Molecular identification of varieties

Varieties of genus Citrus and its relatives show large diversity on their appearance and physiologicalcharacteristics, but some of them often look similar and are difficult to distinguish from others. Molecularidentification of citrus varieties is beneficial to distinguish from similar ones by eliminating to depend onunstable morphological dissimilarity or empiricism. Genotyping analysis by DNA marker has been used for itsaccuracy, reliability, and reproducibility by detecting differences of nucleotide sequence among varieties thatis called nucleotide polymorphism. Type and frequency of nucleotide polymorphism at different loci observedat a set of varieties correlates to genetic distance of them. Scoring genotypes by multiple DNA markers istherefore useful to reveal identity of individual variety, and phylogenetic relationships among citrus varieties. Initial attempts for DNA-based markers analysis used random markers like RAPD or ISSR. These DNA markerswere advantageous by revealing sufficient number of polymorphism with less cost and required no priornucleotide sequence data. But those kinds of markers are not suited for genetic study since they are unstableand less informative dominant markers. Nowadays co-dominant type DNA markers that improved stability,reproducibility and transferability including simple sequence repeat (SSR), insertion/deletion (indels) orsingle nucleotide polymorphism (SNP) are used in studies of citrus. These DNA markers are sufficientlyinformative for detailed genetic analysis but require nucleotide sequences of target organisms to designthem. EST sequences or BAC end sequences were initially applied to design these markers. Recent citrusgenome sequencing analysis revealed many polymorphic nucleotide sequence loci, and it is facilitating DNAmarker development. Further efforts for nucleotide sequencing of various citrus varieties in the future willincrease genome-wide DNA markers and improve their availability. With the rapid advance of D