Biology subjects

Colombo, C. A.

Publications and source records attributed to Colombo, C. A..

3 recordsLinked to original sources

bioRxiv2025

A Transcriptomic Atlas of Macauba Palm Reveals Organ-Specific Gene Expression and Stress-Related Pathways

The macauba palm (Acrocomia aculeata) is an emerging oilseed species with promising applications in biodiesel production, as well as in food and cosmetic industries. Native to the Neotropical, it is incipiently domesticated and distributed across diverse environments and edaphoclimatic conditions. However, genomic studies of macauba are limited due to the scarcity of publicly available sequence data, as it is considered a non-model plant. In this study, we present an exploratory analysis of a transcriptome dataset comprising seven organs (roots, bulbs, male and female flowers, leaves, leaf sheath, and fruits). A total of 22,703 transcripts were assembled into a single reference dataset. Of these, 9,729 transcripts (42.85%) were annotated using KEGG orthology. Gene expression profiling revealed 306, 32, 41, 159, 158 and 916 organ-specific transcripts in leaves, leaf sheaves, bulbs, flowers, fruit and root, respectively. Comparative analysis with African oil palm (Elaeis guineensis) and date palm (Phoenix dactylifera) revealed 55 gene families exclusive to macauba palm. In addition, 221 transcripts related to drought stress were identified, grouped into 112 families. Root libraries revealed 7,091 fungal transcripts - approximately 3.9% of all reads - mainly derived from arbuscular mycorrhizal fungi (AMF) Rhizophagus spp. These findings highlight the central role of signal transduction pathways in response to environmental stresses in macauba palm. The transcriptome dataset generated in this study provides a valuable genomic resource for future genotype-phenotype investigations in macauba palm. Furthermore, the presence of AMF-associated transcripts suggests a potentially important role for these symbiotic fungi in macauba palm growth and development.

plant biology↗

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↗

bioRxiv2024

Genome-Wide Association Insights into the Genomic Regions Controlling Oil Production Traits in Acrocomia aculeata (neotropical native palm)

Macauba (Acrocomia aculeata) is a non-domesticated neotropical palm that has been attracting attention for economical use due to its great potential for oil production comparable to the commercially used oil palm (Elaeis guineenses). The discovery of associations between quantitative trait loci and economically important traits represents an advance toward macauba domestication. Pursuing this advance, this study performs single-trait and multi-trait GWAS models to identify candidate genes related to oil production traits in macauba. We randomly selected 201 palms from a natural population and analysed 13 traits related to fruit production, processing, and oil content. Genotyping was performed following the genotyping-by- sequencing protocol. SNP calling was performed using three strategies since macauba doesnt have a reference genome: using i) de novo pipeline, ii) Elaeis guineenses Jacq. reference genome, and iii) transcriptome of Acrocomia aculeata. Single-trait analysis was fitted using five models from GAPIT, while multi-trait analysis was fitted using a multivariate stepwise method implemented in the software TASSEL. Multi-trait analyses were conducted in all pairwise trait combinations. Results showed statistically significant differences in all phenotypic traits studied, and heritability values ranged from 0.63 to 0.95. Gene annotation detected 15 candidate genes in seven traits in the single-trait GWAS and four candidate genes in 10 trait combinations in the multi-trait GWAS. We provide new insights on genomic regions that mapped candidate genes involved in macauba oil production phenotypes. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in macauba for both domestication and pre-breeding purposes.

genetics↗