Development of a SCAR Marker for the Identification of the Korean Garlic Cultivar ‘Hongsan’

Garlic (Allium sativum L.) cultivars in Korea, particularly the widely adaptable ‘Hongsan’, are challenging to identify in processed forms or seedlings due to the plasticity of phenotypic traits such as clove tip greening. This uncertainty increases the risk of mislabeling and the infringement of breeders’ rights under the UPOV framework. This study aimed to develop a stable SCAR marker for ‘Hongsan’-specific identification using a RAPD-based DNA pooling method. Sixty Operon primers (>60% GC) were screened against ‘Hongsan’ gDNA versus a multi-cultivar DNA pool (‘Daeseo’, ‘Uiseong’, ‘Danyang’, and ‘Namdo’); OPE-01 consistently amplified a unique 1.3 kb band, which was cloned and sequenced, revealing a 1272 bp sequence with a translocation junction (878 + 394 bp), a 18 bp insertion, and an EcoRI site on chromosome 2 (NCBI reference sequence: GCA_030737875.1). SCAR primers SaH191R/SaH513F produced a specific 545 bp amplicon in Hongsan, clearly distinguishing it from other cultivars and parental lines, indicating that the marker locus is related to the paternal line ‘9209’. This RAPD-to-SCAR marker overcomes reproducibility limitations and enables reliable authentication of Hongsan in processing powders and black garlic irrespective of environmental factors. This cost-effective and rapid assay ensures industry transparency, quality control, and IP protection for Korean garlic production.