Table of Contents | Genet. Mol. Res. 2021 (2)
Genetic variability of Aspergillus flavus isolated from commercial peanut and bulgur wheat in Southern Brazil and antifungal activity of essential oils against some of the isolates
Aspergillus flavus produces carcinogenic aflatoxins. This species is divided based on the type of sclerotia produced, designated as “S” for numerous small and “L” for fewer and large. “L” strains are concerning since they are prevalent in corn, peanut, rice, and soil samples. Nearly all “S” strains and approximately 70% of “L” strains produce aflatoxins. Host specificity within isolates is not well understood and needs to be better characterized. We isolated A. flavus from commercial peanut samples from Southern Brazil and investigated their genetic variability and their genetic correlation with four A. flavus isolates previously obtained from commercial bulgur wheat in the same region. We also evaluated the antifungal activity of essential oils on some of the isolates. Eleven “L” type A. flavus strains were isolated from peanut kernels. Eight of these isolates were considered aflatoxigenic, based on thin-layer chromatography and culture techniques. The genetic biodiversity of the A. flavus isolates was analyzed using Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) analyses, which indicated differences according to host, however, did not regarding aflatoxin production. Essential oils of oregano, thyme, cinnamon, lavender, and fennel inhibited the isolate’s growth. In conclusion, A. flavus isolates differ according to host and essential oils have potential to control this fungus.
Gaucher Disease (GD) is an autosomal recessive genetic disorder, caused by a deficiency of the enzyme B-glucocerebrosidase (GBA). In Colombia, despite considerable research on GD, the frequency of the GBA gene variants in the population is unknown, making it difficult to determine the risk of occurrence based on carriers. To identify the variants of the GBA gene, a transversal, descriptive, non-experimental study was carried out with the results obtained from the sequencing of the complete exome of 320 patients with complex disease, without clinical suspicion of GD. Bioinformatics software was used to analyze the clinical significance of the different variants. The population frequency of each variant was calculated, and a network of interaction of the GBA gene was developed. As a result, 41 variants associated with the GBA gene were found; 21/41 of the variants reported have a benign significance, 5/41 of the variants reported were classified as pathogenic or probably pathogenic and 7/41 of the variants reported presented uncertain significance. The gene interaction network showed close associations between GBA and genes PSAP, SCARB2, LAMP2, all of them focused on functions of vacuolar locations, lysosomal and vacuolar lumen instructions, vacuolar and lysosomal membranes. We conclude that the impact on the phenotype highly depends on the pathogenicity of the variants. In our sample, a high frequency of benign variants was found; however, pathogenic variants were detected, which should be the object of study in precision medicine associated with GD.
The quality of fit of a multiple linear regression model often encounters multicollinearity and high dimensionality problems, making it impossible to obtain stable estimates through the traditional method of estimation based on ordinary least squares. To overcome such challenges, dimensionality reduction methods have been proposed, because of their simple theory and easy application. We compared three dimensionality reduction methods: Principal Components Regression (PCR), Partial Least Squares (PLS), and Independent Components Regression (ICR). An important step for dimensionality reduction and prediction is selecting the number of components, as it affects the linear combinations of the explanatory variables. The linear combinations are inserted into the model to predict the response based on a reduced number of parameters. We examined the criteria for the selection of the number of components. The dimensionality reduction methods were applied to genomic and phenotype data. We evaluated 370 accessions of Asian rice, Oryza sativa, which were genotyped for 36,901 SNPs markers considered to predict the genomic values for the number of panicles per plant trait. This data set presented multicollinearity and high dimensionality. The computational time for each method was also recorded. Among the methods, PCR and ICR gave the highest accuracy values, with ICR standing out for presenting estimates of the least biased genomic values. However, ICR required more computational time than the other methodologies.
Differential expression of microRNAs in a hyperoxia-induced rat bronchopulmonary dysplasia model revealed by deep sequencing
We examined the biological roles of microRNAs (miRNAs) in the pathogenesis of bronchopulmonary dysplasia (BPD). Neonatal rats were randomly assigned to hyperoxia (85% O2) and normoxia (21% O2) groups, and each group had eight neonatal. Twenty differentially expressed miRNAs were identified by deep sequencing, of which 10 were up-regulated and 10 were down-regulated in the hyperoxia group. A total of 5,794 molecular related to gene ontology functions were enriched, including cell location and biological processes. rno-miR-29b-3p were up-regulated, and rno-miR-322-5p and rno-miR-335 were down-regulated in the hyperoxia sample based on quantitative real-time PCR. In conclusion, BPD appears to be caused by activation of extracellular matrix -receptor interaction, cytokine-cytokine receptor interaction, RNA transport, cell cycle, and cell adhesion molecule pathways. These miRNAs may play a role in the occurrence and development of BPD. Our study provides new insight into the biological processes of BPD.
Hypertension (or high blood pressure) is a common problem throughout the world, including Vietnam, especially for people over 65. This pathology has various contributing risk factors. Understanding them can help in hypertension awareness, treatment, and control, especially in low-income countries. To help provide more useful information for our population, we conducted a cross-sectional study of 166 randomly-selected patients at Military Hospital 121 in CanTho City, Vietnam. The objective was to identify risk factors that influence hypertension development and progression. These included less than 150 minutes per week of physical activity, low consumption of fruits and vegetables), high body mass index (obesity), and diabetes or chronic kidney disease. We combined the most relevant factors into a risk score. A linear increase in the predicted risk of hypertension with each additional risk factor was detected. Women have a higher level of the predicted prevalence of hypertension (75%). In men, this point was 25%. The evaluated patients' average age was 60 years. We concluded that obese, little plant product consumption, inactive lifestyle, and diabetes development contributed most to hypertension risk in the Vietnam population. Most such risk factors can be corrected by prevention strategies.
Brazil is the world largest producer and exporter of Coffea arabica. In this country, numerous breeding programs have generated a great multiplicity of cultivars with expressive productivity that are adapted to the different regions. Evaluating genetic diversity is critical since it provides parameters for defining breeding strategies. We estimated the genetic diversity among and within 32 cultivars of the Brazilian Coffee Trial using AFLP markers. This trial is composed of the main cultivars developed and some under development by Empresa De Pesquisa Agropecuaria do Estado de Minas Gerais (EPAMIG), Fundação PROCAFÉ, Instituto Agronômico de Campinas (IAC), and Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná). A total of 982 AFLP fragments were generated, of which 97.35% were polymorphic. The percentage of polymorphic loci ranged from 22.8 to 50.5%, with genetic diversity varying from 0.06 to 0.16. Variable levels of genetic diversity observed among cultivars probably derived from the diverse germplasm sources and methods used in the genetic breeding programs, the number of advanced generations of each cultivar, as well as genetic recombination or cross-fertilization during breeding programs. Bayesian cluster analysis, principal component analysis, and Neighbor-Net showed three divergent genetic groups, with a high genetic differentiation index (FST = 0.46). The pairwise FST also revealed high divergence among cultivars. IDR-Paraná had the cultivars with the highest genetic variability among these four Brazilian coffee breeding centers. We found that AFLP markers allowed us to distinguish the cultivars/progenies in the Brazilian National Trial. We conclude that Brazilian coffee germplasm still has considerable genetic variability for the development of new cultivars with high productivity, resistance to disease, superior beverage quality, and adaptation to diverse edaphoclimatic conditions in the different producing regions.
Impact of ancient oxygen levels on mitochondrial genome evolution inferred by supertrees, supermatrices, and relaxed molecular clocks
Evolution of mitochondrial genomes is essential for the adaptation of yeasts to changes in environmental oxygen levels. Although Saccharomyces cerevisiae mitochondrial DNA lacks all complex I genes, respiration is possible because alternative NADH dehydrogenases are encoded by NDE1 and NDI1 nuclear genes. The apparent whole genome duplication (WGD) in the yeast ancestor 100-150 million years ago caused nuclear gene duplications and secondary losses, although its relation to the loss of mitochondrial complex I is unknown. We produced phylogenomic supertrees and a supermatrix tree of 46 mitochondrial genomes, showing that the loss of complex I predates WGD and occurred independently in the S. cerevisiae group and the fission yeast Schizosaccharomyces pombe. The branching patterns did not differ substantially in supertrees and supermatrix phylogenies. We found consistent relations between conserved mitochondrial chromosomal gene order (synteny) in closely related yeasts. Correlation of mitochondrial molecular clock estimates and atmospheric oxygen variation in the Phanerozoic suggests that the Saccharomyces lineage might have lost complex I during hypoxic periods near Permian-Triassic or Triassic-Jurassic mass extinction events, while the Schizosaccharomyces lineage possibly lost complex I during hypoxic environment periods during the Middle Cambrian until the Lower Devonian. The loss of mitochondrial complex I, as a result of low oxygen levels, might not affect yeast metabolism due to a fermentative switch. The return to increased oxygen periods could have favored adaptations to aerobic metabolism. Additionally, we also show that NDE1 and NDI1 phylogenies indicate evolutionary convergence in yeasts in which mitochondrial complex I is absent.
A modified non-liquid nitrogen protocol for extraction of high-quality genomic DNA from the inner bark tissues of Dalbergia cochinchinensis (Fabaceae)
Dalbergia cochinchinensis (Fabaceae) is known as Thai rosewood. It is a Thai native and widespread throughout Thailand. Due to it being a hardwood tree, it became a valuable hardwood tree species for its commercial value for luxury furniture and as a first-class prime timber, which has made it a potentially endangered species. For genetic studies of this tree, we tested four protocols of genomic DNA extraction from the inner bark based on the sodium dodecyl sulfate method and two protocols of the cetyltrimethyl ammonium bromide method, . We evaluated the quantity, purity, and integrity of the extracted genomic DNA from 15 genotypes of D. cochinchinensis using PCR amplification and restriction enzyme digestion to develop a protocol for this species. We found that optimal concentrations of lithium chloride and polyvinylpyrrolidone could improve the quantity and quality of DNA in the extraction buffer without using liquid nitrogen. The highest concentration of high-quality DNA was obtained with protocol M5 (392 ng/µL DNA and a purity ratio of A260/A280 equal to 1.96). In contrast, the commercial Nucleospin Plant II Mini Kit provided the lowest yield of 13.94 ng/µL DNA, with a low purity ratio of A260/A280 (1.58). Start codon targeted \ and sequence-related amplified polymorphism fingerprints further demonstrated that protocol M5 developed for inner bark tissue samples gives good DNA quality and quantity for genetic studies of D. cochinchinensis.
Comparative analysis of tocopherol biosynthesis genes during seed development in the Asian spiderflower, Cleome viscosa (Cleomaceae)
Cleome viscosa (common names, wild mustard, Asian spiderflower, and tick weed) is an annual oilseed crop plant that has a high vitamin E content, with the most active forms being the tocopherols (α, β, γ and δ). These act as antioxidants in plants and are also useful for human health. The gene expression profiles and partial-length cDNA encoding tocopherol cyclase (CvVTE1), homogentisic acid prenyltransferase (CvVTE2), MPBQ methyltransferase (CvVTE3), gamma-tocopherol methyltransferase (CvVTE4), hydroxyphenyl-pyruvate dioxygenase (CvHPPD) and homogentisate solanesyltransferase (CvHST) genes involved with tocopherol biosynthetic enzymes were determined. Partial cDNA sequences of six genes as 694 bp CvVTE1, 375 bp CvVTE2, 387 bp CvVTE3, 402 bp CvVTE4, 334 bp CvHPPD and 461 bp CvHST showed high identity to their homologs in other higher plants. Expression levels of CvVTE1, CvVTE2, CvVTE3, CvVTE4, CvHPPD and CvHST genes were analyzed by real-time quantitative PCR (qPCR) at plant nodes L1-L3 in leaves and 1-4 weeks after fruit set (WAF) of seeds. CvVTE3 and CvHPPD were predominantly expressed in the leaves, while in seeds CvVTE2 was expressed at both 2 and 3 WAF at rates of 231-fold and 224-fold, which coordinated with CvVTE1 and CvVTE3 expression. Co-expression of CvVTE4 and CvHPPD supports high levels of flux toward the synthesis of tocopherols at 4 WAF without any down regulation. We conclude that CvVTE2 plays a key role in tocopherol biosynthesis in C. viscosa seeds.
Severity of rust infection in soybean genotypes with partial resistance as a function of temperature and leaf wetness duration
Soybean cultivars with resistance against Asian soybean rust (ASR) are necessary to maintain plant yield when control methods become ineffective. We examined the influence of temperature (18, 21, 24, 27 and 30°C) and leaf wetness duration (0, 6, 12, 24 and 48 hours) on the penetration and temporal progress of ASR in soybean genotypes with different levels of partial resistance from the Federal University of Uberlandia breeding program. The genotypes were selected in the field from 100 progenies during 15 years under ASR epidemic conditions. Information on inheritance and molecular markers for disease resistance was available for our study. There were significant differences (P=0.001) in the area under the disease progress curve (AUDPC) between genotypes under the interaction of the binomial (temperature x leaf wetness duration - LWD) and for incubation period at different temperatures. No signs or symptoms of rust appeared at temperatures below18°C or above 30°C. The relationship between temperature and LWD affect the AUDPC and temperature affects incubation period. The highest AUDPC values occurred at 24°C and leaf wetting period of 24 hours, and the lowest values were achieved at temperatures above 27ºC. (Cultivar Desafio RR 8473 RSF) showed susceptibility to ASR.ASR lesions started to appear on average at least 15 days after infection in partially resistant genotypesF8 BRSGO Luziânia X Potenza, F8 BRSGO Caiapônia X Potenza, and F8 BRSGO Caiapônia X IAC100, which also had lower AUDPC and severity values, during the monocycle experiment. We conclude that ASR is shifting to a longer incubation period and fast sporulation induction after uredinia formation. These genotypes can be used in the field, with less need for fungicides helping avoid the emergence of new ASR pathotypes and races with low sensitivity to currently used fungicides.
Lactobacilli are the predominant bacterial species colonizing the vaginal surfaces of healthy women, where they play a protective role against opportunistic and polymicrobial infections, such as bacterial vaginosis. Several Lactobacillus species, especially L. crispatus, have been prospected for probiotic applications due to their potential antimicrobial and anti-inflammatory capacities. During the last decade, several genomic studies have been investigating the genetics of L. crispatus strains in an effort to identify novel probiotic strains and evaluate their potential for improving human and animal health. This mini review highlights the main genes associated with L. crispatus protective mechanisms in four novel strains of this species that we recently isolated from healthy Brazilian women of reproductive age. Among the probiotic features of these strains, the roles of a pyruvate oxidase-encoding gene, lactate synthesis related enzymes, bacteriocin genes, and genomic islands, are reviewed, and the next steps for confirming their activity are indicated.
Development and transferability of microsatellite loci for Spondias tuberosa (Anacardiaceae: Sapindales), a species endemic to the Brazilian semi-arid region
The umbu tree (Spondias tuberosa) is one of the best known plants of the Brazilian semi-arid region; it has great potential for the fruit market due to excellent consumer acceptance. This tree is not presently cultivated; fruit commercialization is based on extrativism. Consequently, there has been little research on the genetics of this species. Our objective was to develop, evaluate and transfer single sequence repeat (SSR) loci to S. tuberosa to support work on genetic resources and agronomic improvement of this species. SSR loci for the umbu tree were developed from a new enriched genomic library and evaluated by PCR. Fourteen SSR loci developed for S. radlkoferi were evaluated for use in S. tuberosa, as well as 18 SSR loci previously identified for this species. DNA was extracted from leaf tissue of eight umbu trees available that are part of a germplasm collection located in Petrolina, PE, Brazil. Of the 14 pairs of primers that were tested, six yielded amplicons, and two showed polymorphism in the genotyped samples. All SSR loci of S. radlkoferi transferred to the umbu tree species, yielding amplicons; however, only four were polymorphic in this sample. Among the eighteen available species-specific SSR loci, six were polymorphic for these eight trees. Among the 38 loci that we evaluated, 12 were polymorphic in the sample, including two new loci for S. tuberosa. The number of alleles ranged from 2 to 12, and 10 of them were moderately to highly informative (PIC>0.50), while nine had heterozygosity greater than 0.50. The six new SSR loci and the 14 SSR loci transferred from S. radlkoferi increase the number of available loci for population studies, germplasm collection and resource management for the development of new umbu tree cultivars.
A combination of regression and internal point methods as a hybrid model for estimating oat plant productivity
The internal points method (IPM-Carvalho), with regression analysis, can generate an efficient hybrid model for estimating oat grain productivity. We tested a combination of the internal points method and regression to estimate straw productivity. We also applied this methodology to forecast a harvest index in the elaboration of a hybrid model to estimate oat grain productivity, taking into account nitrogen management and growth regulator use, with biological and environmental indicators. Simulation of oat yield as a function of nitrogen and growth regulator applications, with biological and environmental inputs, can assist in the development of more efficient and sustainable management for this crop. Two experiments were conducted during 2013, 2014, and 2015; one was used to quantify biomass yield and the other to determine grain yield and plant lodging. The experimental design was randomized blocks with four replications in a 4 x 3 factorial scheme in the sources of variation, which were growth regulator (0, 200, 400 and 600 mL ha-1) and nitrogen (30, 90 and 150 kg ha applications. The environmental parameters that were included were rainfall and maximum air temperature. The nitrogen was applied as urea at the expanded fourth leaf stage. The growth regulator was trinexapac-ethyl applied at the stage between the 1st and 2nd visible stem node. Straw productivity was obtained by the IPM model with nitrogen dose and rainfall inputs. The harvest index was obtained by regression as a function of the growth regulator doses. The combination of the internal points method to estimate straw productivity with the use of regression in the forecast of the harvest index proved to be a useful model for estimating oat grain productivity based on biological and environmental parameters, together with nitrogen and growth regulator applications.
Screening cassava germplasm for resistance to the root-knot nematode (Meloidogyne javanica) showed that periclinal chimera, which came from combination of the wild species Manihot fortalezensis and indigenous cultivar UnB 201, resulted in resistance to M. javanica. Apparently periclinal chimera acquired resistance from M. fortalezensis, with its tissue forming a subepidermis and the internal tissue. Apparently, resistance was due to interaction of DNA in the chimera components, since the DNA moves within all plant tissues. This interaction provided the increased vigor observed in periclinal chimera. This is the first report of transferring resistance to a pathogen by periclinal chimera.
Isolation of high-affinity phosphate transporters SbPT1 AND SbPT2 in Sorghum bicolor and their characterization in contrasting genotypes
Phosphate (Pi) availability is highly limited in the acidic soils of the Brazilian savannahs (Cerrado) used for sorghum cultivation. Although several sorghum genotypes contrasting for P use-efficiency have been developed from natural genetic variants, the Pi transport pathway mechanisms in these plants remain unclear. High-affinity Pi transporters play a pivotal role in Pi acquisition by roots and its subsequent mobilization to aerial parts of the plant. We investigated the potential roles of high-affinity Pi transporters in Pi use efficiency in contrasting genotypes of sorghum. A cDNA library prepared from Pi-deprived sorghum seedlings was screened with heterologous Zea mays (maize) Pi transporters ZmPTs, leading to isolation of two homologous sorghum genes referred to as SbPT 1 and SbPT2. Southern analysis revealed that a small gene family represents the SbPTs genes in the sorghum genome. There were significant increases in the transcription levels of SbPT1 and SbPT2 in roots of Pi-deprived seedlings of both Pi-use efficient (101B) and Pi-use inefficient (136B) genotypes. A decrease in the transcript levels of these transporters in 101B and 136B upon Pi replenishment suggested their transcriptional regulation by Pi. Although SbPT1 and SbPT2 were induced in the roots, and in young and old leaves of Pi-deprived sorghum, high transcription levels were observed exclusively in the stems of Pi-efficient genotype 101B under Pi-deprivation. This suggests a role of SbPTs in the efficient mobilization of Pi from the root to the shoot, which could be one of the factors conferring higher Pi-use efficiency in this genotype.