SNP-based genetic diversity of a network of germplasm banks to establish a core collection for the tropical fruit Hancornia speciosa

Abstract

Hancornia speciosa is a tropical fruit and an important food resource native to Brazil. Its fruits, commercialized in natura or as a frozen pulp or ice cream, are an outstanding source of vitamins C, E, folates, and carotenoids. Despite its economic relevance, the species is still exploited in an extractive manner by harvesting natural populations, and no commercial varieties are available. A network of germplasm banks has been established from seeds and vegetative material collected in different regions throughout the Brazilian Atlantic Forest and Cerrado biomes. Nonetheless, resources are limited to maintain and evaluate all germplasm accessions for plant breeding. We used SNP markers generated by DArTSeq to assess the genetic diversity and population structure of 508 individual plant accessions conserved across three germplasm banks of H. speciosa and proposed a core collection for the species to be targeted for phenotypic characterization efforts. Significant genetic differentiation was found among the germplasm banks (Fst 0.221), with moderate genetic diversity and substantial inbreeding within each one, likely resulting from a Wahlund effect due to within-bank substructure as genetic entries were sampled from disjunct populations. A structure analysis assigned most of the germplasm accessions to two genetic groups, although some admixed individuals were observed. A core collection of 138 accessions (27.11%) was proposed, covering 98% of the currently conserved genetic diversity in the germplasm network. Although the proposed core collection provides a solid representation of the currently conserved genetic diversity for breeding, our results indicate that additional sampling of natural populations not yet surveyed should be pursued.