Through 10,000 years of domestication: the flavor code of grape wine

“Grape wine luminous cup, want to drink pipa immediately urge.” Wang Han’s “Liangzhou Words” shows that grapes were already the main raw material for winemaking in the Tang Dynasty.

Why have people been so obsessed with wine for thousands of years? What exactly determines the flavor factors of a wine?


At the Shenzhen Institute of Agricultural Genomics of the Chinese Academy of Agricultural Sciences (hereinafter referred to as the Institute of Genomics), there is such a group of scientists, who are not satisfied with shallow “taste” and stop, so they follow the footprints of “delicious”, trace the domestication history of grapes for more than 10,000 years, and explore the flavor code hidden in the years.

On June 6, Beijing time, the Proceedings of the National Academy of Sciences (PNAS) published online the latest research results of Zhou Yongfeng, a researcher at the Institute of Genomics, in the field of grape population genetics and breeding. This study is the first to use machine learning and multiple genetic methods to reveal the formation mechanism of grape flavor, analyze the impact of domestication on the grape genome, and further clarify the history of grape domestication. This research helps the utilization of grape wild resources and provides theoretical support for the next step of grape cultivation.

Wine grape flavor: thanks to wild grapes

Grapes originated in West Asia and soon spread all over the world. During the Western Han Dynasty in China, there was a record of Zhang Qian sending an envoy to the Western Regions to bring back grapes.

“For every thousand grapes there are a thousand flavors”, the key factor that determines flavor – the grape variety. Zhou Yongfeng, co-corresponding author of the paper, told China Science News that at present, the mainstream grape varieties whether fresh food or wine are mostly foreign selected varieties, and China’s wine market, especially the high-end wine market, has long been occupied by Western imported wines.


Why are wine grape varieties originating in Europe more popular?

“We found that this is closely related to genetic infiltration from wild grapes in Europe.” Zhou explained that gene introgression is the flow of alleles from one species or population to another.

They analyzed more than 300 resequencing data, including major cultivars and wild grapes, and conducted accurate and detailed studies of the history of differentiation, involution intensity and timing between populations.

Their use of ancestral simulation not only reconfirmed the history of grape domestication for more than 10,000 years, but also further refined the history of domestication and differentiation between wild grapes and fresh food and wine grapes in Europe and the Near East. It was found that in the past 2,000 years or so, cultivated grapes, especially wine grapes, had a continuous genetic exchange, that is, a hybrid process, with European wild grapes.

Based on the population genetic analysis of machine learning, the study found that 1.82% of the entire wine grape genome came from the progressive infiltration of European wild grapes, and these regions were enriched with multiple metabolic pathway genes, indicating that European wild grapes had an important impact on the aroma and other traits of wine grapes.

Present wine used to be drunk by the ancients

Contemporary cultivation of grapes is mainly propagated by clonal propagation. Previous studies have found that some modern grape varieties are clones of European medieval varieties. In other words, some of the surviving viticultural varieties may retain their appearance in ancient times, in the sense that we taste the same wine as the ancients.

Xiao Hua, co-first author of the paper and a postdoctoral fellow at the Institute of Genomics, told China Science News that even if they are cloned individuals, their genetic sequences are not static. In continuous clonal reproduction, variations accumulate in the genome in the form of heterozygotes, affecting grape breeding. During the cultivation of live seedlings, the researchers found that offspring grown from grape seeds were difficult to survive, in part because of the sequelae caused by clonal reproduction.

Forward simulations have found that within 100 generations, clonal populations can more quickly select favorable variants and eliminate harmful variations, but most of the remaining variants are present in the genome in the form of heterozygotes. Hybrid populations take longer, such as more than 500 generations, to reach a new equilibrium, but for infiltrated peripheral alleles, hybrid populations have greater selection efficiency and can remove more harmful variations. The study revealed the patterns of change hidden by genetic variants behind different ways of reproduction.

Cultivate high-quality grape varieties

Zhou Yongfeng said that at present, crop breeding technology has developed to the whole genome design breeding stage, that is, selective rapid aggregation of beneficial variants and removal of harmful mutations in the breeding process, so as to achieve the purpose of rapid and efficient breeding. However, the application of modern breeding technology in the process of grape breeding is very limited, and grape breeding is still in the 2.0 stage for the time being, that is, hybrid breeding, mainly because the breeding system is backward and still relies on large-scale and long-term cross-screening breeding. Most of the table grape varieties widely planted in China come from Japan, while wine grapes come from Europe and the United States, and the problem of seed industry stuck neck is particularly prominent.


However, China has rich wild grape resources, and there are nearly 40 species in China among more than 70 species of grapes. “How to make full use of the rich genetic resources of these wild grapes, accelerate the implementation of modern breeding technology and cultivate new excellent grape varieties are the most important grape breeding goals and strategies at this stage.” Zhou Yongfeng said.

Due to the high added value of wine, grapes are one of the crops with the highest economic value. However, at present, China’s high-end wines are heavily dependent on imports. Zhou Yongfeng believes that cultivating new varieties of wine grapes with China’s own intellectual property rights through seed industry innovation is the only way for China to change from a wine importer to an exporter.

The reviewers of the paper believe that the study is very interesting, and it publishes important results on the origin, timing and infiltration of grapes. The adaptation and maladaptive interactions caused by infiltration are not only relevant to grapes, but also to many other plants and animals, and can be further applied in grape biology research and genomic design breeding.

The research was supported by the National Foundation of China Overseas Outstanding Youth Fund, the US National Science Foundation, and the Agricultural Science and Technology Innovation Stability Support Fund. (Source: China Science News, Li Chen, Ma Xinyi)

Related paper information:

(Photo courtesy of the Institute of Genomics, Chinese Academy of Agricultural Sciences)

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