Biology subjects

Alves-Pereira, A.

Publications and source records attributed to Alves-Pereira, A..

9 recordsLinked to original sources

bioRxiv2024

Sample Size Impact (SaSii): an R script for estimating optimal sample sizes in population genetics and population genomics studies

Obtaining large sample sizes for genetic studies can be challenging, time-consuming, and expensive. However, small sample sizes may generate biased or imprecise results. Many studies have suggested the minimum sample size necessary to obtain robust and reliable results, but it is not possible to define one ideal minimum sample size that fits all studies. Here, we aim to present SaSii (Sample Size Impact), a R script to help researchers to define minimum sample size and to indicate minimum sample size patterns for some taxa groups. The patterns were obtained by analyzing previously published datasets with SaSii and can be used as a starting point for the sample design of population genetics and genomic studies. Our results showed that it is possible to estimate an adequate sample size that accurately represents the real population and does not require the scientist to take time to write any program code, extract and sequence samples or use population genetics programs, making it easier to gather this information. We also confirmed that sample sizes of five to twenty-five for SNP and fifteen to thirty for SSR can be used for most plant species, giving a better direction for new studies.

bioinformatics↗

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

Molecular attributes of the tropical tree Avicennia schaueriana involved in the response and tolerance to low temperatures

Mangroves are coastal ecosystems of great socioenvironmental importance that are highly threatened by human activities. Mangrove trees live under harsh environmental conditions, which makes them sensitive to extreme weather events, particularly freezing events. Such events are unpredictable and have catastrophic consequences for mangrove trees; therefore, understanding and anticipating the impacts of such events are essential for directing future mitigation measures. Freezing cold currently limits the distribution of mangroves to tropical and subtropical latitudes worldwide. Mangrove trees are seriously affected by freezing conditions and suffer severe metabolic fluctuations due to photosystem and cellular structure damage. However, land plants more broadly have developed sophisticated mechanisms of resistance to freezing during their evolution, and the central molecular mechanisms involved in this process are consistent. However, the known information is restricted to models of herbaceous plants, such as Arabidopsis thaliana, that are native to temperate habitats, and there is a research gap regarding tropical trees such as mangroves. This work aimed to improve the understanding of the molecular aspects of the response and tolerance to freezing in mangrove trees using Avicennia schaueriana as a model. This species occurs within the colder range limits of South American mangroves and shows evidence of the existence of two functional groups that are locally adapted to the equatorial (EQ) and subtropical (ST) portions of the Brazilian coast. We investigated the transcriptional profiles of seedlings from both functional groups under freezing shock (-4{degrees}C) in a time series. We analyzed transcriptomic data by combining differential expression, coexpression network and protein interaction data. Our results allowed us to describe the profile of the molecular response of A. schaueriana to freezing and the divergence in the behavior of the EQ and ST functional groups. In EQ plants, the response strongly depended on the action of abscisic acid (ABA) and stress signals throughout the experiment. Notably, ABA negatively affects plant growth and promotes the accumulation of carotenoids, anthocyanins and lipids through chlorophyll degradation. On the other hand, in the ST, there were fewer hormones active in the process of primary growth maintenance and metabolic normalization. The accumulation of substances is mainly based on sucrose, anthocyanin and lipid levels, and lipid synthesis is not dependent on chlorophyll degradation. Based on these results, we hypothesize that susceptibility to freezing damage is greater in EQ mangroves than in ST mangroves. Therefore, we recommend that this fact be considered when managing this species, especially at higher latitudes, which are more prone to lower temperatures and extreme freezing events.

plant biology↗

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↗

bioRxiv2022

Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleraceae and E. precatoria) from different Brazilian biomes

The Brazilian palm fruits and hearts-of-palm of Euterpe edulis, E. oleracea and E. precatoria are an important source for agro-industrial production, but overexploitation requires conservation strategies to maintain genetic diversity. Chloroplast genomes have conserved sequences, which are useful to explore evolutionary questions. Besides the plastid DNA, genome skimming allows the identification of other genomic resources, such as single nucleotide polymorphisms (SNPs), providing information about the genetic diversity of species. We sequenced the chloroplast genome and identified gene content in the three Euterpe species. We performed comparative analyses, described the polymorphisms among the chloroplast genome sequences (repeats, indels and SNPs) and performed a phylogenomic inference based on 55 palm species chloroplast genomes. Finally, using the remaining data from genome skimming, the nuclear and mitochondrial reads, we identified SNPs and estimated the genetic diversity among these Euterpe species. The Euterpe chloroplast genomes varied from 159,232 to 159,275 bp and presented a conserved quadripartite structure with high synteny with other palms. In a pairwise comparison, we found a greater number of insertions/deletions (indels = 93 and 103) and SNPs (284 and 254) between E. edulis/E. oleracea and E. edulis/E. precatoria when compared to E. oleracea/E. precatoria (58 indels and 114 SNPs). Also, the phylogeny indicated a closer relationship between E. oleracea/E. precatoria. The nuclear and mitochondrial genome analyses identified 1,077 SNPs and high divergence among species (FST = 0.77), especially between E. edulis and E. precatoria (FST = 0.86). These results showed that, despite the few structural differences among the chloroplast genomes of these Euterpe palms, a differentiation between E. edulis and the other Euterpe species can be identified by point mutations. This study not only brings new knowledge about the evolution of Euterpe chloroplast genomes, but also these new resources open the way for future phylogenomic inferences and comparative analyses within Arecaceae.

evolutionary biology↗

bioRxiv2021

Selective signatures and high genome-wide diversity in traditional Brazilian manioc (Manihot esculenta Crantz) varieties

Knowledge about crops genetic diversity is essential to promote effective use and conservation of their genetic resources, because genetic diversity enables farmers to adapt their crops to specific needs and is the raw material for breeding efforts. Currently, manioc (Manihot esculenta ssp. esculenta) is one of the most important food crops in the world and has the potential to help achieve food security in the context of on-going climate changes. In this study we assessed the patterns of genome-wide diversity of traditional Brazilian manioc varieties conserved in the gene bank of the Luiz de Queiroz College of Agriculture, University of Sao Paulo. We used single nucleotide polymorphisms to evaluate the organization of genetic diversity and to identify selective signatures contrasting varieties from different biomes with samples of maniocs wild relative M. esculenta ssp. flabellifolia. We identified signatures of selection putatively associated with resistance genes, plant development and response to abiotic stresses. This presumed adaptive variation might have been important for the initial domestication and for the crops diversification in response to cultivation in different environments. The neutral variation revealed high levels of genetic diversity within groups of varieties from different biomes and low to moderate genetic divergence among biomes. These results reflect the complexity of maniocs biology and its evolutionary dynamics under traditional cultivation. Our results exemplify how the smallholder practices contribute to the conservation of maniocs genetic resources, maintaining variation of potential adaptive significance and high levels of neutral genetic diversity.

genetics↗

bioRxiv2021

Filling gaps: fishing, genetics, and conservation of groupers, especially the comb grouper (badejo) (Mycteroperca acutirostris), in SE Brazil (2013-2020)

There are large gaps in our knowledge of the biology of important fish consumed by people in tropical countries, which makes conservation difficult. Small-scale fisheries are difficult to study and regulate, especially in countries with no systematic species monitoring. It is even more difficult to estimate the influence of these fisheries on vulnerable fish species and to diagnose possible damage to local fish populations. In this study, 490 individuals of badejo, or comb grouper (Mycteropeca acutirostris), were observed at the Posto 6 fishery in Copacabana, Rio de Janeiro, for the periods of 2013-2014 and 2018-2020. A pattern of decreasing catches was observed for comb grouper. Therefore, provided that the fishing gear and the number of fish have remained the same, the apparent decrease in comb grouper needs to be further investigated. The results provide information regarding the reproduction of comb grouper, with major spawning season around spring (September-December) and additional spawning during April in SE Brazil. Samples from 96 groupers along the coast of Brazil were obtained, and genetic analyses were conducted. The genetic information obtained for grouper species enabled us to determine the relative genetic proximity of M. acutirostris and Mycteroperca bonaci and to obtain information that can be useful for aquaculture and conservation.

ecology↗

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↗

bioRxiv2019

High-resolution Linkage Map with Allele Dosage Allows the Identification of an Apomixis Region and Complex Traits in Guinea Grass (Megathyrsus maximus)

Forage grasses are mainly used in animal feed to fatten cattle and dairy herds. Among tropical forage crops that reproduce by seeds, guinea grass (Megathyrsus maximus) is considered one of the most productive. This species has several genomic complexities, such as autotetraploidy and apomixis, due to the process of domestication. Consequently, approaches that relate phenotypic and genotypic data are incipient. In this context, we built a linkage map with allele dosage and generated novel information about the genetic architecture of traits that are important for the breeding of M. maximus. From a full-sib progeny, a linkage map containing 858 single nucleotide polymorphism (SNP) markers with allele dosage information expected for an autotetraploid was obtained. The high genetic variability of the progeny allowed us to map ten quantitative trait loci (QTLs) related to agronomic traits, such as regrowth capacity and total dry matter, and 36 QTLs related to nutritional quality, which were distributed among all homology groups (HGs). Various overlapping regions associated with the quantitative traits suggested QTL hotspots. In addition, we were able to map one locus that controls apospory (apo-locus) in HG II. A total of 55 different gene families involved in cellular metabolism and plant growth were identified from markers adjacent to the QTLs and apomixis locus by using the Panicum virgatum genome as a reference in comparisons with the genomes of Arabidopsis thaliana and Oryza sativa. Our results provide a better understanding of the genetic basis of reproduction by apomixis and traits important for breeding programs that considerably influence animal productivity as well as the quality of meat and milk.

plant biology↗