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Discriminant Analysis of Principal Components. Density plot considering the first principal component of the 38 Croton tetradenius plants that were evaluated in Sergipe, Brazil. Each peak represents the individuals in a municipality, as follows: Red: Porto da Folha; Green: Poço Redondo; Blue: Lagarto; Purple: Pacatuba
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Croton tetradenius Baill. is an aromatic plant species whose essential oils have high economic importance. Its incorporation into Active Germplasm Banks is essential for conservation and future use, yet its genetic variability must be observed. The objective of this study was to estimate the genomic diversity and structure of C. tetradenius in the...
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... This can be confirmed by the highest levels of inbreeding observed for the locations from Roraima and Amazonas. Regarding the estimates of genetic diversity, the locations from the Amazon biome presented low values of diversity, similar to data obtained for an aromatic shrub plant species occurring widely in Northeast Brazil, Croton tetradenius (H O = 0.072; H E = 0.086) assessed with SNP markers [27], agreeing with our initial hypothesis. The Cha- padinha location from the Cerrado biome, on the other hand, presented higher genetic diversity indexes, similar to those obtained for mango trees (H O = 0.183-0.215; ...
Platonia insignis is a fruit tree native to Brazil of increasing economic importance, with its pulp trading among the highest market values. This study aimed to evaluate the structure and genomic diversity of P. insignis (bacurizeiro) accessions from six locations in the Brazilian States of Roraima, Amazonas, Pará (Amazon biome), and Maranhão (Cerrado biome). A total of 2031 SNP markers were obtained using genotyping-by-sequencing (GBS), from which 625 outlier SNPs were identified. High genetic structure was observed, with most of the genetic variability (59%) concentrated among locations, mainly between biomes (Amazon and Cerrado). A positive and significant correlation (r = 0.85; p < 0.005) was detected between genetic and geographic distances, indicating isolation by distance. The highest genetic diversity was observed for the location in the Cerrado biome (HE = 0.1746; HO = 0.2078). The locations in the Amazon biome showed low genetic diversity indexes with significant levels of inbreeding. The advance of urban areas, events of burning, and expansion of agricultural activities are most probably the main factors for the genetic diversity reduction of P. insignis. Approaches to functional analysis showed that most of the outlier loci found may be related to genes involved in cellular and metabolic processes.
... Currently, one of the most used molecular markers to estimate plant diversity and genetic structure are the single-nucleotide polymorphism (SNP) markers (Alves-Pereira et al. 2019). These markers allow identifying the variation of a single nucleotide in an automated way and at a moderate cost, thus enabling the analysis of genetic diversity on a genomic scale (Brito et al. 2021). ...
Chaco is the largest remaining continuous tropical dry forest on the American continent and has one of the highest deforestation rates in the world. Copernicia alba Morong ex Morong & Britton is a typical species of Chaco forests and has been subjected to predatory extraction in its areas of occurrence. This study aims to assess the diversity and genetic structure of C. alba populations in the Brazilian Chaco region. By employing single-nucleotide polymorphism (SNP) markers, this research seeks to generate insights to guide effective management and conservation strategies for this palm tree. To obtain the SNPs, genomic libraries were developed using the genotyping-by-sequencing (GBS) approach. Populations showed considerable levels of genetic diversity (HE). The inbreeding coefficient (f) was negative for all populations, indicating an excess of heterozygotes. Additionally, clear signs of genetic flow were observed, indicating low to moderate genetic differentiation between populations. We detected 65 outlier SNPs associated mainly with general metabolic processes. Despite these results, conservation efforts should be adopted to avoid the loss of genetic variation. Conservation in situ or ex situ is pointed out as an important strategy for the preservation of C. alba populations, prioritizing sampling throughout the distribution area. The information obtained in this study will contribute to the conservation of genetic diversity, increasing the chances of the natural populations of C. alba persisting over time.
... The mating system and life cycle shape genetic diversity in plants in such a way that a deficit of heterozygotes may be due to the loss of randomness in the crosses of a population (Glémin et al. 2006), and breeding among closely related individuals from the same population and self-fertilization can play a very important role in inbreeding (Abu Awad and Billiard 2017). As far as we know, there are no previous reports of genetic diversity of SNPs from species that are closely related to cirio, so the values reported here will be particularly use- (Borrell et al. 2018;Blyth et al. 2020;Jia et al. 2020;Stojanova et al. 2020;Brito et al. 2021). ...
An important research goal for plant species of conservation concern is to identify and spatially delimit genetically distinct populations and understand their degree of connectivity. Here, we evaluated structure, diversity, and genetic connectivity using neutral genetic markers in cirio (Fouquieria columnaris), a unique succulent tree restricted to the northwestern Sonoran Desert in Mexico. Using genome-wide sequencing, 1,137 biallelic single nucleotide polymorphisms (SNPs) were identified in 55 individuals from 7 sites (6 on the Baja California Peninsula, 1 in coastal Sonora), belonging to populations that were previously shown to constitute distinct lineages according to chloroplast DNA. There was relatively minor cytonuclear discordance, which was attributed to the northernmost peninsular site; when that site was removed, there was concordance between chloroplast and nuclear DNA matrices. We recognize four genetic groups as demographically independent units. Pairwise comparisons of nuclear genetic differentiation between localities (Jost’s D) ranged from 0.035 to 0.008. We detected positive inbreeding values and diversity patterns associated with historical bottlenecks and habitat fragmentation. There was asymmetric gene flow from the small Sonoran mainland population to the much larger northern peninsular population, an unexpected result that may be influenced by pollinators. The most strongly differentiated populations based on SNPs were Sierra Bacha on the Sonoran coast with the southernmost peninsular site, Tres Vírgenes. Within the Peninsula there was a statistically significant pattern of isolation by distance. Our findings provide a detailed view of the genetic structure and connectivity of this emblematic tree that may help guide conservation actions.
... Knowledge of genetic diversity and structure is important for the conservation and effective use of genetic resources (Huang et al. 2016;Brito et al. 2021). This is the first study to use SNP markers obtained by the GBS method to assess the diversity and genetic structure of P. platycephala populations in Northeast Brazil. ...
... According to Lyons and Lauring (2017), selection disfavors substitution rates by transversions, as they are less likely to conserve the biochemical properties of the original amino acid; thus, transversions are considerably more harmful than transitions. Thus, if the rate of transitions is high, they are more likely to be conservative and will occur more frequently simply because of a transition mutation bias (Brito et al. 2021). Genetic diversity in plant species is strongly affected by historic and demographic factors, population size, and reproductive system (Crispim et al. 2021). ...
Parkia platycephala Benth. is a native species with high nutritional and ecological potential that is used in forest recovery and restoration. However, studies on the diversity and population genetic structure of this species are limited. Therefore, 5036 nucleotide polymorphism loci (resulting from genotyping by sequencing) were used to investigate the diversity and population structure of P. platycephala in two localities of Northeast Brazil. One of the evaluated areas comprised the Conservation Unit, Sete Cidades National Park, the other location consisted of the trees located around the park. A high level of genetic diversity was found for both populations, with similar values of expected heterozygosity (HE = 0.29), showing the existence of a considerable level of genetic variation. Analysis of molecular variance revealed that most of the diversity (99.06%) was distributed within populations. The results of the genetic structuring indicated little divergence between the plants, suggesting that the evaluated groups could be considered a single population. Few loci under selection (outliers) were identified; thus, no significant evidence of adaptive divergence was found. The results indicate that P. platycephala trees inside and outside the Conservation Unit maintain high genetic diversity, which has potential for use in breeding programs and for the production of seedlings for forest restoration. Furthermore, the importance of the Sete Cidades National Park for in situ conservation of this species is highlighted.
... The SNPs result from a specific modification due to interchange of a single base (Grover and Sharma 2016). As they are abundant and widely distributed in the genomes (Ganal et al. 2009;Kethom et al. 2019), they allow more accurate estimation of genetic diversity in natural populations (Chung et al. 2017;Nadeem et al. 2018;Kethom et al. 2019), even in non-model species, such as medicinal and aromatic plants (Wang et al. 2016;Otto et al. 2017;Marakli 2018;Do et al. 2019;Brito et al. 2021). ...
... The transition bias frequently occurs in plants (Stern and Orgogozo 2008), as was observed in the present study and for the species Jatropha curcas L. (Gupta et al. 2012) and Croton tetradenius Baill. (Brito et al. 2021). Two sources of origin have been reported to explain the transition bias. ...
... Similar results were observed for the species C. urucarana (21.72%; Costa et al. 2020) and C. tetradenius (5%; Brito et al. 2021), in which lower genetic variation was observed among the populations than within the populations. The value observed for the F ST statistic (0.071) indicates that the populations studied have moderate genetic differentiation (Silva-Júnior et al. 2020apud Wright 1978Leviyang and Hamilton 2011). ...
Croton grewioides Baill. is a medicinal and aromatic species with proven biological activity. Considering the economic potential of the species, the use of molecular markers for genetic diversity studies is of utmost importance to develop viable strategies for its management, conservation, and use. Thus, the aim of this study was to evaluate the genetic diversity and structure of natural populations of C. grewioides using SNP markers, and select genotypes to compose the species collection in an Active Germplasm Bank. Genotypes were sampled from two populations, the first in the state of Sergipe (SE) and the second in the state of Bahia (BA). A total of 6,942 high quality SNPs were identified through genotyping-by-sequencing (GBS). Genetic diversity was estimated by observed and expected heterozygosities (Ho: 0.211 < He: 0.225), the Shannon Index (I: 0.357), inbreeding coefficient (f: 0.056), and number of exclusive alleles (BA: 1296 and SE: 799). Analysis of molecular variance (AMOVA) showed greater genetic variation within the populations. The multivariate analyses performed (Discriminant analysis of principal components—DAPC; bayesiana—Structure; Principal Components Analysis—PCA; and the dendrogram based on Rogers’ genetic distance) allowed separation of the genotypes according to the population of origin. Thirteen (13) genotypes from the SE population and 17 from the BA population were selected to compose the species collection. The selection of genotypes coming from the two populations studied is fundamental for effective conservation of the genetic variability detected.
