Identification and evaluation of core microsatellite panel for fingerprinting in oil palm

The aim of the present study was to identify the core microsatellite panel from different genetic backgrounds of oil palm (Indian and African countries) and validate it in progenies from different crosses. Molecular characterization of 311 African germplasm and 4 germplasm blocks consisting of 420 palms including 120 exotic germplasm was performed using 500 simple sequence repeats (SSRs). The polymorphism parameters such as polymorphism information content (PIC), allelic richness, gene diversity (He), and heterozygosity (Ho) were used to develop the core SSR panel of 30 loci. High PIC was observed in the exotic germplasm (0.91) followed by African germplasm (0.84). High polymorphism was observed in germplasm block 7, with a mean PIC of 0.62, 0.64 for gene diversity (He) and 0.41 for heterozygosity (Ho), followed by higher PIC (0.50) in African germplasm and higher gene diversity (0.61) in germplasm block 3. High allele number (10) was observed with African germplasm followed by the germplasm block 7 (8). Based on the polymorphism parameters, the 150 SSRs were further reduced to 30 microsatellites distributed across all 16 chromosomes of the oil palm, designated as core microsatellite panel. This was validated on four crosses and two self-crosses. The clustering patterns resulting from the 150 SSR panel and the core SSR panel were similar in all 6 crosses, indicating that the developed SSR panel is sufficient to identify true-to-type, finger printing and for identifying illegitimate palms.

The online version contains supplementary material available at 10.1007/s13205-025-04262-0.