Summary
Name
Oryza sativa subsp. japonica cv. Nipponbare
Description

Oryza sativa (rice) is a monocotyledonous flowering plant of the family Poaceae and is one of the most important crop plants in the world, providing the principal food source for half of the world's population. Oryza sativa subsp. japonica is one of three major subspecies of rice, the others being indica and javanica. Oryza sativa subsp. japonica is short-grained and high in amylopectin so that the grains stick together when cooked, which distinguishes it from subsp. indica which is long grained and not sticky. Oryza sativa subsp. japonica is grown in dry fields, mainly in temperate or colder climates such as Japan. Oryza sativa has a haploid chromosome number of 12, containing 370 Mb with 30,000 protein-coding genes. Rice was an obvious choice for the first whole genome sequencing of a cereal crop. It is the smallest of the major cereal crop genomes and is the easiest to transform genetically. The cultivar sequenced from the japonica subspecies was Nipponbare

Taxonomy
Division
Plants and Fungi
Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Genbank Common Name
Japanese rice
Infraspecific Taxon
cultivar Nipponbare
Common Name
Oryza sativa japonica Nipponbare
Other Name
Japonica rice
Synonym
  • Oryza sativa (japonica cultivar-group)
  • Oryza sativa subsp. japonica
Annotations
Publication
Analysis
Analysis Table
Analyses
NameProgramDate Constructed
Whole Genome Assembly and Annotation of Oryza sativa (v7.1)Performed by MSUJul 12th, 2018
CGSNL annotation and manual curation dataRAPDBDec 2nd, 2020
InterPro (5.48-83.0) Annotations of RAPDB InterProScanApr 15th, 2021
Transcriptional rice responses to PGPR BurkholderiaGenetrop standard mapping (BWM)Jun 14th, 2019
Gene expression profiling of reproductive meristem types in early rice inflorescences by laser microdissectionMapping against Niponvarre MSUv7 suing STAR, used of DESq2 for DE analysisJan 1st, 2018
Transcriptome of Oryza glaberrima in response to Meloidogyne graminicolaMapping against Niponvarre MSUv7 suing STAR, used of DESq2 for DE analysisJan 13th, 2019
Genetic characterization of rice cultivated in Burkina FasoPython script developed by François to set up the data file and R script developed by Philipe to analyze the dataJan 13th, 2021
Transcriptome of Oryza sativa in response to Meloidogyne graminicola Mapping against MSU7 using TopHat2 and count files generated by htseq-count (i-trop, Alexis Dereeper) Jan 1st, 2018
Genome-wide association mapping for shoot growth and water uptake dynamics in a panel of O. glaberrima rice accessionsSNP calling from MSU/GWAS by MLM (Tassel)Nov 10th, 2021
Small RNA sequencing of Rice leaves infected with the African Xanthomonas oryzae pv. oryzae strain BAI3Mapping against IRGSP1 genome. sRNA reads coverage--based inferrence of small RNA loci and identification of differentially expressed ones with Deseq2Dec 17th, 2021
Small RNA sequencing of Rice leaves infected with strains of the oryzae or oryzicola pathovars of Xanthomonas oryzaeMapping against IRGSP1 genome. sRNA reads coverage--based inferrence of small RNA loci and identification of differentially expressed ones with Deseq2Jan 3rd, 2020
Dynamic and Coordinated Expression Changes of Rice Small RNAs in Response to Xanthomonas oryzae pv. oryzaeMapping against IRGSP1 genome. sRNA reads coverage--based inferrence of small RNA loci and identification of differentially expressed ones with Deseq2Jan 3rd, 2022