Comparative Genetic Analysis between the Jeju ‘Inchangkyool’ and Chinese ‘Ichangensis’ (Citrus ichangensis) using Internal Chloroplast trnL-trnF Intergenic Spacers and Transcribed Spacer Sequence Regions

'Inchangkyool' varieties, which are believed to have been cultivated in Jeju for a long time, have leaves and flowers with a lemon-like fragrance. They have been suggested to be given the same scientific name as Citrus ichangensis, which is known to originate from China’s Southwest and Midwest regions. However, the genetic characterization of ‘Inchangkyool’ has not been reported, and literature is not readily available. Hence, in this study, 30 citrus chloroplast (cp)DNA (trnL-trnF) regions and nuclear ribosomal DNA internal transcribed spacer (ITS) regions were tested to identify the genetic relationship between ‘Inchangkyool’ and C. ichangensis and the origin of ‘Inchangkyool’ cultivars. Our results indicated that the total nucleotide sequence length of the trnL-trnF intergenic spacer (IGS) region and the G + C content was 373 bp and 36.73%, respectively, in the cpDNA of C. ichangensis and ‘Inchangkyool’, whereas the ITS1 regions were 247 and 248 bp and the ITS2 regions were 228 and 226 bp, respectively. Furthermore, the sequence lengths of the total ITS (ITS1 + 5.8S rDNA + ITS2) regions were 638 and 637 bp, respectively, whereas the G+C content was 70.16%, 71.26%, 69.03%, 70.61%, 64.6%, and 65.49%, respectively - showing differences in the nuclear ribosomal DNA region. However, the nucleotide sequence length of the 5.8S rDNA region was 163 bp and the G + C content was 54.6%, which were the same for both varieties. In addition, sequence divergence and phylogenetic analysis of the trnL-trnF and ITS regions in chloroplast DNA showed that the sequence divergence of the trnL-trnF region on the chloroplast was 0–0.008. This result indicates that ‘Inchangkyool’ is most closely related to Jeju eight native citrus cultivars including ‘Dongjeongkyool’. It is also closely related to C. ichangensis cultivars and six common citrus cultivars. In other words, the ‘Inchangkyool’ cultivar was inherited from the same maternal line as the Chinese C. ichangensis. The divergence values of the nuclear ribosomal DNA region between ‘Inchangkyool’ and ‘Dongjeongkyool’ and C. ichangensis were 0.008 and 0.026, respectively. These results indicated that ‘Inchangkyool’ was most closely related to ‘Dongjeongkyool’, and was farther from the C. ichangensis cultivar. In addition, phylogenetic relationships found ‘Inchangkyool’ to belong to the same group as the ‘Dongjeongkyool’ cultivar of jeju native citrus cultivars and a different group from C. ichangensis. From the above results, it is suggested that ‘Inchangkyool’ cultivar has been classified from the same maternal cultivar as the C. ichangensis in China, but has been obtained through long-term crossing with the same species as ‘Dongjeongkyool’. Moreover, based on the above results, it is believed that a distinct cultivar name for ‘Inchangkyool’ can be presented.