Vianna, S. A. | Search bioRxiv

bioRxiv2024

Genetic variations associated with adaptation processes in Acrocomia palms: A comparative study across the Neotropic for future crop improvement

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 Acrocomia, 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 A. aculeata, A. totai, and A. intumescens across the Neotropic. Our results reveal two major gene pools in A. aculeata, 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. A. totai presented a pronounced genetic structure, with SNPs under selection indicating a recent diversification driven by climatic and geological factors, especially in the Pantanal biome. A. intumescens displays genetic structuring shaped by the endemic process of biogeographic barriers within the Caatinga biome, with potential shared ancestry with A. aculeata. 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 Acrocomia 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 Acrocomia in sustainable development and renewable energy production.

genomics↗

bioRxiv2020

Whole-genome SNP analysis elucidates the genetic population structure and diversity of Acrocomia species

Acrocomia (Arecaceae) is a genus widely distributed in tropical and subtropical America that has been achieving economic interest due to the great potential of oil production of some of its species. In particular A. aculeata, due to its vocation to supply oil with the same productive capacity as the oil palm even in areas with water deficit. Although eight species are recognized in the genus, the taxonomic classification based on morphology and geographic distribution is still controversial. Knowledge about the genetic diversity and population structure of the species is limited, which has limited the understanding of the genetic relationships and the orientation of management, conservation, and genetic improvement activities of species of the genus. In the present study, we analyzed the genomic diversity and population structure of seven species of Acrocomia including 117 samples of A. aculeata covering a wide geographical area of occurrence, using single nucleotide Polymorphism (SNP) markers originated from Genotyping By Sequencing (GBS). The genetic structure of the Acrocomia species were partially congruent with the current taxonomic classification based on morphological characters, recovering the separation of the species A. aculeata, A. totai, A. crispa and A. intumescens as distinct taxonomic groups. However, the species A. media was attributed to the cluster of A. aculeata while A. hassleri and A. glauscescens were grouped together with A. totai. The species that showed the highest and lowest genetic diversity were A. totai and A. media, respectively. When analyzed separately, the species A. aculeata showed a strong genetic structure, forming two genetic groups, the first represented mainly by genotypes from Brazil and the second by accessions from Central and North American countries. Greater genetic diversity was found in Brazil when compared to the other countries. Our results on the genetic diversity of the genus are unprecedented, as is also establishes new insights on the genomic relationships between Acrocomia species. It is also the first study to provide a more global view of the genomic diversity of A. aculeata. We also highlight the applicability of genomic data as a reference for future studies on genetic diversity, taxonomy, evolution and phylogeny of the Acrocomia genus, as well as to support strategies for the conservation, exploration and breeding of Acrocomia species and in particular A. aculeata.

genetics↗