Effects of trimer repeats on Psidium guajava L. gene expression and prospection of functional microsatellite markers.

Most research on trinucleotide repeats (TRs) focuses on human diseases, with few on the impact of TR expansions on plant gene expression. This work investigates TRs' effect on global gene expression in Psidium guajava L., a plant species with widespread distribution and significant relevance in the food, pharmacology, and economics sectors. We analyzed TR-containing coding sequences in 1,107 transcripts from 2,256 genes across root, shoot, young leaf, old leaf, and flower bud tissues of the Brazilian guava cultivars Cortibel RM and Paluma. Structural analysis revealed TR sequences with small repeat numbers (5-9) starting with cytosine or guanine or containing these bases. Functional annotation indicated TR-containing genes' involvement in cellular structures and processes (especially cell membranes and signal recognition), stress response, and resistance. Gene expression analysis showed significant variation, with a subset of highly expressed genes in both cultivars. Differential expression highlighted numerous down-regulated genes in Cortibel RM tissues, but not in Paluma, suggesting interplay between tissues and cultivars. Among 72 differentially expressed genes with TRs, 24 form miRNAs, 13 encode transcription factors, and 11 are associated with transposable elements. In addition, a set of 20 SSR-annotated, transcribed, and differentially expressed genes with TRs was selected as phenotypic markers for Psidium guajava and, potentially for closely related species as well.

Exploring the versatility of sesquiterpene biosynthesis in guava plants: a comparative genome-wide analysis of two cultivars.

Psidium guajava L., a fruit crop belonging to the Myrtaceae family, is highly valued for its nutritional and medicinal properties. The family exhibits a diverse chemical profile of essential oils and serves as a valuable resource due to its ecological interactions, adaptability, and dispersal capacity. The Myrtaceae family has been extensively studied for its terpenoids. Genetic studies have focused on foliar terpene yield in species from the Eucalypteae and Melaleucaceae tribes. To understand the evolutionary trends in guava breeding, this study predicted terpene synthase genes (TPS) from different cultivars. Through this analysis, 43 full-length TPS genes were identified, and approximately 77% of them exhibited relative expression in at least one of the five investigated plant tissues (root, leaf, bud, flower, and fruit) of two guava cultivars. We identified intra-species variation in the terpene profile and single nucleotide polymorphisms (SNPs) in twelve TPS genes, resulting in the clustering of 62 genotypes according to their essential oil chemotypes. The high concentration of sesquiterpenes is supported by the higher number of TPS-a genes and their expression. The expansion for TPS sub-families in P. guajava occurred after the expansion of other rosids species. Providing insight into the origin of structural diversification and expansion in each clade of the TPS gene family within Myrtaceae. This study can provide insights into the diversity of genes for specialized metabolites such as terpenes, and their regulation, which can lead to a diverse chemotype of essential oil in different tissues and genotypes. This suggests a mode of enzymatic evolution that could lead to high sesquiterpene production, act as a chemical defense and contribute to the adaptive capacity of this species to different habitats.

Genomic studies of the additive and dominant genetic control on production traits of Euterpe edulis fruits.

In forest genetic improvement programs for non-domesticated species, limited knowledge of kinship can compromise or make the estimation of variance components and genetic parameters of traits of interest unfeasible. We used mixed models and genomics (in the latter, considering additive and non-additive effects) to evaluate the genetic architecture of 12 traits in juçaizeiro for fruit production. A population of 275 genotypes without genetic relationship knowledge was phenotyped over three years and genotyped by whole genome SNP markers. We have verified superiority in the quality of the fits, the prediction accuracy for unbalanced data, and the possibility of unfolding the genetic effects into their additive and non-additive terms in the genomic models. Estimates of the variance components and genetic parameters obtained by the additive models may be overestimated since, when considering the dominance effect in the model, there are substantial reductions in them. The number of bunches, fresh fruit mass of bunch, rachis length, fresh mass of 25 fruits, and amount of pulp were strongly influenced by the dominance effect, showing that genomic models with such effect should be considered for these traits, which may result in selective improvements by being able to return more accurate genomic breeding values. The present study reveals the additive and non-additive genetic control of the evaluated traits and highlights the importance of genomic information-based approaches for populations without knowledge of kinship and experimental design. Our findings underscore the critical role of genomic data in elucidating the genetic control architecture of quantitative traits, thereby providing crucial insights for driving species' genetic improvement.

Genome-wide identification, expression profile and evolutionary relationships of TPS genes in the neotropical fruit tree species Psidium cattleyanum.

Terpenoids are essential for plant growth, development, defense, and adaptation mechanisms. Psidium cattleyanum (Myrtaceae) is a fleshy fruit tree species endemics from Atlantic Forest, known for its pleasant fragrance and sweet taste, attributed to terpenoids in its leaves and fruits. In this study, we conducted genome-wide identification, evolutionary and expression analyses of the terpene synthase gene (TPS) family in P. cattleyanum red guava (var. cattleyanum), and yellow guava (var. lucidum Hort.) morphotypes. We identified 32 full-length TPS in red guava (RedTPS) and 30 in yellow guava (YlwTPS). We showed different expression patterns of TPS paralogous in the two morphotypes, suggesting the existence of distinct gene regulation mechanisms and their influence on the final essential oil content in both morphotypes. Moreover, the oil profile of red guava was dominated by 1,8-cineole and linalool and yellow guava was enriched in α-pinene, coincident in proportion to TPS-b1 genes, which encode enzymes that produce cyclic monoterpenes, suggesting a lineage-specific subfamily expansion of this family. Finally, we identified amino acid residues near the catalytic center and functional areas under positive selection. Our findings provide valuable insights into the terpene biosynthesis in a Neotropical Myrtaceae species and their potential involvement in adaptation mechanisms.

Genomic and epigenomic variation in Psidium species and their outcome under the yield and composition of essential oils.

Diploid and polyploid species derived from the euploid series x = 11 occur in the genus Psidium, as well as intraspecific cytotypes. Euploidy in the genus can alter the gene copy number, resulting in several "omics" variations. We revisited the euploidy, reported genomic (nuclear 2C value, GC%, and copy number of secondary metabolism genes) and epigenomic (5-mC%) differences in Psidium, and related them to essential oil yield and composition. Mean 2C values ranged from 0.90 pg (P. guajava) to 7.40 pg (P. gaudichaudianum). 2C value is intraspecifically varied in P. cattleyanum and P. gaudichaudianum, evidencing cytotypes that can be formed from euploid (non-reduced) and/or aneuploid reproductive cells. GC% ranged from 34.33% (P. guineense) to 48.95% (P. myrtoides), and intraspecific variations occurred even for species without 2C value intraspecific variation. Essential oil yield increased in relation to 2C value and to GC%. We showed that P. guajava (diploid) possesses two and P. guineense (tetraploid) four copies of the one specific TPS gene, as well as eight and sixteen copies respectively of the conserved regions that occur in eight TPS genes. We provide a wide "omics'' characterization of Psidium and show the outcome of the genome and epigenome variation in secondary metabolism.

Development of inclusion complexes of 2-hydroxypropyl-ß-cyclodextrin with Psidium guajava L. essential oil by freeze-drying and kneading methods for application as Aedes aegypti L. larvicide.

Inclusion complexes (ICs) of 2-hydroxypropyl-ß-cyclodextrin with the essential oil (EO) from Seculo XXI cultivar of Psidium guajava were prepared using kneading (KN) and freeze-drying (FD) methods. The resulting ICs clusters have a nanometric size, with a diameter of approximately 80 and 40 nm for KN and FD, respectively. Complexation efficiency was 80.3% and 50.8% for KN and FD methods, respectively. The larvicidal activity of the EO in DMSO on A. aegypti had LC50 and LC90 values of 51.49 and 64.51 µg mL-1, respectively. For the KN method, the toxicity corresponded to 77.54 and 107.29 µg mL-1 for LC50 and LC90, respectively. FD method demonstrated toxicity at concentrations above 600 µg mL-1. Thus, ICs enable the use of EO in breeding sites for A. aegypti, thus being potential products to be commercially exploited.

Patterns of genetic diversity and structure of a threatened palm species (Euterpe edulis Arecaceae) from the Brazilian Atlantic Forest.

The detection of distribution patterns of genetic diversity of plant and animal species has contributed to the understanding of biodiversity and evolutionary history of the Atlantic Forest. We used microsatellite markers to access the genetic diversity and structure of 26 populations and 527 adult individuals of Euterpe edulis, a native palm which is an important food resource for fauna and is intensively exploited due to economic reasons. We found high genetic diversity and inbreeding in all populations analyzed. We report highest rates of inbreeding for this species, which could reflect the anthropic impacts of selective cutting, fragmentation, and change in foraging behavior from pollinators and less availability and mobility of large dispersers. We detected by STRUCTURE, two genetic groups, Northern and Southern, which divide the Brazilian Atlantic Forest geographically. These groups have low genetic admixtures, but we found a region of lineage hybridization in the contact zone with low recent gene flow. Distribution pattern of this species corroborates results from previous studies reporting the Last Glacial Maximum (LGM) have shaped the structuring of the species through movements of forests' expansion and contraction. The STRUCTURE analysis of each group revealed the presence of genetic subgroups with low rates of recurrent gene flow. Southern subgroups have higher rates of admixtures than the Northern subgroups, revealing greater historical connectivity of forests in this region.

Genetic Diversity and Population Structure of Psidium Species from Restinga: A Coastal and Disturbed Ecosystem of the Brazilian Atlantic Forest.

The Atlantic Forest is one of the most threatened biomes in the world. Here, we use a common set of microsatellite markers to assess the genetic diversity and population structure of three species from the genus Psidium (P. guajava, P. macahense, and P. guineense), located in a disturbed environment of the Atlantic Forest, the restinga, in Espírito Santo, Brazil. Psidium guajava populations presented the highest number of alleles (95) followed by P. guineense (81) and P. macahense (68). The genetic variability was high (P. guajava = 0.71; P. guineense = 0.74; P. macahense = 0.63), with greater variation within populations (72 to 84%) than among populations (15 to 27%), reflecting elevated values of genetic differentiation (P. guajava, FST: 0.15; P. macahense, ØST: 0.27; P. guineense, ØST: 0.21). The populations were clustered into two main groups and considered moderately structured. This is the first report of genetic studies and evidence of polyploidy to P. macahense. Our results may provide information that can be used in management and conservation strategies, to preserve the diversity of Psidium populations.

Genetic diversity and structure of landrace accessions, elite lineages and cultivars of common bean estimated with SSR and SNP markers.

Common bean (Phaseolus vulgaris L.) is an important source of proteins, fibers and minerals for humans, being grown mainly in developing countries and representing a source of income for small farmers. In this work, a set of 206 Brazilian landraces and 59 elite lineages and cultivars were genotyped with 23 SSR (Simple Sequence Repeats) and 251 SNPs (Single-Nucleotide Polymorphism) markers. The ideal number of groups, according to STRUCTURE, was K = 2 for both SNPs and SSRs. This could be expected considering the two original gene pools-Andean (AND) and Mesoamerican (MES). The matrices of genetic simple matching dissimilarity for SSRs and SNPs were highly correlated; therefore, the allelic data of the markers was combined and analyzed to understand the genetic relationships of the studied collection. The neighbor-joining analysis considering the genetic distance of simple matching grouped the 265 genotypes into 17 subgroups. The markers SSR and SNP presented high power to discriminate among the genotypes. The ample genetic diversity observed in the work collection makes it a valuable source for the conservation, sustainable management and exploration in breeding programs of the crop.

Phytochemical analysis and effect of the essential oil of Psidium L. species on the initial development and mitotic activity of plants.

The use of allelopathic compounds is an alternative for weeds control, since they present low toxicity when compared with the synthetic herbicides, that may cause several damages, as the contamination of the environment. Our objective was to determine the chemical composition and allelopathic properties of the essential oils of Psidium cattleianum, P. myrtoides, P. friedrichsthalianum, and P. gaudichaudianum on the germination and root growth of Lactuca sativa and Sorghum bicolor, and to evaluate their action on the cell cycle of root meristematic cells of L. sativa. The main compound found in all the studied species was (E)-caryophyllene (P. cattleianum-23.4 %; P. myrtoides-19.3%; P. friedrichsthalianum-24.6% and P. gaudichaudianum-17.0%). The different essential oils were tested at different concentrations on L. sativa and S. bicolor, reducing germination, germination speed index, and root and shoot growth of lettuce and sorghum seedlings. The cytotoxicity and aneugenic potential of these oils were evidenced by the reduction of the mitotic index and increase of the frequency of chromosomal alterations in L. sativa. The essential oils of the species of Psidium studied have potential to be used in weeds control.

Toxicological effects of comercial formulations of fungicides based on procymidone and iprodione in seedlings and root tip cells of Allium cepa.

In this study the phytotoxic, cytotoxic, genotoxic and mutagenic effects of two commercial fungicide-active compounds, procymidone (PR) and iprodione (IP), were determined. The parameters evaluated were germination and root growth, mitotic index, chromosomal and nuclear aberrations, and molecular analyses were also performed in the model plant Allium cepa L. The results demonstrated that the active compounds PR and IP were phytotoxic, delaying germination and slowing the development of A. cepa seedlings. Moreover, PR and IP showed cytogenotoxicity towards A. cepa meristematic cells, inducing chromosomal changes and cell death. The mutagenic activity of the active compounds was demonstrated by the detection of DNA changes in simple sequence repeat (SSR) and inter-simple sequence repeat (ISSR) markers in the treated cells compared to the negative control. Together, these results contribute to a better understanding of the damage caused by these substances in living organisms and reveal a promising strategy for prospective studies of the toxic effects of environmental pollutants.