Lemon (Citrus limon), an interspecific hybrid between sour orange and citron, has been widely used as a rootstock along with trifoliate orange. Though lemons are superior to trifoliate orange in terms of their high seed germination rate throughout the year, one of the obstacles to using lemons as rootstocks is the lack of reliable, lemon-specific molecular markers to discriminate buds of the micro-grafted scion from those of the lemon rootstock. In order to obtain lemon-specific molecular markers, we compared the whole-plastid genomes available from four citrus species (lemon, pummelo, sweet orange, and mandarin) and developed seven plastid insertion/deletion (InDel) markers. The plastid InDel markers were applied to 46 citrus accessions that included lemons (17 accessions), grapefruit, mandarin, pummelo, sour orange, orange, papeda, tangor, and tangelo groups. The resulting dendrogram revealed that the citrus accessions used in this analysis could be distinctly classified into seven clusters. Lemons formed a separate cluster and had identical allele sizes for each InDel locus among all accessions investigated. This set of InDel markers could be a useful molecular tool for the rapid and clear discrimination of micro-grafted scions and lemon rootstocks during the production of virus-free citrus trees. The plastid InDel markers with maternal inheritance features can also be used to analyze the phylogenetic origin of various citrus cultivars including lemons.

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