The construction of high-quality rice pan-genome was successful

Pan-genomic characteristics of rice in 111 parts of rice germplasm. Courtesy of the Chinese Academy of Agricultural Sciences

Recently, the Rice Molecular Design Technology and Application Innovation Team of the Institute of Crop Sciences of the Chinese Academy of Agricultural Sciences cooperated with Shanghai Jiao Tong University to construct a high-quality rice pan-genome based on the second- and third-generation whole genome sequencing data of 111 representative rice resources, and obtained high-quality reference genomes of 9 representative rice populations, including 5 defect-free rice genomes. The relevant data provides an important basis for in-depth exploration of genomic variations and excellent genes to cultivate breakthrough new rice varieties. The results are published online in Genome Research.

According to Wang Wensheng, a researcher at the Institute of Crop Sciences of the Chinese Academy of Agricultural Sciences, the team published a paper in Nature in 2018 to resequenc and big data analyze 3,010 rice from 89 countries around the world, which represented about 95% of the genetic diversity of the 780,000 core germplasm in the world, constructing the first complete Asian cultivated rice pan-genome. However, previous research was based on second-generation sequencing data, and the quality of data built using third-generation sequencing technology is higher.

The pan-genome constructed in this study adds three generations of sequencing data on the basis of the original, so the pan-genome constructed is more accurate, more continuous, and more complete, containing a non-redundant new sequence of 879 Mb, involving 19319 new protein-coding genes (2132 new gene families).

Compared to second-generation sequencing data, third-generation sequencing data have lower false-positive rates when detecting gene presence-deletion variants (PAV), especially for genes containing duplicate sequences. In addition, 14471 presence-deletion variants were detected to be significantly associated with multiple agronomic traits, suggesting that the gene presence-deletion variant may have made an important contribution to rice phenotypic variation.

The high-quality rice genome, pan-genome and gene presence-deletion variation obtained in this study are conducive to promoting the research of rice functional genome, and at the same time help to dig deep into genomic variations and excellent genes, providing an important basis for cultivating breakthrough new rice varieties.

The research has been supported by the National Natural Science Foundation of China, the Hainan Yazhou Bay Seed Laboratory Unveiling Project, the Chinese Academy of Agricultural Sciences Science and Technology Innovation Project and the National High-level Talent Support Program. (Source: China Science Daily Li Chen)

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