Genetic diversity and marker-assisted inbreeding in papaya

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 proportion of the genetic variation occurring in “Solo” and “Formosa” groups. This seems to be promising for success in further developments of new hybrids in breeding programs.

► Molecular markers can reduce the time to develop papaya inbred lines.
► The inbreeding coefficient is unequal for different genotypes after self-pollinated.
► Genetic variability could be maintained after several cycles of selection in papaya.
► There was no correlation among inbreeding levels and any agronomic trait.
► Clustering analysis were consistent with the papaya classification according to the fruit type.