Azevedo-Filho, J. | bioRxiv Science

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↗

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↗