SNP genotype data set in variant calling format (vcf) for Acrocomia species.

Population genetic research has evolved, focusing on selection processes using single nucleotide polymorphisms (SNP) genotyping techniques to study crop traits and domestication. This study explores the adaptation process of three neotropical palms of <i>Acrocomia</i>, a genus that has high potential for oil extraction. Our research focuses on their genetic structure, evolutionary significance, and implications of the selection signatures for breeding efforts. We employed Genotyping-by-Sequencing (GBS) with a focus on outlier SNP markers for identifying adaptive genetic processes in <i>A. aculeata</i>, <i>A. totai</i>, and <i>A. intumescens</i> across the Neotropic. Our results reveal two major gene pools in <i>A. aculeata</i>, a North American and a South American group mainly influenced by dispersal and biogeographic barriers, with putative selective signatures linked to fatty acid and carotenoid biosynthesis, pathogen resistance, and environmental stress adaptation. <i>A. totai</i> presented a pronounced genetic structure, with SNPs under selection indicating a recent diversification driven by climatic and geological factors, especially in the Pantanal biome. <i>A. intumescens</i> displays genetic structuring shaped by the endemic process of biogeographic barriers within the Caatinga biome, with potential shared ancestry with<i> A. aculeata.</i> Correlations between allele frequencies and climatic variables highlight adaptation to diverse environments, principally semi-arid, with the annual mean temperature being one of the most influential. Candidate genes associated with fatty acid and carotenoid biosynthesis, as well as pathogen resistance and drought tolerance, indicate targets for domestication. Despite challenges in reduced representation sequencing, this study underlines the potential of <i>Acrocomia</i> as a novel crop, offering prospects in oil production, biofuels, and sustainable agriculture. Future efforts should prioritize whole-genome sequencing and genotype-environment interaction studies to realize the full potential of <i>Acrocomia</i> in sustainable development and renewable energy production.