Rice Super-Population Variation Map

Detailed knowledge of the genetic variations in diverse crop populations forms the basis for genetic crop improvement and gene functional studies. In the present study, we analyzed a super-large-scale rice population (10,548 samples) to construct a rice super-population variation map (RSPVM). This map consisted of 54,378,986 single nucleotide polymorphisms (SNPs) and 11,119,947 insertion/deletion mutations (InDels) derived from 10,548 cultivated and wild accessions of rice. 356 Asian cultivated rice long sequencing reads data were collected and structural variants were identified. And based on this, a graph pangenome was constructed, and then 184,736 presence/absence variations (PAVs) were identified in 10,548 accessions.

Here, the user can query and download the following information:

1.Material information (356 accessions dataset or 10,548 accessions)
2.SNP and InDel
3.Structure variation (356 accessions or 10,548 accessions)
4.Population variant frequency
5.Download rare variation

If you encounter any problems during use, please contact us: shanglianguang@163.com.


Wang T., He W., Li X., Zhang C., He H., Yuan Q., Zhang B., Zhang H., Leng Y., Wei H., Xu Q., Shi C., Liu X., Guo M., Wang X., Chen W., Zhang Z., Yang L., Lv Y., Qian H., Zhang B., Yu X., Liu C., Cao X., Cui Y., Zhang Q., Dai X., Guo L., Wang Y., Zhou Y., Ruan J., Qian Q., Shang L. (2023). A rice variation map derived from 10,548 rice accessions reveals the importance of rare variants. Nucleic Acids Research. doi: https://doi.org/10.1093/nar/gkad840

Construction of RSPVM