Population genomics of the neotropical palm Copernicia prunifera (Miller) H. E. Moore: Implications for conservation

• Published in: PloS one 2022-11, Vol.17 (11), p.e0276408-e0276408
• Main Authors: Costa, Marcones Ferreira, Morales-Marroquín, Jonathan Andre, de Araújo Batista, Carlos Eduardo, Alves-Pereira, Alessandro, de Almeida Vieira, Fábio, Zucchi, Maria Imaculada
• Format: Article
• Language: English
• Subjects: Agricultural industry; Biological diversity; Brazil; Breeding; Coastal plains; Conservation; Conserved sequence; Copernicia prunifera; Deforestation; Discriminant analysis; Environmental aspects; Enzymes; Evolution; Genetic aspects; Genetic diversity; Genetic structure; Genomes; Genomics; Genotyping; Growth; Heterozygotes; Inbreeding; Methods; Natural populations; Natural selection; Nucleotides; Outliers (statistics); Palms; Plant extracts; Plant population genetics; Population; Population genetics; Population structure; Populations; Prevention; Protection and preservation; Single-nucleotide polymorphism; Sustainability management; Vegetation; Wildlife conservation
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0276408

Copernicia prunifera (Miller) H. E. Moore is a palm tree native to Brazil. The products obtained from its leaf extracts are a source of income for local families and the agroindustry. Owing to the reduction of natural habitats and the absence of a sustainable management plan, the maintenance of the natural populations of this palm tree has been compromised. Therefore, this study aimed to evaluate the diversity and genetic structure of 14 C. prunifera populations using single nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing (GBS) to provide information that contributes to the conservation of this species. A total of 1,013 SNP markers were identified, of which 84 loci showed outlier behavior and may reflect responses to natural selection. Overall, the level of genomic diversity was compatible with the biological aspects of this species. The inbreeding coefficient (f) was negative for all populations, indicating excess heterozygotes. Most genetic variations occurred within populations (77.26%), and a positive correlation existed between genetic and geographic distances. The population structure evaluated through discriminant analysis of principal components (DAPC) revealed low genetic differentiation between populations. The results highlight the need for efforts to conserve C. prunifera as well as its distribution range to preserve its global genetic diversity and evolutionary potential.