Overview for Oryza sativa Japonica (Asian rice Japonica)

Asian rice (Oryza sativa), the most commonly grown rice species, contains two main subspecies: the sticky, short-grain (Oryza sativa Japonica) and the non-sticky, long-grain (Oryza sativa Indica) rice varieties. Oryza sativa Indica is grown mainly in hot climates of Southern Asia, while Oryza sativa Japonica is mainly grown in temperate climates such as Japan. It has a diploid genome of ~500 Mb. For Oryza sativa Japonica, 37,960 genes and 25,135,669 SNPs are stored in agReg-SNPdb.

Statistics

(Last updated on 08.02.2022)

Number of chromosomes	14
Number of genes	37,960
Number of SNPs	25,135,669

Click on a chromosome to download the data stored in agReg-SNPdb for the complete chromosome

Chromosome	Number of SNPs	Number of Genes
1	2,581,619	5,271
10	1,713,783	2,112
11	2,273,779	2,423
12	2,094,503	2,174
2	2,117,842	4,215
3	2,043,810	4,548
4	2,497,050	3,355
5	1,958,709	3,029
6	2,134,381	3,155
7	2,029,301	2,871
8	2,072,841	2,586
9	1,618,051	2,110
Mt	0	53
Pt	0	58

Distribution of rSNPs relative to the TSS

Input data (Ensembl Plants)

Plant	Assembly version	Download links
Oryza sativa Japonica (Asian rice Japonica Group)	IRGSP-1.0	Reference genome SNPs Genes (downloaded on 08 November 2021)