Phylogenomic analysis and SNP fingerprinting construction of Camellia oleifera Abel. germplasm resources using SLAF-seq technology

Camellia oleifera Abel., a species of Theaceae plants widely cultivated in southern China, is highly valued for its production of oils and pharmaceutical compounds. However, the large-scale cultivation of C. oleifera cultivars faces significant challenges due to difficulties in accurate identification. To address this, developing DNA fingerprinting is crucial for identifying superior germplasm and enhancing the classification and utilization of C. oleifera resources. In this study, we utilized SNP markers derived from specific-locus amplified fragment sequencing (SLAF-seq) to investigate the phylogenetic relationships and genetic diversity among 25 widely cultivated C. oleifera cultivars. The analysis revealed three distinct genetic clusters, indicating high levels of genetic differentiation. Notably, the C. oleifera cultivar CR-153 exhibited the highest genetic diversity, making it a promising candidate genetic pool for future breeding programs aimed at improving C. oleifera . The results also suggest that cultivars such as CL-4, DL-1 and XL-1; as well as XL-3 and XL-210, may share ancestry or have undergone introduction events. Furthermore, we developed a DNA fingerprinting system incorporating genes relevant to economic traits and abiotic resistance, enabling rapid classification and molecular breeding of C. oleifera . Overall, these findings provide valuable insights into the genetic resources of cultivated C. oleifera in southern China, offering practical guidelines for future breeding programs, scientific resource management, and the enhancement of economically important traits. • Camellia oleifera Abel. cultivars demonstrate excellent potential for industrial production. • The phylogenetic relationships of 25 widely cultivated cultivars were investigated. • The CR-153 cultivar exhibits the highest genetic diversity, making it a candidate genetic pool. • The revealed DNA fingerprinting facilitates fast identification and cultivation management.