Scientists construct high-quality rice pan-genome

  Science and Technology Daily (Reporter Ma Aiping) Recently, the Rice Molecular Design Technology and Application Innovation Team of the Institute of Crop Science, Chinese Academy of Agricultural Sciences, in cooperation with Shanghai Jiaotong University, based on 111 second- and third-generation whole genome sequencing data of representative rice resources, constructed a High-quality rice pan-genome, high-quality reference genomes of 9 representative populations of rice were obtained, including 5 rice genomes without deficiency.

The relevant data provides an important basis for in-depth mining of genomic variation and excellent genes, and the cultivation of new breakthrough rice varieties.

The relevant research results were published online in Genome Research.

  According to Wang Wensheng, a researcher at the Institute of Crop Science of the Chinese Academy of Agricultural Sciences, the team published a related paper in Nature in 2018, re-sequencing and big data analysis of 3,010 rice samples from 89 countries around the world. Rice represents 780,000 core accessions worldwide, thus constructing the first complete pan-genome of Asian cultivated rice.

However, the previous research was based on the second-generation sequencing technology for data construction. In comparison, the data constructed using the third-generation sequencing technology will be of higher quality.

  The pan-genome constructed in this study has added three-generation sequencing data on the original basis. Therefore, the constructed pan-genome is more accurate, continuous and complete, including 879Mb of non-redundant new sequences, involving 19,319 new protein-coding genes. (2132 new gene families).

Compared with next-generation sequencing data, third-generation sequencing data has a lower false-positive rate in detecting gene presence-deletion variants (PAVs), especially for genes containing repetitive sequences.

In addition, the study also detected 14,471 presence-deletion variants that were significantly associated with multiple agronomic traits, indicating that gene presence-deletion variants may have important contributions to rice phenotypic variation.

The high-quality rice genome, pan-genome, and gene presence-deletion variation resources obtained in this study are conducive to promoting the research of rice functional genome, and at the same time, it is helpful to deeply mine genome variation and excellent genes, and provide a breakthrough for the cultivation of new rice varieties. Important reference.

  The research was supported by the National Natural Science Foundation of China, the Hainan Yazhou Bay Seed Laboratory "Revealing the Leaders" project, the Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences, and the National High-level Talent Support Program.