Genetic diversity analysis of Euterpe edulis based on different molecular markers

Abstract

Knowledge of the genetic diversity and population structure of species can facilitate conservation and guide management programs. However, the type of molecular markers used can affect estimates of genetic divergence and population structure. Here three types of molecular markers were used to estimate the genetic diversity and population structure of Euterpe edulis, a palm endemic to the Atlantic Forest and economically and ecologically important. The objective was to estimate the parameters of genetic diversity and population structure for two other types of molecular markers (SNP and SilicoDArT) in addition to the commonly used one (SSR) to the species. We used single nucleotide polymorphism (SNP), SilicoDArT, and microsatellite (SSR) markers in 138 E. edulis individuals sampled from 15 sites. Euterpe edulis individuals were grouped into 11 clusters using SNPs and SilicoDArT and six groups using SSR data. The SNP and SilicoDArT data showed less divergence between the individuals within each cluster in comparison to the results derived from the SSR data. The probability of reassigning individuals to their cluster of origin revealed an average association with the original clusters was 0.92 for SNPs (n = 100), 0.71 for SSR (n = 8), and 0.99 for SilicoDArT (n = 445). The genetic divergence is high among sites using SNP markers, whereas SSRs showed the largest genetic divergence is found within each site. The overall heterozygosity values for each site in the eight SSR (He = 0.69; Ho = 0.59) markers were almost four times higher than those values inferred using SNPs (data 7833 SNP, He = 0.15; Ho = 0.13; data 100 SNP, He = 0.14; Ho = 0.12). Within each site, we found low inbreeding rates using both markers (SNP and SSR). In addition, population structure analysis identified two strongly supported geographical groups, one northern and one southern Brazilian Atlantic Forest group, for both markers. This study contributes to the understanding of the population genetics and population structure of E. edulis and may have important implications for its conservation. In addition, our results suggest that SNP and SilicoDArT markers are more effective for evaluating population structure, but SSR is more capable of detecting diversity among individuals for this species.