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Cultivar · Rice cultivar

Nipponbare

Nipponbare is a Japanese temperate japonica rice cultivar best known as the international reference genome for rice. Its map-based genome sequence, published in 2005, underpins a large body of rice genetics and genomics research.

Dated referenceLast reviewed: 2026-07-12Updated: 2026-07-12
Illustrative diagram · AgricultureID (original)

Record

Cultivar / variety
Variety of
Rice
Botanical taxon
Oryza sativa (temperate japonica group)
Type
Inbred line (temperate japonica; reference cultivar)
Breeding method
Cross-breeding (pedigree selection)
Origin
Japan
Registry status
Historical
Adaptation
Temperate japonica adaptation (temperate East Asian rice conditions)
Intended use
Staple food grain, Reference material for rice genetics and genomics research

Registry listing or variety protection is jurisdiction- and date-specific and does not by itself indicate current commercial availability, universal cultivation approval, patent status, or a recommendation.

Nipponbare is a temperate japonica rice cultivar from Japan. While it is a food-grade short-grain rice, it is best known internationally as the reference genome for rice: its map-based genome sequence was produced by the International Rice Genome Sequencing Project and published in 2005, and it remains the standard reference assembly used across rice research.

Because so much rice genetics and genomics work is anchored to Nipponbare, the cultivar functions as a common coordinate system for genes, markers, and comparative studies. This page focuses on its documented role as a reference cultivar rather than on regional cultivation recommendations.

Origin and classification

Nipponbare is a temperate japonica cultivar developed in Japan. Temperate japonica rices are typically short-grained, adapted to temperate growing conditions, and associated with a sticky, tender cooked texture, in contrast to the long-grain indica rices of the tropics. AgricultureID does not assert a specific release year or breeding institution for Nipponbare, as these details are not reproduced here from an authoritative primary registry.

Botanical taxon
Oryza sativa (temperate japonica group)
Origin
Japan
Grain type
Short, round japonica grain
Cooked texture
Sticky and tender, typical of temperate japonica rice

Role as the rice reference genome

Nipponbare is the cultivar whose genome was sequenced by the International Rice Genome Sequencing Project, with the map-based sequence published in 2005. This high-quality, map-based assembly became the standard reference to which other rice genomes, genes, and markers are compared. As a result, Nipponbare is one of the most intensively studied plants in crop science and is a routine reference in rice molecular genetics.

Rice was the first crop cereal to have a high-quality reference genome of this kind, partly because of its relatively compact genome and its central importance as a food crop. Nipponbare’s reference role is the main reason a Japanese table-rice cultivar is so widely cited in international research.

Use and status

As a food crop, Nipponbare is a short-grain japonica table rice suited to temperate conditions. Its wider importance, however, is as a research reference. It is treated here as a historical and reference cultivar; its current commercial cultivation and registry standing in any particular country are not asserted on this page.

Relationships

Evidence-backed connections in the knowledge graph.

Scope & limitations

Geographic scope: A Japanese temperate japonica cultivar used worldwide as the rice reference genome; discussed here as a reference and research cultivar rather than a regional growing recommendation.

Climate context: Temperate japonica rice adapted to temperate East Asian conditions; grain and texture characteristics are typical of the japonica group.

  • Nipponbare is presented mainly as a reference cultivar; its current commercial cultivation and registry standing in specific countries are not asserted here.
  • A specific release year and breeding institution are not stated because they are not reproduced here from an authoritative primary registry.
  • Genome assembly versions and gene annotations are updated over time and should be taken from current genomics resources.

Sources

This article draws on the following authoritative sources. See our sources & methodology for how they are selected.

  1. [1]IRRI — International Rice Research Institute (opens in a new tab)

    International Rice Research Institute (IRRI)

    High

    Cited for: Nipponbare’s role as the rice reference genome and japonica characterization

    Type:
    Research institute
    Jurisdiction:
    Global
    Accessed:
    2026-07-12
  2. [2]NCBI Taxonomy (opens in a new tab)

    U.S. National Center for Biotechnology Information (NCBI)

    High

    Cited for: Oryza sativa (Japonica group) classification and reference-genome context

    Type:
    Reference database
    Jurisdiction:
    Global
    Accessed:
    2026-07-12
  3. [3]GBIF — Global Biodiversity Information Facility (opens in a new tab)

    Global Biodiversity Information Facility (GBIF)

    High

    Cited for: Species classification (Oryza sativa)

    Type:
    Reference database
    Jurisdiction:
    Global
    Accessed:
    2026-07-12