SNP-based analysis reveals high genetic structure and diversity in umbu tree (Spondias tuberosa Arruda), a native and endemic species of the Caatinga biome

Abstract

Umbu (Spondias tuberosa Arruda) is an endemic fruit tree restricted to the Brazilian seasonally dry tropical forest called Caatinga. This study aimed to evaluate the structure and genomic diversity of umbu trees from seven locations in the Caatinga biome, distributed among four Brazilian states. Using genotyping-by-sequencing (GBS), a total of 5,336 SNPs were obtained, of which 250 showed outlier behavior. Therefore, 5,086 neutral SNPs were used for population structure and genetic diversity analyses. Both discriminant analysis of principal components (DAPC) and neighbor-joining cluster analyses classified the accessions into four groups, with a genetic structure observed among groups, disagreeing with our initial hypothesis of low genetic structure between locations. Isolation by distance (r² = 0.974; p = 0.0015) was detected. Moderate to high levels of genetic diversity were found, with the average observed heterozygosity (H_O = 0.221) higher than the expected heterozygosity (H_E = 0.199) and with negative inbreeding coefficient (F_IS) values. Most genetic variation was found within locations, although high diversity between locations (22.1%) was observed. The results obtained are important for understanding the levels and distribution of genetic variation, suggesting that most locations are priorities for conservation actions, contributing with different alleles to the species' gene pool in Brazil.