◎Writing丨Science and Technology Daily reporter Zhao Hanbin
◎ Planning丨 Zhao Yingshu, Teng Jipu, Lin Lijun
As one of the world's four major fruits and one of the world's largest cash crops with the largest combined production value, grapes have important economic, social and cultural value. But where did table grapes and wine grapes originate? How long did it take to be domesticated artificially ... These questions have always plagued the scientific community.
Recently, young Chinese scientist Dong Yang and 79 scientists from 17 countries along the "Belt and Road" mentioned the history of grape cultivation to 11,000 years ago, solved the academic controversy over the origin of grapes for more than 100 years, constructed a high-precision kinship genealogy map covering almost all cultivated grape genetic resources, and provided a new technical path for grape directional breeding and design breeding.
Looking back at the road of scientific research, with fruitful results, the reporter followed scientists along the "Belt and Road" to a whirlwind journey through 10,000 years.
1
Darwin made a start, but did not give a conclusion
Over the past 15,000 years, humans have domesticated more than 300 species of animals and plants. Through the floods, the transition from a hunter-gatherer society to an agrarian society.
The introduction and domestication of plants refers to artificial selection and cultivation to adapt wild or exotic plants to the local natural environment and be used by people, and its essence is to retain or discard the different traits and phenotypes caused by changes in genetic diversity in layers of selection and improvement, forming varieties and strains of agricultural crops.
There are about 60 fertile wild species of the grape, about 28 in North America and about 30 in East Asia, and they prefer to grow on temperate slopes, ravines, shrublands and mixed coniferous forest margins between 200 and 1,500 meters above sea level.
Because they have not been domesticated by artificial introduction, wild grapes have small grains, low yields, and sour taste, and they are often dioecious, which means that only half of the grapes in nature can bear fruit. "The ancients selected mutated hermaphrodites and domesticated them artificially, preserving and spreading them." Dong Yang, a professor at Yunnan Agricultural University, said that the yield of cultivated grapes is much higher than that of wild grapes, and the form, color and aroma are also diversified.
With the progress of human civilization, as a fruit and wine raw material, grapes have gradually been distributed and varied, and there are currently about 11,000 varieties registered in the world.
In the first chapter of On the Origin of Species, Darwin describes a very interesting phenomenon: domestic animals and domestic plants are very different from their wild ancestors. Years later, he wrote "Mutation of Animals and Plants under Domestic Domestication," a detailed account of domesticated animals and plants. But when and where domestication of animals and plants was carried out, Darwin started without giving a conclusion, leaving a century-old puzzle, of which grapes were one.
Under natural conditions, it takes hundreds of thousands of years to form a new species, and in the artificial domestication environment, it only takes thousands of years to form a relatively independent species, and the morphology and characteristics of many domestic species are very different from their wild ancestors, forming reproductive isolation and meeting the standards of new species. Artificial domestication is very different from natural selection, and many species characteristics meet the needs of artificial domestication, but it is not conducive to natural reproduction in nature, but it is conducive to artificial breeding.
Internationally, viticulture is an independent discipline parallel to horticulture, which shows people's preference and dependence on grapes.
Most grapeology textbooks agree that cultivated grapes originated about 8,000 years ago; At the same time, there has been controversy about the origin of grapes, with different answers in different textbooks, but most believe that grapes originated near the Mediterranean Sea and are of a single regional origin, and table grapes and wine grapes may also have originated in order.
"In response to many questions, in 2017, we carried out the first phase of exploratory research, collecting 472 grape genetic resources for genomic analysis across the country and in Asia." At that time, Dong Yang said, they only tried to explore whether the genomic approach could be applied to the analysis of genetic resources in grapes.
"At that time, we suggested that modern grapes may have originated in the Black Sea region, exactly where it is not clear, and the origin was about 7460 years ago." Sheng Jun, former president and professor of Yunnan Agricultural University, told Science and Technology Daily that the result was very controversial after it was proposed. In order to carry out in-depth scientific research and improve the theory, the research team of the Key Laboratory of Biological Big Data of Yunnan Agricultural University soon launched another study.
2
Join hands with scientists from 17 countries to reveal the genetic code of grapes
Previously, our lack of large-scale genomic genetic variation data made it impossible to resolve the history of grape domestication and spread, which also seriously hindered the trait improvement of grapes.
In a 2017 study, Dong Yang and others were surprised to find that among all grape varieties in the world, Chinese grapes can be described as "maverick".
"Our grapes more or less have the genetic shadow of the 'Jingxiu' variety, which on the one hand shows that 'Jingxiu' is very important for grape breeding; at the same time, it also tells us that the genetic circle of Chinese grapes is very narrow, resulting in the Korean grape resources affected by it are also very narrow." Dong Yang said that Japan also first introduced some varieties from China, and later used some varieties in Europe and the United States as breeding materials to cultivate summer black grapes that are disease-resistant, abundant and shelf-stable, as well as varieties of sunshine rose grapes with crispy flesh and juicy, rose fragrance, non-cracked fruit, and non-threshing.
Jinsha River hot and dry valley grape planting demonstration site.
"If we understand the origin, domestication and migration of grapes, we can target their varieties." Dong Yang explained that as with many fruit tree breeding, early people used natural mutations – that is, bud changes and cuttings to breed grapes.
To solve this set of problems, it is necessary to start on a global scale in order to obtain valuable results, which means to collect as many samples of cultivated grapes as possible around the world. This would have been almost impossible just a few years ago.
Dong Yang, known as "alien" by colleagues and peers, is young, active, energetic and has extraordinary organizational skills. He immediately sent a whirlwind of invitations to colleagues around the world through the Internet, asking them to collect sample data and existing information to China, and quickly received responses from scientists from 17 countries.
"Fortunately, the collaboration began in early 2019 and 5,000 samples and data were collected by the end of that year." Sheng Jun said.
Some of these samples are from Chile, Australia and other countries in the southern hemisphere, some from the United States, Britain, Germany, France, Japan and other countries, and more are the collaboration of scientists from countries along the "Belt and Road". Connecting their countries on the map closely matches the ancient overland "Silk Road" route.
Participating countries and main sample collection sites.
The 5,000 samples, not all of which were independent varieties, but about 800 of them were of close genetic background and were defined as clones, which had to be sequenced and filtered, which required great patience and extensive knowledge in the disciplines. "After careful combing and investigation, we eliminated some samples with duplicate names and wrong names, and then sequenced and compared, and the kinship between them could be clearly and accurately revealed. This is the biggest difficulty in research. Dong Yang said.
"The advancement of the grape project relies heavily on international cooperation. In this collaboration, we adopt a very strict method of sample delivery and sign Material Transfer License Agreements (MTAs) with each partner. Chen Wei, an associate professor at Yunnan Agricultural University, said that in this way, it can be clarified that the ownership and source of the sample are clearly traceable; There is also a mechanism in place for the sharing of research results: after each unit provides samples, it has priority access to the data generated by it and can analyze them independently.
"In the collaboration, sample mail delivery has a particularly strong impact." Dong Yang said that due to the impact of the new crown epidemic, many collaborators can only stay at home to work, but the materials are in offices and laboratories. Even email communication and confirmation can be tedious.
An Australian collaborator, who asked not to be named, is in his seventies and lives a hermit life, living alone on a mountain farm. "Every time I look for him, I have to contact his family. His family drove for a long time and then told him about our needs. When he gets to town and finds his computer, he can answer our emails. But overall, the communication was very good. Dong Yang said.
Three collaborators from Georgia provided very important samples of wild grapes. One of them was not proficient in English. "On every exchange, we asked his colleagues to contact him, and although he was late in answering emails, he was very supportive of our work and gave us a lot of guidance, sometimes in English mixed with Georgian language, or with the help of translation software." Dong Yang said.
All this has been difficult to advance during the new crown epidemic. In the past three years, the world has changed, data and results have been continuously produced, and two of the scientists involved have unfortunately passed away.
Speaking of this, Dong Yang's lenses have become a layer of mist.
3
The earliest domesticated fruit appeared on the cover of Science
On March 3, 2023, the collaboration of 79 scientists finally came to fruition and appeared on the cover of Science.
The two most striking words are "domestication" and "grapes", and the text is titled "Double domestication in grape evolution and the origin of its traits". At the same time, the journal also distributed a number of praiseworthy comments. The study's creators will also be invited to the 2023 Science Annual Meeting.
The research results appear on the cover of Science.
"This is a major achievement in the research of grape biological resources led by young scientists in the mainland, using ultra-large-scale genomic data and complex data analysis methods, and uniting global scientists. It is not only the pride of China's young scientists who are committed to national scientific and technological self-reliance, but also a model of cooperation between Chinese science and technology and the world's scientific and technological innovation. Wang Xueqin, secretary of the party group and director of the Yunnan Provincial Department of Science and Technology, said that at the same time, it also reminds us that in order to solve the problem of common development, human beings need international cooperation and open sharing more than ever.
In the era of molecular biology, the taxonomic community judges the association and evolutionary history of species, no longer based solely on appearance, but according to the similarity of the genome - similar are one source, and then through the DNA sequence variation law to calculate the "molecular clock", which can accurately reflect the time of species differentiation.
Through complex sequencing analysis, Dong Yang and his team found that 11,000 years ago, due to climate change, wild grapes naturally differentiated into two groups, East and West, and the ancients domesticated and improved grape varieties almost simultaneously on the eastern coast of the Near East Mediterranean Sea and the South Caucasus, 1,000 kilometers apart. With migration and trade, grapes were also spread throughout the world.
About 11,000 years ago, two separate artificial domestication events began, forming a dual-origin pattern.
"Domestication comes with a strong sense of purpose. With continuous selection, wild and cultivars were completely separated, resulting in today's grape varietal pattern. Chen Wei said that the earliest domesticated crop by humans was wheat, about 15,000 years ago. But what the first domesticated fruit was is not clear before. New research proves that grapes are the first domesticated fruits of humans.
In the study, the data generated exceeded 40TB, and the storage space and computing power required were also a big problem, and the impact of the new crown epidemic was even more prominent at this time. Based on the previous work, the young team tried their best to innovate algorithms, adjust control parameters, creatively formed a set of computing and data analysis methods, and successfully built the world's largest database of grape genetic resources.
"It seems that all possible problems have been encountered, but they have all been solved, and this is the charm of scientific research - constantly have problems, keep solving problems, and life is like this." Dong Yang had a "past a thousand sails" demeanor.
In solving doubts, they also put forward many new ideas. Previously, most vitiological views believed that European wine grapes originated from local wild species, and the newly constructed high-quality reference genome proved that this was not the case. This changes the basic message of viticulture: the question of origin is central, and the mode of domestication is key to understanding the formation of grape genetic resources. The clear articulation of all doubts is epoch-making.
"This article can be on the cover of Science because of the scientific method and detailed data." Dong Yang said.
"This is an era of big science and big cooperation. It was put on the cover because it was a big project of international cooperation that solved problems that the whole world wanted to know. Sheng Jun said.
Some commentators pointed out that the newly proposed "dual center of origin of grapes" model corrects the previous theory of single origin center in the scientific community, proves that wine grapes and table grapes originated at the same time in different regions, and the genetic background at the beginning of origin was significantly different, forming a consistent view of grape origin and migration, and rewriting the textbook of grape research.
The commentary published by Science argues that the domestication of plants, which underpinned the rise of human civilization, is increasingly recognized as a complex interaction in the cultural landscape. By reporting on grape domestication, Dong Yang and others revealed more complexities in food sources.
4
Precisely designed and targeted selection produces original high-quality grapes
Zhang Qian, who was claimed by Sima Qian to have the merit of "gouging out" the Western Regions. In the second year of the founding of the Western Han Dynasty (139 BC), on the order of Emperor Wudi of the Han Dynasty, Zhang Qian led a team to open up the north-south road from the Han Dynasty to the Western Regions, and opened up land transportation between China and Central Asia, West Asia, South Asia and even Europe, becoming the representative of the pioneers of the Silk Road.
"Our data also show that 2,500 years ago, grapes entered mainland Xinjiang from West Asia and then spread inland along trade routes." Dong Yang introduced that in Xi'an, the unearthed grape seeds and wine, as well as some remains of the winery, can fully prove the history of the spread of grapes, and the introduction time is about 330 years earlier than the Zhang Qian period.
"We also found some special traits that are very important in grapes, such as genes that map the special aromatic traits of rare ancient varieties of muscadine grapes. This gene is extremely rare in existing grape varieties. Dong Yang said.
"In the future, we can apply this gene to make crystal grapes have a musky type, and the farmers' income will definitely be very good!" Dr. Zhu Yifan, who has traveled to Europe for many years and now joins Yunnan Agricultural University's grape project seed development research, said.
The grape research team of Yunnan Agricultural University used tomatoes as a model to achieve efficient gene editing of grapes. The picture shows the tomato model experiment.
More than 11,000 varieties, different fruit types, color, sweetness, aroma type, dazzling. "Previously, we conducted 29 phenotypic traits of grapes for three consecutive years, and through genomic association analysis, we discovered a large number of genes related to agricultural traits and analyzed their functions, which can provide a vital tool for precision grape breeding in the future." Zhu Yifan said.
At present, the research team has brought together more than 1,000 grape varieties and more than 170 grape phenotypic traits, including fruit shape, aroma, secondary metabolites, and even some traits in root details, and systematically explored the genes associated with them.
Zhu Yifan et al. also paid great attention to different domestication branches, especially the different genes of wine grapes and table grapes in different domestication branches. "In the future, we may be able to devise some methods of grape breeding on the computer, telling the breeder what variety to use to cross with what variety, and what kind of genetic background and genotype offspring to select, so that the variety selection can be carried out accurately and quickly."
Zhu Yifan revealed that at present, some relevant work has been carried out in full swing. Through precise design and directional cross-breeding, China can also produce original high-quality grapes in the future.
Researchers from the grape research team at Yunnan Agricultural University are selecting wine grape samples.
On the eve of press time, Zhu Yifan and they found a key gene to control the early ripening of grapes. "Introducing these genes into crystal grapes can make it more beautiful in color, taste, and maybe let people eat freshly picked grapes during the Spring Festival!" More importantly, Sheng Jun said, this series of research will also provide reference for the development of apples, citrus, bananas, and other types of crops, which are called the "four major fruits" along with grapes.
Further reading
Make good use of genomic tools to produce more original results
"At present, 70% of table grape varieties in mainland China rely on imports, and there are no high-end varieties with independent intellectual property rights; Almost all wine grapes in the country are imported varieties. Sheng Jun, former president and professor of Yunnan Agricultural University, who has long been engaged in food science research, told reporters that this requires researchers to write papers on the ground and firmly hold the safety of the seed industry, including fruits, in the palm of their hands.
In recent years, global fruit production has shown a rapid development trend. Relevant data show that China, India and Brazil are among the top three in fruit production and planting area. Among them, in 2022, the mainland grape planting area will be 510.8945 million mu, and the output will be 14.3143 million tons.
Under the leadership of Sheng Jun, Yunnan Provincial Key Laboratory of Biological Big Data was established. "Gene sequencing is a tool. But the in-depth application of this tool will reveal many secrets for us, find a lot of scientific research clues and future applications. Sheng Jun said.
Due to its unique vertical climatic zone and rich hot and dry river valleys, Yunnan has unique advantages in both fresh food and wine grapes, and has become an important production area and a high-quality cultivation area in the mainland. At present, the grape planting area in Yunnan Province is about 600,000 mu, and the highest output is 1.6 million tons.
"If we cultivate less varieties independently, the market will not be large." Zhu Youyong, academician of the Chinese Academy of Engineering and honorary president of Yunnan Agricultural University, said that the publication of the results of the origin of grape domestication and the construction of high-precision pedigree maps have provided strong support for solving the problems and pain points of grape breeding.
"But publishing results is only the first step in innovation in the seed industry." This "model of the times" urged the young team to base themselves on genome research, innovate and tackle key problems, carry out directional breeding as soon as possible, strengthen agricultural chips, and provide better varieties for the development of characteristic industries, especially the table grape industry.
"We will further give full play to the advantages of disciplines and social services, fully support Professor Dong Yang's team to transform scientific research results into first-line application technology, promote the upgrading of the grape industry, and better serve regional development." Li Yonghe, president of Yunnan Agricultural University, said. To this end, Yunnan Agricultural University awarded a scientific research award fund of 10 million yuan to the teams of Dong Yang and Zhu Yifan.
Dong Yang revealed to reporters that the grape business is still continuing, using genomic tools, and new results will be born this year. The team's focus has shifted to global models of domestication of domestic chickens, cherry and cherry blossom origins, domestication of medicinal plants, and high-quality genomic studies of tea.
Identifying genes related to egg production traits in domestic chickens can significantly increase egg production; Genome analysis of cherry blossoms and cherries preliminarily determined that they originated in the Greater Shangri-La region; Screening and controlling tea plant height dwarf genes can not only reveal the history of the evolution of large-leaf tea to small-leaf tea, but also optimize the planting mode of tea gardens. Introducing artificial domestication and genomics ideas into the cultivation of Chinese herbal medicine can cultivate more medicinal plants with stable efficacy for the country... The grape team of Yunnan Agricultural University is working hard to make the goal of more blossoming and fruiting just around the corner.
Source: Science and Technology Daily