Conventional methods for the selection of papaya inbred lines are time-consuming. Procedures involving
the use of molecular markers can reduce this time considerably, by indirect selection of homozygous
plants. The objective of this study was to use microsatellite markers in marker-assisted selection (MAS)
to develop new papaya inbred lines, and categorize the inbred lines into useful groups based on the
molecular profiles and agronomic traits. Thirty-six lines from F4 (Calimosa × Common papaya) and S3
derivate from open-population accessions of germplasm, and 6 controls were used for the molecular
analysis with 27 microsatellite primers. Twelve polymorphic and 15 monomorphic microsatellite primers
were identified, allowing the identification of 59 alleles, with an average of 2.19 alleles per primer. The
observed heterozygosity values (Ho) were low for both the markers (0.00–0.24) and the individual lines
(0.00–0.19). The inbreeding coefficient(f) ranged from 0.80 to 1.00. Eleven papaya inbred lines and checks
(landrace, cultivars, and other pure lines) showed complete inbreeding (f = 1). A broad genetic variability
for all agronomic traits analyzed, especially for productivity (10.34–86.39 t ha−1), was observed and was
confirmed using agronomic and molecular data simultaneously to group the new papaya inbred lines and
checks. Hierarchical and silhouette-width method using Gower’s dissimilarity revealed 9 major clusters.
Despite the fact that self-pollination and selection lead to reduction of genetic variability, papaya inbred
lines are proved to be genetically diverse representing a large proportionofthe genetic variationoccurring
in “Solo” and “Formosa” groups. This seems to be promising for success in further developments of new
hybrids in breeding programs.