| Summary: | In this study, we used SNP markers to access the genetic components occurrence of genetic differentiation resulting from the selection processes applied to collect and maintain the germplasm bank of <i>Elaeis oleifera</i> (Kunth) Cortés from the Brazilian Amazon rainforest. A set of 1667 higher quality SNPs—derived from a previous GBS study—was used for genomic characterization and calculation of genetic parameters. There is differentiation in the distribution of alleles between populations for 78.52% of the tested loci. Genotypic diversity test results indicated strong evidence of genotypic differentiation between populations. Sixteen out of the nineteen tested deviated significantly from the expected allele frequencies in HWE, reinforcing the hypothesis that there was maybe a selection in the evaluated populations. A group of 568 loci with a higher probability of being under selection effects were selected, both directional and stabilizing. In total, 1546 and 1274 SNPs aligned in the genomes of <i>E. oleifera</i> and <i>E. guineensis</i> Jacq., respectively. These markers showed a wide distribution throughout the genome of the two species. In conclusion, the <i>E. oleifera</i> GB from the Brazilian Amazon rainforest has specific genetic structures and good genetic variability within populations.
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