Ripe millet. Photo courtesy of the millet variety exhibition base in Lvdian, Yichuan, Henan
What was the staple food eaten by the ancestors of Mentougou in Beijing more than 10 thousand years ago? What did Qinghai people use to make noodles more than 4000 years ago? 6,000 years ago, the population of the Central Plains increased greatly for the first time because of what crops?
Archaeology has proved that the answer is millet, which is commonly known as millet.
Recently, Nature-Genetics published online the first high-quality pan-genome map of millet completed by Diao Xianmin, a researcher at the Institute of Crop Science of Chinese Academy of Agricultural Sciences. This study not only proved that China is the only origin of millet from the genome level, but also created a precise and efficient breeding method of millet genome, which laid a theoretical foundation and provided a technical path for cultivating breakthrough varieties.
Li Jiayang, a researcher at the Institute of Genetics and Developmental Biology of Chinese Academy of Sciences and an academician of China Academy of Sciences, pointed out that this is the first high-quality map pan-genome in the field of coarse cereals, which is of special importance for future breeding applications. This achievement is not only another milestone in millet research, but also the best interpretation of "small crops, great achievements" and will bring important impetus to other crop research.
Identity change of millet
Millet belongs to the genus Setaria in Gramineae, which is the oldest domesticated crop in the world and the main crop formed in Asian/Chinese farming civilization.
The earliest millet found in archaeology appeared in the site of Donghulin in Mentougou District, Beijing, 11,500 years ago. There is no millet in Europe earlier than 3500 years ago.
Diao Xianmin, the correspondent of the paper, told China Science Journal that millet had long occupied the position of staple food in farming culture before the arrival of agricultural production system with high input (water conservancy, fertilizer and pesticide).
From Xia and Shang Dynasties to Wei, Jin, Southern and Northern Dynasties, millet has always occupied a primary position in grain. Especially in the Wei, Jin, Southern and Northern Dynasties, millet in the south developed unprecedentedly and reached the peak of historical prosperity. During the Sui and Tang Dynasties, millet entered the first recession, and the status of rice and wheat rose, replacing the traditional status of millet, forming a pattern of southern rice and northern wheat, but millet was still the core crop at that time.
Since modern times, with the breakthrough of green revolution of wheat, rice and other crops, the advantage of millet as a staple food has been gradually weakened. "In fact, it is only nearly 40 years since millet changed from a big crop to a small crop." Diao Xianmin said that Heilongjiang was the largest millet planting province in China in the early days of the founding of New China. In 1978, the millet planting area in Heilongjiang Province reached 20 million mu, but now the total millet planting area in China is only 20 million mu.
However, millet, the kernel of millet, has high nutritional value, which makes it a popular miscellaneous grain.
In recent years, with the increasingly obvious problems of climate change, agricultural sustainability and food security, scientists have placed new hopes on millet with the characteristics of drought tolerance, barren tolerance, strong environmental adaptability, easy transformation and easy laboratory operation.
Diao Xianmin has been engaged in millet research since 1987, and has collected more than 1,500 materials of Setaria from more than 20 species. "China’s millet farm varieties and bred varieties are the most abundant in the world. There are about 27,000 farm varieties, and the breeding level is the most advanced in the world. "
Diao Xianmin said that in order to make better use of these materials, it is necessary to accurately identify the genotype and phenotype of millet. "Now, compared with other big crops, the yield level of millet is still very low. The yield per mu of millet is generally 250 kg ~300 kg without watering and fertilization; Typical high-yield fields have water and fertilizer, with a maximum yield of 700 kg. This is mainly because we have no clear understanding of the population structure, evolutionary relationship and history of wild species, farm species and bred species of millet. "
These problems include that the level of genomic variation of millet is not very clear, especially there is no information on structural variation; The information of resource phenotype identification record is incomplete; It is not clear which genes, segments and loci have been selected during the domestication and breeding of millet. "This requires us to study more deeply."
Draw the first miscellaneous grains "heavenly book"
"The research published now is actually a part of the above-mentioned big project and a by-product. It is not decided to do it in a short time, but with the deepening of research and technological progress, it has been integrated with breeding and production needs and accumulated for a long time. Research results." As the chief scientist of the national millet sorghum industrial technology system, Diao Xianmin hopes to thoroughly understand the millet crop, and cultivate better varieties on this basis, so that millet can play its due role in the grain system.
Because of this, millet has become the first crop with map-pan genome in miscellaneous grains.
The so-called pan-genome refers to all the genetic information of a species, while the graph genome contains all the structural variations in the genome of a species. In other words, the map-pan-genome is the clearest, most detailed and comprehensive genome information of a species that can be drawn by using the current science and technology, which is equivalent to the "heavenly book" of the species genome.
Diao Xianmin’s team analyzed 1,844 core germplasm resources such as wild millet, farmed millet and modern bred millet, assembled 110 high-quality genomes of millet and Setaria from scratch, drew the first genome variation map of Setaria, recognized the basic situation of millet resource variation, and systematically analyzed the genome variation during the domestication and improvement of millet.
He Qiang, the co-first author of the paper and a postdoctoral fellow at the Institute of Crop Science, Chinese Academy of Agricultural Sciences, introduced that the species of Setaria could be clearly clustered by using high-magnification sequencing of 1844 core germplasm-foxtail millet and Setaria viridis. Among them, Setaria viridis is divided into 4 subgroups. Before Setaria viridis was domesticated into millet, there was an older subgroup C3, which was more geographically distributed and had stronger environmental suitability, which was of great significance for improving the environmental suitability of millet in the future.
Liu Xu, a researcher at the Institute of Crop Science of the Chinese Academy of Agricultural Sciences and an academician of the China Academy of Engineering, said that this confirmed the theory of the single origin center of millet, namely the origin center of China, and was a typical representative of resource research using new technologies.
Not only that, they also studied how millet was domesticated and improved. He Qiang introduced that they identified a total of 4582 structural variations related to millet domestication, 152 structural variations related to millet breeding improvement, and identified 680 structural variation-related genes that were continuously selected in domestication improvement, which were mainly enriched in metabolic pathways such as reproduction, photoperiod, pigment and nitrogen utilization.
2023 is the International Year of Millet. The Food and Agriculture Organization of the United Nations believes that millet deserves attention and has a place in people’s dietary structure, because millet can grow in harsh climatic conditions, which can help solve the problem of food shortage. Contribute to a healthy diet; Climate resilience; There is much to be done in improving the livelihood of small farmers; Xiaomi trade can enhance the diversity of the global food system; There are many innovative uses in the fields of treatment and pharmacy.
Diao Xianmin believes that publishing the map of millet pan-genome is the best support of China scientists for the International Year of Millet.
Establish a breeding database
It is already a huge task just to map the pan-genome. However, the team of Diao Xianmin did not stop there.
"What is different from other work is that we have done a lot of phenotypic identification." Diao Xianmin said that they relied on 17 units to investigate the basic agronomic traits of 680 materials and 22 environments in 13 places across the country for 10 years, which is the real multi-year and multi-point experimental data.
"We not only investigated the common traits such as plant height, panicle length, tiller number and grain weight per panicle, but also studied the drought resistance, grain dropping, beige color and grain quality traits in germination stage, seedling stage and whole life cycle, and formed 68 traits and 226 groups of phenotypic data, which is actually a phenotypic group." Diao Xianmin said that they focused on more practical character identification related to breeding. For example, they made a three-year drought-resistance survey in Xinjiang, a three-year drought-resistance survey in Shanxi, and a drought-resistance survey in Hengshui, Hebei.
More importantly, they also docked the two big data, the map pan-genome and the phenotype group, and discovered a total of 1084 phenotypic-related loci, of which structural variation accounted for 5.8%.
Tang Sha, the co-first author of the paper and an associate researcher at the Institute of Crop Science, Chinese Academy of Agricultural Sciences, told reporters that structural variation in the genome could not be seen before the genome was mapped. However, some important agronomic characters of millet, such as starch, flowering period and ear weight, are determined by structural variation genes.
"With these genes and their information, we can build a molecular breeding module. This information provides a method for genotype and phenotype mutual estimation and phenotype estimation by genotype, which is genome-wide selection breeding. " Diao Xianmin said that this is a database from which you can know what is the optimal gene for a certain trait. With this family background, good genes can be gathered together in breeding in the future, providing molecular and phenotypic basis for future breeding.
"This makes us more clearly see the importance of genome structural variation in discovering gene functions." Qian Qian, a researcher at the Institute of Crop Science of the Chinese Academy of Agricultural Sciences and an academician of the China Academy of Sciences, said.
Han Bin, director of the Center for Excellence and Innovation in Molecular Plant Science of China Academy of Sciences and academician of China Academy of Sciences, said: "The phenotypic prediction accuracy of whole genome selection in this study is over 90%, which shows us the application potential of whole genome selection in millet breeding. I think this research is not only a classic work of’ pan-genome-quantitative inheritance-breeding’ in millet but also in crop field, which has important guiding significance for future crop genetic improvement. "
Related paper information:https://doi.org/10.1038/s41588-023-01423-w
