Super pan genome helps mining and utilization of genetic variation in Rice Germplasm Resources
By: Date: 2022-07-22 Categories: foodtechnology Tags: ,
Recently, the Shenzhen Institute of agricultural genomics, Chinese Academy of Agricultural Sciences, in cooperation with many domestic universities and scientific research institutions, assembled 251 high-quality rice genomes, and constructed the super pan genome with the largest population size, fully annotated genome and the most systematic genome in rice. The completion of this map will greatly promote the mining of rice functional genes and the utilization of rice germplasm resources. Relevant achievements were published in cell research.
 
Through geographical distribution sources, genotypes and phenotypic variations, 202 highly representative core germplasm materials of Asian cultivated rice, 28 common wild rice, 11 African cultivated rice and 10 short tongue wild rice were carefully selected for sequencing and assembly. In order to accurately compare the genetic variation of alleles in different rice materials, researchers also used high-quality population genomes to construct a pan genome map based on genome sequence alignment, and performed gene annotation and sequence integration for each variation site. This map contains the most comprehensive multiple allelic information of rice gene sequence at present, and provides an important basis for the study of rice comparative genomics and evolutionary genomics.
 
In order to make efficient and convenient use of these massive genomic data, researchers also built a database ricsuperspirdb( http://www.ricesuperpir.com/)。 Through data retrieval, we can efficiently obtain the genome sequence and genome annotation of a specific rice variety. We can also select any sample genome as the reference genome to view the whole genome comparison results and genome variation with all materials. The database has important scientific significance and practical value for the study of rice gene function and the utilization of germplasm resources.
 
The research was supported by the National Natural Science Foundation of China and the national key research and development program.
 
Original link:https://www.nature.com/articles/s41422-022-00685-z