Institute of Fruit Tree and Tea Science, NARO

Publication of Mikan Genome Database (MiGD)

-Efficient development of DNA markers for cultivar identification and breeding of new cultivar-

National Agriculture and Food Research Organization (NARO) has developed and published a database "Mikan genome database (MiGD)" to support the development of DNA markers in citrus. This database enables the easy search for DNA polymorphism information necessary to develop DNA markers for about 10 species and cultivars of Citrus species and wild species in related genera. This database will be very useful to yield DNA markers for identifying important genes, marker assisted breeding and cultivar identification.


Genome sequences have been deciphered in various plants with the development of next-generation sequencing technology. In 2017, NARO decoded the whole genome sequence of satsuma mandarin (Citrus unshiu) of the citrus family. Recently, the entire genome sequence of trifoliate orange (Poncirus trifoliata) was decoded. In addition, other research institutes have decoded and released the genome sequences of eight types of citrus fruits such as orange (C. sinensis), clementine (C. clementina), and their related species. Development of DNA markers is important to identify useful genes using map-based cloning, and for subsequent selection of superior individuals and cultivar identification.

NARO has developed a database, called "MiGD", to support the development of citrus DNA markers and its publication on the Web. Currently, the database hosts information for around 10 kinds of citrus fruits and their related species (satsuma mandarin, trifoliate orange, orange, clementine, ponkan (Citrus reticulata), two varieties of pomelo (C. grandis), citron (C. medica,) and two wild relatives of citrus. This database enables easy identification of slight differences (polymorphisms) in genome sequence between species and cultivars, which is necessary for DNA marker development. It is also possible to view the whole genome sequence information and gene annotation information of satsuma mandarin and trifoliate orange, and ~2,700 existing DNA marker information available for all citrus fruits.

This database will be very useful for agricultural experiment station to promote citrus breeding and for custom department to prevent import violation/infringement of breeder's rights. URL of Mikan Genome DB (MiGD)

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