Genetic diversity and relationship analyses of mango (Mangifera indica L.) germplasm resources with ISSR, SRAP, CBDP and CEAP markers

• ISSR, SRAP, CBDP and CEAP markers were used to evaluate the genetic diversity of mango. • Combined use multiple molecular markers is more accurate for genetic relationship analysis. • Nine mango seedlings were found the potential parents or sister lines. • CEAP marker was better than other markers for genetic diversity study. Forty-eight mango accessions were compared for genetic diversity and relationships based on four molecular marker assays, namely, inter-simple sequence repeat (ISSR), sequence-related amplified polymorphism (SRAP), CAAT-box derived polymorphism (CBDP), and cis-element amplified polymorphism (CEAP). Comparative analyses of the marker assays based on Nei's genetic diversity (H), Shannon's information index (I), polymorphism information content (PIC), the marker index (MI), and resolving power (Rp) revealed that (i) the CEAP markers provided the most information according to the PIC, MI and Rp values; (ii) the CBDP and ISSR markers exhibited valuable information according to the H and I values. The correlation values (r) of the Mantel test ranged from 0.334 (ISSR and CEAP) to 0.819 (CEAP and the combination of the four marker assays). The unweighted pair group method with arithmetic mean (UPGMA) cluster results showed that a single-marker assay can accurately reflect the genetic relationships of some mango samples but cannot accurately reflect the genetic relationships of all mango samples and that when multiple markers are used to evaluate the genetic relationships of mango germplasm resources, the results are more accurate than those of a single-marker assay. The combined cluster analysis of the molecular marker types shows higher discrimination according to genetic relationships. Nine mango accessions were suggested to be likely parental or sister lines based on the combination of the ISSR, SRAP, CBDP, and CEAP marker assays.