3000 rice data mining

In the past two years, the China National Gene Bank has completed crop resequencing and project cooperation including the 3000 rice project, the thousand plant project, the ten thousand plant genome project, the Ruili Botanical Garden digital project, etc. The national gene bank has fully opened up the project data resources and researchers can use The analysis, mining and utilization of big data help the breeding work.

Cooperating with multiple institutions to carry out rice breeding work, including more than 3000 rice copies, representing 95% of the global rice genetic diversity. The project research paper was published in "Nature".

Led by the Institute of Crop Science of the Chinese Academy of Agricultural Sciences, 16 units including IRRI, Shanghai Jiaotong University, BGI, Shenzhen Agricultural Genomics Research Institute, Anhui Agricultural University and other 16 units have jointly completed the "3000 Asian Cultivated Rice Genome Studies", and completed the study on April 2018. Published on "Nature" in the month. The research conducted an in-depth discussion on the law of rice origin, classification and domestication, revealed the origin and population genomic variation structure of Asian cultivated rice, and analyzed the genomic genetic diversity of rice core germplasm resources.

3000 rice (from 89 countries and regions in the world) represents the core collection of about 95% diversity of 780,000 rice germplasms in the world. Through the re-sequencing of the whole gene, the average sequencing depth of each sample was 14X, and a total of 32M high-quality SNPs and InDels were detected using the resequencing data. The structure and differentiation of Asian cultivated rice populations are described and divided more carefully and accurately, from the traditional 5 populations to 9 populations. The study focused on the analysis of 453 SVs with a sequencing depth of >20X. The evolutionary tree constructed using SVs is similar to the evolutionary tree constructed by SNP. A large number of SVs may be the genetic basis of different degrees of hybrid sterility and the decline of XI and GJ hybrids. At the same time, the pan-genome of Asian cultivated rice was constructed, including 12,770 (62.1%) core gene families and 9,050 (37.9%) distributed gene families. Found 12,000 full-length new genes and thousands of incomplete new genes. The core genes are relatively old, and most of the new genes are younger and shorter in length.

[1]: Wang, W., Mauleon, R., Hu, Z. et al. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature 557, 43–49 (2018). https://doi.org/10.1038/s41586-018-0063-9