SNP List of Rice (Nipponbare) MNU Mutant Lines

From the gene names (accessions) and genomic positions listed in the zip file, you can identify the mutant lines that carry specific mutations. The mutant lines are available from the National BioResource Project (NBRP).

This list was generated by detecting SNPs using PED from NGS sequences of Nipponbare MNU-treated mutant lines developed at Kyushu University (Kubo et al. 2024). The reference genome used was IRGSP-1.0. The files are organized by chromosome, indicating the positions of mutations and the lines carrying them. Additionally, the mutation positions within the genes indicated by the Rice Annotation Project (RAP) and the primer sequences for amplifying these mutation sites are also included.

By searching the files with a gene name, you can identify the mutations within that gene and the lines carrying those mutations.

The files are tab-delimited lists that can be imported into Excel. To import, go to the Data tab in Excel, click "From Text/CSV," and select the chromosome file. Column 11 corresponds to the IRGSP accession. You can filter by accession or by the gene abbreviation in Column 10.

To obtain seeds, please apply through the seed request page of NBRP (Kyushu University): https://miriq.agr.kyushu-u.ac.jp/request.php

Column order is chromosome number, position, line name, ref, alt, genotype, allele frequency, number of reads, mutation type, gene name, RAP ID, position of nucleotide sequence of gene, position of amino acid sequence of gene, left primer, right primer, amplified size.

The PED software is available at: https://github.com/akiomiyao/ped

Miyao, A., Kiyomiya, J.S., Iida, K. et al. Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data. BMC Bioinformatics 20, 362 (2019). https://doi.org/10.1186/s12859-019-2955-6