Genome-wide SNP analysis to assess the genetic population structure and diversity of Acrocomia species

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, and 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 present SaSii (Sample Size Impact), an R script to help researchers define the minimum sample size. Based on empirical and simulated data analysis using SaSii, we present patterns and suggest minimum sample sizes for experiment design. The patterns were obtained by analyzing previously published genotype 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 without requiring the scientist to write any program code, extract and sequence samples, or use population genetics programs, thus simplifying the process. We also confirmed that the minimum sample sizes for SNP (single-nucleotide polymorphism) analysis are usually smaller than for SSR (simple sequence repeat) analysis and discussed other patterns observed from empirical plant and animal datasets.

Genome-wide association insights into the genomic regions controlling vegetative and oil production traits in Acrocomia aculeata

BACKGROUND

Macauba (Acrocomia aculeata) is a non-domesticated neotropical palm that has been attracting attention for economic use due to its great potential for oil production comparable to the commercially used oil palm (Elaeis guineensis). The discovery of associations between quantitative trait loci and economically important traits represents an advance toward understanding its genetic architecture and can contribute to accelerating macauba domestication. Pursuing this advance, this study performs single-trait and multi-trait GWAS models to identify candidate genes associated with vegetative and oil production traits in macauba. Eighteen phenotypic traits were evaluated from 201 palms within a native population. Genotyping was performed with SNP markers, following the protocol of genotyping-by-sequencing. Given that macauba lacks a reference genome, SNP calling was performed using three different strategies: using i) de novo sequencing, ii) the Elaeis guineenses Jacq. reference genome and iii) the macauba transcriptome sequences. After quality control, we identified a total of 27,410 SNPs in 153 individuals for the de novo genotypic dataset, 10,444 SNPs in 158 individuals using the oil palm genotypic dataset, and 4,329 SNPs in 167 individuals using the transcriptome genotypic dataset. The GWAS analysis was then performed on these three genotypic datasets.

RESULTS

Statistical phenotypic analyses revealed significant differences across all studied traits, with heritability values ranging from 63 to 95%. This indicates that the population contains promising genotypes for selection and the initiation of breeding programs. Genetic correlations between the 18 traits ranged from -0.47 to 0.99. The total number of significant SNPs in the single-trait and multi-trait GWAS was 92 and 6 using the de novo genotypic dataset, 19 and 11 using the oil palm genotypic dataset, and 1 and 2 using the transcriptome genotypic dataset, respectively. Gene annotation identified 12 candidate genes in the single-trait GWAS and four in the multi-trait GWAS, across the 18 phenotypic traits studied, in the three genotypic datasets. Gene mapping of the macauba candidate genes revealed similarities with Elaeis guineensis and Phoenix dactylifera. The candidate genes detected are responsible for metal ion binding and transport, protein transportation, DNA repair, and other cell regulation biological processes.

CONCLUSIONS

We provide new insights into genomic regions that map candidate genes associated with vegetative and oil production traits in macauba. These potential candidate genes require confirmation through targeted functional analyses in the future, and multi-trait associations need to be scrutinized to investigate the presence of pleiotropic or linked genes. Markers linked to traits of interest could serve as valuable resources for the development of marker-assisted selection in macauba for its domestication and pre-breeding.

Development of microsatellite markers and evaluation of the genetic diversity of the edible sea anemone Paracondylactissinensis (Cnidaria, Anthozoa) in China

Paracondylactissinensis Carlgren, 1934 is a sea anemone with economic value in China. The wild population of P.sinensis has been shrinking due to overfishing and environmental pollution, which have caused price instability. In winter, the price of P.sinensis can reach 25 USD per kilogram. Up to now, there are no genetic markers developed for P.sinensis, preventing a further exploration of their population genetic diversity. In this study, the full-length transcriptome of P.sinensis was sequenced and microsatellite DNA markers (simple sequence repeats [SSRs]) were developed from those transcripts. A total of 52 primer pairs, which can amplify specific polymorphic bands in PCR experiments, were designed for the SSR markers. Genetic diversity and population genetics were analysed for P.sinensis populations collected from the coasts of Taizhou and Rizhao using six microsatellite DNA loci. While inbreeding was detected in both populations (Fis > 0), the overall number of alleles (Na = 11.3) and bottleneck analysis suggested that the genetic diversity of P.sinensis has not been greatly impacted. Clustering analyses using STRUCTURE, principal coordinate analysis and unweighted pair group method with arithmetic mean tree revealed that the Taizhou population diverged from the Rizhao population; however, the genetic differentiation between the populations was moderate. Human-mediated commercial activities may be the principal reasons for the gene flow between the populations. Our study provides the first evaluation of the genetic resources of wild P.sinensis populations in China, which can serve as a useful reference for future comparative studies on population genetics and may guide policy-makers in initiating strategies for germplasm conservation and artificial breeding.

Training set optimization is a feasible alternative for perennial orphan crop domestication and germplasm management: an Acrocomia aculeata example

Orphan perennial native species are gaining importance as sustainability in agriculture becomes crucial to mitigate climate change. Nevertheless, issues related to the undomesticated status and lack of improved germplasm impede the evolution of formal agricultural initiatives. Acrocomia aculeata - a neotropical palm with potential for oil production - is an example. Breeding efforts can aid the species to reach its full potential and increase market competitiveness. Here, we present genomic information and training set optimization as alternatives to boost orphan perennial native species breeding using Acrocomia aculeata as an example. Furthermore, we compared three SNP calling methods and, for the first time, presented the prediction accuracies of three yield-related traits. We collected data for two years from 201 wild individuals. These trees were genotyped, and three references were used for SNP calling: the oil palm genome, de novo sequencing, and the A. aculeata transcriptome. The traits analyzed were fruit dry mass (FDM), pulp dry mass (PDM), and pulp oil content (OC). We compared the predictive ability of GBLUP and BayesB models in cross- and real validation procedures. Afterwards, we tested several optimization criteria regarding consistency and the ability to provide the optimized training set that yielded less risk in both targeted and untargeted scenarios. Using the oil palm genome as a reference and GBLUP models had better results for the genomic prediction of FDM, OC, and PDM (prediction accuracies of 0.46, 0.45, and 0.39, respectively). Using the criteria PEV, r-score and core collection methodology provides risk-averse decisions. Training set optimization is an alternative to improve decision-making while leveraging genomic information as a cost-saving tool to accelerate plant domestication and breeding. The optimized training set can be used as a reference for the characterization of native species populations, aiding in decisions involving germplasm collection and construction of breeding populations.

Genotyping-by-sequencing informs conservation of Andean palms sources of non-timber forest products

Conservation and sustainable management of lineages providing non-timber forest products are imperative under the current global biodiversity loss. Most non-timber forest species, however, lack genomic studies that characterize their intraspecific variation and evolutionary history, which inform species' conservation practices. Contrary to many lineages in the Andean biodiversity hotspot that exhibit high diversification, the genus Parajubaea (Arecaceae) has only three species despite the genus' origin 22 million years ago. Two of the three palm species, P. torallyi and P. sunkha, are non-timber forest species endemic to the Andes of Bolivia and are listed as IUCN endangered. The third species, P. cocoides, is a vulnerable species with unknown wild populations. We investigated the evolutionary relationships of Parajubaea species and the genetic diversity and structure of wild Bolivian populations. Sequencing of five low-copy nuclear genes (3753 bp) challenged the hypothesis that P. cocoides is a cultigen that originated from the wild Bolivian species. We further obtained up to 15,134 de novo single-nucleotide polymorphism markers by genotyping-by-sequencing of 194 wild Parajubaea individuals. Our total DNA sequencing effort rejected the taxonomic separation of the two Bolivian species. As expected for narrow endemic species, we observed low genetic diversity, but no inbreeding signal. We found three genetic clusters shaped by geographic distance, which we use to propose three management units. Different percentages of missing genotypic data did not impact the genetic structure of populations. We use the management units to recommend in situ conservation by creating new protected areas, and ex situ conservation through seed collection.

Biometric variability of inflorescence and flower traits among ex situ accessions of the neotropical oilseed palm Acrocomia Mart

The oilseed palm genus Acrocomia is suitable for sustainable oil production in South America. The high phenotypic diversity of wild populations poses a challenge for the delimitation of the genus. Comparing the inflorescence architecture, a first-order panicle, and staminate and pistillate flower traits could be a valuable tool in resolving the taxonomic disarray. Thus, this study aims to characterize the differences in the inflorescence architecture and floral structures of three common and economically significant Acrocomia species: A. aculeata, A. totai, and A. intumescens. Biometric traits of the inflorescence architecture and floral structures of various Acrocomia accessions in an ex situ germplasm collection in Brazil were assessed. The unweighted pair group method with arithmetic mean (UPGMA) cluster analysis based on the Gower distance was used to measure dissimilarities between the individual plants of the accessions. To our best knowledge, this study provides the first evidence of the presence of second-order rachillae in the genus Acrocomia. Evaluated traits showed a high level of variation within and between accessions, emphasizing the phenotypic diversity of the genus. The accessions of A. totai were distinguishable from those of the other two species by their inflorescence architecture and flower traits. The dissimilarities between A. aculeata and A. intumescens were not sufficient to differentiate both. In conclusion, the quantitative assessment of inflorescence and floral traits is a valuable tool for taxonomic resolution of the genus.

Structure and emulsifying properties of unprecedent glucomannan oligo- and polysaccharides from Amazonia Acrocomia aculeata palm fruit

Acrocomia aculeata fruit pulp contains oil (4.1-82.8 % fresh matter) and carbohydrates (6.6-98.0 % fresh matter). To date, only the oil fraction is valorized because very little is known about the nature of carbohydrates. This study explores new ways of adding value to this pulp by developing simple and efficient extraction processes for its carbohydrate components and characterizing their structure and physicochemical properties over two harvest periods. A water-soluble monosaccharide fraction F1 (solubility limit (SL): 98.5-99.3 g/L) (yield: 21 % dry pulp (DP)), a water-soluble polysaccharide fraction F2 (SL: 93.3-95.3 g/L) (yield: 26 % DP) and two additional water-insoluble polysaccharide fractions F3 and F4 (SL: <8 g/L) (yields: 10 and 19 % DP, respectively) were isolated. NMR structural characterizations of fraction F2 revealed it to be a linear glucomannan with β-(1 → 4) osidic linkages between d-Manp and d-Glcp residues. F2 is unique for its d-Manp/d-Glcp ratio of 3:1 and the position of its acetyl group (13-14 %, C-2 d-Manp). Finally, the polysaccharide showed a molecular weight (Mw) variation ranging from 8.2 × 104 to 1.1 × 103 Da over the two harvest periods, with remarkable emulsifying properties associated with a low Mw of F2 (stability >6 months, 1 % w/v in a water-in-oil emulsion).

Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns

The Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food and energy industries; Bactris gasipaes, important for palm heart; Copernicia alba and C. prunifera, worldwide known for wax utilization; and Syagrus romanzoffiana, of great ornamental potential. Copernicia spp. showed the largest chloroplast genomes (C. prunifera: 157,323 bp and C. alba: 157,192 bp), while S. romanzoffiana and B. gasipaes var. gasipaes presented the smallest (155,078 bp and 155,604 bp). Structurally, great synteny was detected among palms. Conservation was also observed in the distribution of single sequence repeats (SSR). Copernicia spp. presented less dispersed repeats, without occurrence in the small single copy (SSC). All RNA editing sites were C (cytidine) to U (uridine) conversions. Overall, closely phylogenetically related species shared more sites. Almost all nodes of the phylogenetic analysis showed a posterior probability (PP) of 1.0, reaffirming the close relationship between Acrocomia species. These results elucidate the conservation among palm chloroplast genomes, but point to subtle structural changes, providing support for the evolutionary dynamics of the Arecaceae family.

Genetic diversity and genome-scale population structure of wild Indian major carp, Labeo catla (Hamilton, 1822), revealed by genotyping-by-sequencing

Labeo catla (catla) is the second most commercially important and widely cultured Indian major carp (IMC). It is indigenous to the Indo-Gangetic riverine system of India and the rivers of Bangladesh, Nepal, Myanmar, and Pakistan. Despite the availability of substantial genomic resources in this important species, detailed information on the genome-scale population structure using SNP markers is yet to be reported. In the present study, the identification of genome-wide single nucleotide polymorphisms (SNPs) and population genomics of catla was undertaken by re-sequencing six catla populations of riverine origin from distinct geographical regions. DNA isolated from 100 samples was used to perform genotyping-by-sequencing (GBS). A published catla genome with 95% genome coverage was used as the reference for mapping reads using BWA software. From a total of 472 million paired-end (150 × 2 bp) raw reads generated in this study, we identified 10,485 high-quality polymorphic SNPs using the STACKS pipeline. Expected heterozygosity (He) across the populations ranged from 0.162 to 0.20, whereas observed heterozygosity (Ho) ranged between 0.053 and 0.06. The nucleotide diversity (π) was the lowest (0.168) in the Ganga population. The within-population variation was found to be higher (95.32%) than the among-population (4.68%) variation. However, genetic differentiation was observed to be low to moderate, with F_st values ranging from 0.020 to 0.084, and the highest between Brahmani and Krishna populations. Bayesian and multivariate techniques were used to further evaluate the population structure and supposed ancestry in the studied populations using the structure and discriminant analysis of principal components (DAPC), respectively. Both analyses revealed the existence of two separate genomic clusters. The maximum number of private alleles was observed in the Ganga population. The findings of this study will contribute to a deeper understanding of the population structure and genetic diversity of wild populations of catla for future research in fish population genomics.

Production of Protein Concentrates from Macauba (Acrocomia aculeata and Acrocomia totai) Kernels by Sieve Fractionation

Macauba palm fruits (Acrocomia aculeata and Acrocomia totai) are emerging as sources of high-quality oils from their pulp and kernels. The protein-rich macauba kernel meal (MKM) left after oil extraction remains undervalued, mainly due to the lack of suitable deoiling parameters and integrated protein recovery methods. Therefore, the present study aimed to produce protein concentrates from MKM using sieve fractionation. The deoiling parameters, comprising pressing, milling, and solvent extraction, were improved in terms of MKM functionality. The combination of hydraulic pressing, milling to 1 mm, and the hexane extraction of A. aculeata kernels resulted in MKM with the highest protein solubility (77.1%), emulsifying activity index (181 m²/g protein), and emulsion stability (149 min). After sieve fractionation (cut size of 62 µm), this meal yielded a protein concentrate with a protein content of 65.6%, representing a 74.1% protein enrichment compared to the initial MKM. This protein concentrate showed a reduced gelling concentration from 8 to 6%, and an increased emulsion stability from 149 to 345 min, in comparison to the MKM before sieving. Therefore, sieve fractionation after improved deoiling allows for the simple, cheap, and environmentally friendly recovery of MKM proteins, highlighting the potential of macauba kernels as a new source of protein.

A Review of an Artificial Intelligence Framework for Identifying the Most Effective Palm Oil Prediction

Machine Learning (ML) offers new precision technologies with intelligent algorithms and robust computation. This technology benefits various agricultural industries, such as the palm oil sector, which possesses one of the most sustainable industries worldwide. Hence, an in-depth analysis was conducted, which is derived from previous research on ML utilisation in the palm oil in-dustry. The study provided a brief overview of widely used features and prediction algorithms and critically analysed current the state of ML-based palm oil prediction. This analysis is extended to the ML application in the palm oil industry and a comparison of related studies. The analysis was predicated on thoroughly examining the advantages and disadvantages of ML-based palm oil prediction and the proper identification of current and future agricultural industry challenges. Potential solutions for palm oil prediction were added to this list. Artificial intelligence and ma-chine vision were used to develop intelligent systems, revolutionising the palm oil industry. Overall, this article provided a framework for future research in the palm oil agricultural industry by highlighting the importance of ML.