A 10K liquid-phase single nucleotide polymorphism array for genetic diversity analysis and cultivar identification in elephant grass and its hybrid

Elephant grass (Pennisetum purpureum) and its hybrid with hybrid pennisetum (Pennisetum purpureum × Pennisetum americanum) are important high-yield forage grasses in tropical and subtropical regions. To analyze their genetic diversity and mine breeding-related functional genes, we developed a custom 10K liquid-phase single nucleotide polymorphism (SNP) array containing 11,486 SNPs based on the purple elephant grass (Pennisetum purpureum 'Red') reference genome and performed high-throughput genotyping on 83 core accessions. Population structure analysis revealed that the tested materials could be clearly divided into two major groups which align with their distinct ancestry and hybridization history. Analysis of the SNP mutation spectrum showed that transition events (A > G, C > T) predominated (approximately 58.7% in total). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses indicated that the captured variations were significantly enriched in functional categories related to stress resistance, signal transduction, and basic metabolism. On the basis of a genetic similarity analysis, we classified the germplasm into 58 genetic groups and selected 50 highly discriminative core SNPs to construct cultivar-specific fingerprints. This study established, for the first time in forage grasses, a medium-density liquid-phase array genotyping system integrated with functional loci, providing an efficient tool and gene resources for germplasm identification, resource management, and molecular breeding in elephant grass and hybrid Pennisetum.