Soybean graphic structure pan-genome map

Genomics research ushers in a new breakthrough! Researchers from the Institute of Genetics and Developmental Biology in China have made significant progress in soybean genome research. For the first time in plants, the study has realized the construction of a graphical structure-based genome, breaking through the traditional form of linear genomic sourcing, and will lead the next generation of genomics research ideas and methods, which the reviewers call “the milestone work of genomics.” The findings were published online June 17 in the journal Cell, an international authoritative academic journal.

Soybean graphic structure pan-genome map

Genomics is the core and foundation of life science research. Traditional genomics studies store different bases on chromosomes in linear form and are based on a reference genome to obtain genetic information about a species. “Because of genetic variation between different individuals in a species, the linear genome does not reflect genetic variation in different individuals at the same time, which greatly limits the identification and analysis of genetic variations in different individuals. Tian Zhixi, author of the paper and a researcher at the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences, said that building a new type of pan-genome containing all genetic information from a species has become an important task and frontier challenge in genomics research.

Soybean domestication originated in China and spread widely around the world, providing the main plant oil and protein resources for human beings. Now, China is the main consumer and importing country of soybeans, soybean external dependence is high. Strengthening soybean research and increasing soybean production in China are very important to ensure national food security. High-quality reference genome is the basis of basic research and applied research on crop breeding.

“Our team found that there was a large genetic variation between different soybean seed resources, and that a single or minority genome did not represent all genetic variations in the soybean population, in a deep resequencing of soybean seed resources and in a population genetic analysis. Soybean basic research and molecular design breeding urgently need new genomic resources that represent different soybean seed materials. Tian Zhixi stressed.

At the same time, in the 1960s, the first “green revolution” characterized by the reduction of crop strains and semi-dwarf breeding doubled the world’s rice and wheat production, solving the problem of food and clothing. “However, over the past 60 years, there has been no significant breakthrough in average soybean yields relative to other staple crops, and there is an urgent need for a ‘green revolution’ in soybean production. Liang Chengzhi, co-author of the paper and a researcher at the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences, said.

To this end, the researchers conducted a deep resequencing and group structure analysis of 2,898 soybean seed materials from the world’s major soybean producing countries, and selected 26 of the most representative soybean seed materials, including 3 wild soybeans, 9 farm species and 14 modern cultivated varieties. Using the latest assembly strategy, the research team carried out high-quality genomic assembly and precise annotation of 26 soybean seed materials, conducted systematic genome comparisons, constructed high-quality graphical-based pan-genomes, and excavated large-scale fragment structural variations that could not be identified by traditional genomes. At the same time, the study also identified 15 structural variations that lead to fusion between different genes, which provides important clues for the study of the emergence of new genes.

Tian Zhixi said that the construction of high-quality graphical structure of the pan-genome, not only itself has important theoretical significance and application value, but also for the past has been carried out a large number of re-sequencing data provided a new analytical platform, will enable the data to achieve a “second life.” Soybean seed material selected in this pan-genome study is not only representative of genetic diversity, but also has important breeding and production value. The release of the pan-genome and related genetic variation of 2898 seed materials provides an extremely important resource and platform for soybean research, and will vigorously promote soybean molecular design and breeding, helping to realize the “green revolution” of soybeans.