‘Mikan’ means citrus fruits in Japanese. Mikan Genome Database (MiGD) is a citrus polymorphism resource for breeding, physiology, genomics and genetics of citrus. MiGD provides the following contents: (1) comparative genome browser which shows genome-wide variants and depth of coverage of re-sequencing data among nine citrus species, (2) the annotation for satsuma mandarin (Citrus unshiu) and trifoliate orange (Poncirus trifoliata) genomes which newly assembled by MiGD team, (3) CAPS maker database including 2,696 primer sets and restriction enzyme with electrophoresis photos, (4) BLAST service against gene and genome sequences of four citrus species, and (5) genome sequence and annotation data of C. unshiu and P. trifoliata.
Bioinformatics Team, Advanced Analysis Center, NARO
Citrus Genome Research Unit, Institute of Fruit Tree and Tea Science, NARO
Shizuoka University
Kawahara Y, Endo T, Omura M, Teramoto Y, Itoh T, Fujii H, Shimada T (2020) Mikan Genome Database (MiGD): integrated database of the genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding. Breeding Science. [doi: 10.1270/jsbbs.19097]
Kumagai M, Kim J, Itoh R and Itoh T (2013) TASUKE: a web-based visualization program for large-scale resequencing data. Bioinformatics. 29 (14): 1806-1808. [doi: 10.1093/bioinformatics/btt295] [PMID: 23749962]
Numa H and Itoh T (2014) MEGANTE: A Web-based System for Integrated Plant Genome Annotation. Plant and Cell Physiology, 55(1): e2. [doi: 10.1093/pcp/pct157] [PMID: 24253915]
Ninomiya T, Shimada T, Endo T, Nonaka K, Omura M and Fujii H (2015) Development of citrus cultivar identification by CAPS markers and parentage analysis. Hort Res (Japan), 14: 127-133. (In Japanese with English abstract) [doi: 10.2503/hrj.14.127]
Nonaka K, Fujii H, Kita M, Shimada T, Endo T, Yoshioka T and Omura M (2017) Identification and parentage analysis of citrus cultivars developed in Japan by CAPS markers. Hort J, 88: 208-221. [doi: 10.2503/hortj.OKD-026]
Fujii, H., T. Narita, H. Oshino, T. Kawakami, H. Goto, T. Yoshioka, M. Omura and T. Shimada (2019) CAPS markers with stability and reproductivity for discriminating major citrus cultivars in Japan. DNA polyporphism. 27: 71-79.
Ohta S, Endo T, Shimada T, Fujii H, Omura M et al. (2015) Construction of genetic linkage map and graphical genotyping of pseudo-backcrossed F2 (BC’2) progeny to introduce a CTV resistance from Poncirus trifoliata (L.) Raf. into Citrus by introgression breeding. Tree Genet Genom. 11: 797. [doi: 10.1007/s11295-014-0797-y]
Shimada T, Fujii H, Endo T, Omura M. et al. (2014) Construction of a citrus framework genetic map anchored by 708 gene-based markers. Tree Genet Genom. 10: 1001-1013. [doi: 10.1007/s11295-014-0738-9]