BackgroundMost of the satsuma mandarin (Citrus unshiu Marc.) cultivars grown on Jeju Island farms, Korea, are difficult to improve through hybridization because of polyembryony and male sterility. Therefore, their improvement has mostly been based on the selection of nucellar embryo and bud mutation. These cultivars are supplied to breeders and farms at the seedling stage, which renders their identification based only on morphological traits. In addition, because these seedlings originate from nucellar embryo and bud mutation selection, they are genetically very similar. Therefore, the present study was carried out to develop markers that can specifically and rapidly distinguish ‘Haryejosaeng,’ which is generally supplied to breeders, from other satsuma mandarin cultivars that are planted on farms.ResultsPolymerase chain reaction (PCR) was performed to distinguish ‘Haryejosaeng’ from other 8 cultivars (‘Haryejosaeng’- breeder’s stock, ‘Miyagawa wase,’ ‘Okitsu wase,’ ‘Yura wase,’ ‘Miyamoto wase,’ ‘Ueno wase,’ ‘Yonezawa wase,’ and ‘Nichinan 1 gou’) using 6 single nucleotide polymorphism (SNP) markers specific for ‘Haryejosaeng’ and one SNP primer pair, which was used as the negative control. Using a multiplex PCR, SNP markers P1 (HL-SNP-SCAF_2-23997586-F and HL-SNP-SCAF_2-23997586-R), P2 (HL-SNP-SCAF_2-36059523-F and HL-SNP-SCAF_2-36059523-R), and P5 (HL-SNP-SCAF_9-30793978-F and HL-SNP-SCAF_9-30793978-R) simultaneously yielded 165, 150, and 526 bp amplicons, respectively, for Haryejosaeng only. The SNP markers were further validated by high-resolution melting analysis. The multiplex PCR based on P1/P5 and P2/P5 was also used to identify ‘Haryejosaeng’ on a farm growing 17 different cultivars of satsuma mandarin.ConclusionsWe developed specific molecular markers for accurate identification of ‘Haryejosaeng,’ which can be performed by multiplex PCR to save time and cost associated with the supply of ‘Haryejosaeng’ to farms.