DNA reveals the origin of East Asia’s favorite sweet bean 

Red adzuki beans are a beloved staple in East Asia. Cooks tuck a sweet paste made from them inside mochi, swirl it into mooncakes and layer it beneath custard in taiyaki. But despite its popularity, which people were the first to start using this bean remained murky — until now. 

Scientists have analyzed the DNA of nearly 700 varieties of adzuki across Asia. Some of these plants grow in the wild. People have been farming — or cultivating — other types. The beans’ genes now suggest that adzuki was first cultivated in Japan between 3,000 and 5,000 years ago. Only later did people start growing a wide variety of these red beans in China.  

The investigation also uncovered DNA tweaks, or mutations, that gave rise to the beans’ rich red hue. 

“I was surprised by basically everything,” says Cheng-Ruei Lee. He studies evolutionary genetics at National Taiwan University in Taipei. That field of science looks at how variations in DNA lead organisms to evolve new traits. Lee is part of a team that shared its new findings May 29 in Science. 

History written in DNA 

Adzuki beans grow in pods on bushy plants. They have a naturally sweet, nutty flavor. Fossils of ancient beans hinted that Japan’s Jomon people might have grown adzuki. The Jomon were hunter-gatherers who lived as early as 16,000 years ago.  

But red bean DNA had pointed to a different origin story. Beans from China show a wider variety in their DNA than those in Japan. Such diversity is typically only seen in plants that people started to cultivate a very long time ago. 

The new DNA analysis helps make sense of these conflicting data.  

A plant’s nuclear genome is made up of the DNA tucked inside the nuclei of its cells. Plants inherit their nuclear DNA from both parents. And red beans grown in China do show the most diversity in their nuclear genomes, Lee’s team found.  

But the team found another important clue in a different source of the bean’s DNA. This DNA is tucked in structures within plant cells known as chloroplasts. In red beans, only female plants pass this DNA to their offspring. And this type of DNA evolves more slowly. That chloroplast DNA in Chinese red beans closely matches what’s found in wild Japanese beans. 

There’s only one way that these pieces of evidence can fit together, Lee says. People first started growing red beans in Japan, and the practice later spread to China. There, people cross-bred Japanese red beans with local, wild Chinese red beans.  

Today, Chinese red beans now show a much wider variety in their DNA. But their chloroplasts still hold traces of their ancient Japanese ancestors.  

Red bean paste is a common filling for East Asian pastries, such as this taiyaki from Japan (left) and these sesame balls from China (right). But where in Asia these beans were first cultivated had been a long-debated topic.

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Turning red 

Through farming, adzuki beans also got a makeover. Wild beans are pale with dark mottled spots. The farmed varieties are red all over.  

Lee’s team found one mutation in beans’ DNA that affects how they process pigment. It allows red pigments to spread across the coats of their seeds. The deletion of another gene, or chunk of DNA, gets rid of the mottled pattern that’s still seen in the wild. 

The researchers tracked how those two mutations emerged over time. They also looked at a third mutation seen in the farmed beans. It’s in a gene that reduces the odds that a bean pod will break open. For farmers who want to easily harvest whole beans, that’s a useful trait. But it’s not very helpful for wild plants, which rely on their pods bursting to spread seeds.  

All three mutations seen in farmed beans began to spread around 10,000 years ago. That was long before people started farming the plants in Japan. 

Since these traits are of little help in the wild, Lee says, their early spread may reflect human preferences. Red has long been considered lucky. What’s more, the Jomon people are known to have used red coloring in their pottery. 

The new findings bolster the idea that the Jomon people were more than foragers. They could have been shaping their perfect red bean, eventually domesticating it between 3,000 and 5,000 years ago. Fossils had already offered some evidence for that, Lee notes. Finally, he notes, there “is evidence from plant genetics, too.”