Development of Hermaphrodite Salacca (Salacca zalacca) SNAP Marker: A Novel Conservation Tool

Abstract

Abstract Salacca (Salacca zalacca) or snake fruit is a tropical fruit, which is considered to be originated from Indonesia. One of the challenges in salacca conservation is the wide genetic diversity of the plants due to their natural cross-breeding. Most S. zalacca are dioecious plants by having fertile female and male flowers on different individuals, except for Salak Bali which is regarded to be monoecious. Morphological and cytogenetic markers have failed to differentiate the salacca plants’ sex types during the vegetative phase, thus the molecular marker is an alternative. We explored the specific salacca gene sequence on various sex types of salacca plants to identify sex-related single nucleotide polymorphism. The SNAP markers were then developed using the chosen SNP and validated on a total of 30 salacca samples. Nine samples of salacca’s female, male, and hermaphrodites were amplified using designed primers. The produced bands were sequenced and analyzed using Geneious Prime software. The analysis implied 9 SNPs on the 446 bp of salacca’s specific partial sequences. The SNAP markers were designed based on SNP validation showed that the marker potentially used a hermaphrodite-specific marker. The development of molecular markers as an early salacca sex type detection tool may be helpful in fruit cultivation, accelerating the plant breeding program, as well as on conservation management.