of Rice Production & Technology Co., Ltd.)
The Tōgō series has been trademarked under the brand name "Shikiyutaka" and is now cultivated throughout Japan, except for Hokkaidō in the far north. Known for its excellent flavor even when served cold, the rice is in high demand for commercial uses such bento box meals or rice balls, which are often sold and eaten at room temperature.
"It is a continually evolving rice variety that takes advantage of insights from genome decoding. Our goal at the Research Institute is to keep creating new types that delight both producers and consumers."
Next-generation varieties carefully selected at the genetic level are born in this "breeding house."
This article was originally written in Japanese by Tatsuyuki Fukui for the "Public Relations Meidai" web magazine and published on January 24, 2024. Unless otherwise stated, photos were taken by the author. The Nagoya University International Communications Office has translated and edited it for clarity while preserving the original content's intent. Certain information might be outdated. For the original Japanese version, please see here.