title: Minimal marker: an algorithm and computer program for the identification of minimal sets of discriminating DNA markers for efficient variety identification.
abstract: DNA markers are frequently used to analyze crop varieties, with the coded marker data summarized in a computer-generated table. Such summary tables often provide extraneous data about individual crop genotypes, needlessly complicating and prolonging DNA-based differentiation between crop varieties. At present, it is difficult to identify minimal marker sets--the smallest sets that can distinguish between all crop varieties listed in a marker-summary table--due to the absence of algorithms capable of such characterization. Here, we describe the development of just such an algorithm and MinimalMarker, its accompanying Perl-based computer program. MinimalMarker has been validated in variety identification of fruit trees using published datasets and is available for use with both dominant and co-dominant markers, regardless of the number of alleles, including SSR markers with numeric notation. We expect that this program will prove useful not only to genomics researchers but also to government agencies that use DNA markers to support a variety of food-inspection and -labeling regulations.
authors.affiliation: Citrus Research Division, NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization, 485-6 Okitsunaka-cho, Shimizu-ku, Shizuoka 424-0292, Japan. hfujii@affrc.go.jp
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Fujii
authors.forename: Tatsushi
authors.initials: T
authors.lastname: Ogata
authors.forename: Takehiko
authors.initials: T
authors.lastname: Shimada
authors.forename: Tomoko
authors.initials: T
authors.lastname: Endo
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Iketani
authors.forename: Tokurou
authors.initials: T
authors.lastname: Shimizu
authors.forename: Toshiya
authors.initials: T
authors.lastname: Yamamoto
authors.forename: Mitsuo
authors.initials: M
authors.lastname: Omura
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D018744:DNA, Plant / Q000235:genetics*; D030561:Databases, Nucleic Acid / Q000706:statistics & numerical data; D005638:Fruit / Q000145:classification* / Q000235:genetics*; D017343:Genes, Plant; D005819:Genetic Markers; D005838:Genotype; D007564:Japan; D018895:Microsatellite Repeats; D012984:Software; D013045:Species Specificity; D014197:Trees / Q000145:classification* / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers