SNP Marker Development and DNA Fingerprinting for Pennisetum giganteum (JUJUNCAO) Based on RNA-seq

Pennisetum giganteum (JUJUNCAO) exhibits strong adaptability, substantial biomass accumulation, and a rich nutritional profile. As a high-yielding and premium-quality multipurpose grass, it can be utilized for cultivating edible and medicinal fungi, enhancing ecological conditions, and serving as livestock and poultry feed. In this study, we used 32 P. giganteum germplasm accessions to develop species-specific SNP molecular markers, investigate genetic diversity, and construct a DNA fingerprinting database. SNP primers were designed using transcriptome sequencing data from representative P. giganteum samples and applied for polymerase chain reaction (PCR) amplification across all germplasm accessions. Subsequent detection via polyacrylamide gel electrophoresis (PAGE) enabled genetic diversity analysis and DNA fingerprinting. Fifteen pairs of primers with polymorphism and clear bands were screened out from the 46 pairs of primers designed. A total of 151 polymorphic loci were detected, with an average of 10.06 polymorphic loci generated per pair of primers. The Nei’s gene diversity index of the P. giganteum germplasm accessions ranged from 0.3418 to 0.4980, with an average of 0.4732. Shannon’s diversity index ranged from 0.5253 to 0.6912, with an average of 0.6650, showing a high degree of polymorphism. Cluster analysis classified the germplasm accessions of P. giganteum into four major groups: Group I (8 accessions), Group II (12 accessions), Group III (5 accessions), and Group IV (7 accessions). A comprehensive DNA fingerprint profile for all 32 accessions was successfully established using two core primer pairs. These findings significantly enrich the molecular marker repository for P. giganteum , providing a valuable reference framework for marker development in the Pennisetum genus. This is anticipated to accelerate research progress in germplasm identification, cultivar protection, and marker-assisted breeding.