Current issues

Table of contents: 2022

Research Article

The Solanaceae family comprises about 100 genera and 2,500 species, with a cosmopolitan distribution and greatest diversity in the Neotropical region. In Brazil, 36 genera and 506 species have been identified, including 236 endemic species. The family has a high diversity of species of economic importance as a source of food, medicinal extracts, and for ornamental use. The species are sources of bioactive secondary metabolites, with diverse applications. We made ae structural and functional characterization and developed three-dimensional models of putrescine N-methyltransferase (PMT) proteins, a key enzyme of secondary metabolism, involved in biosynthesis of nicotine, tropane alkaloids, and calistegines. We examined 48 PMT sequences from Solanaceae species available in public databases. A hydrophilic characteristic of PMT was found for all species, and the isoelectric point demonstrated a somewhat acidic character (5.4 - 6.6). We identified four functional domains in the PMT sequences. Cluster analysis by Neighbor-Joining was consistent with recent taxonomic classifications of the species.

Genet. Mol. Res. 2022
DOI: 10.4238/gmr19076
Research Article

Sclerotinia stem rot is a common soybean disease caused by the fungus Sclerotinia sclerotiorum, resulting in economic losses in Brazil and worldwide. The development of resistant cultivars is a good option for the management of this disease; however, it has been difficult, largely due to the variability found in the fungus. We assayed for the genetic resistance (vertical and horizontal) of soybean cultivars inoculated with various isolates of S. sclerotiorum. Twenty soybean cultivars were selected and tested; 10 were relatively resistant and 10 relatively susceptible to the pathogen. The cultivars were inoculated with mycelium from four fungal isolates: Mauá da Serra, Ingaí, and Nazareno, collected from soybean production areas and UFLA 24, an isolate normally used by the Lavras University Laboratory of Plant Resistance to Diseases team, for assays with the detached-leaf method. The experiment was conducted in a completely randomized design. Detached-leaves at V2 trefoil were placed on an agar disk containing the mycelium and each leaflet was considered a replicate. After 72 hours, the leaflets were evaluated using a scoring scale ranging from 0 (no symptoms) to 5 (susceptible). Statistical analyses were performed using the diallel method (Griffing IV model), which provided information on the vertical and horizontal resistance of the cultivars, as well as the aggressiveness of the isolates. The soybean cultivars BRS Baliza RR, M-SOY 8001, Emgopa 316 and M-SOY 8329 showed horizontal resistance; BRS Favorita RR, Emgopa 315, MG/BR 46 (Conquista), 7166RSF IPRO, BRS Silvânia RR and BRS Milena presented specific resistance to most isolates The UFLA 24 and Ingaí fungal isolates were the most aggressive, indicating that these isolates should be preferred for evaluating the level of resistance of soybean genotypes.

Genet. Mol. Res. 2022
DOI: 10.4238/gmr19074
Research Article

Pigeonpea is a multipurpose species and can be used for grain, forage production, and as a soil improver. In Brazil, the scarcity of productive cultivars adapted to various growing conditions contribute to the underutilization of this legume crop. The genotype × environment (G×E) interaction is one of the main challenges to the development and recommendation of cultivars. Estimates of adaptability and stability parameters make it possible to predict the behavior and effects of the G×E interaction to reduce possible inconsistencies in cultivar recommendation. From this perspective, we assessed the adaptability and stability parameters for grain yield of 21 pigeonpea lines developed in the breeding program of this pulse at Embrapa Semiárido, Petrolina, PE, Brazil, and the variety ‘guandu Petrolina’ (control), in order to recommend new cultivars for general use. The genotypes were evaluated in eight environments, with experiments conducted in five irrigated and three rainfed environments using a randomized complete block design with three replications. Grain yield was corrected by covariance based on the average plant stand. The Eberhart and Russel, AMMI, and GGE Biplot methods were used in this study. The coefficient of variation for the experiments was 12.41%, with data transformed to square root. The effects of genotypes, the environments, and the genotype-by-environment interaction were highly significant (p < 0.01). The mean grain yield of the genotypes was 1,516 kg ha-1. Lines 87, 100, and 158 simultaneously showed wide adaptability and good predictability according to the three methods, with mean yields of 1,530, 1,701, and 1,812 kg ha-1, respectively, and reaching yields of up to 2,725, 2,928, and 2,955 kg ha-1 in some environments. These lines are indicated for recommendation as new pigeonpea cultivars for the semi-arid region of Brazil.

Genet. Mol. Res. 2022
DOI: 10.4238/gmr19066
Research Article

The challenge presented by the SARS-CoV-2 pathogen has changed the global perception about virus diseases. In Wuhan, China the first case of the disease called COVID-19 (Coronavirus Disease 2019) was reported in December 2019 and quickly reached 215 countries. The pathogenic SARS-CoV-2 virus has an RNA genome composed of a positive-sense single-strand, harboring 14 ORFs that encode 50 proteins composed of typical structural proteins. The spike protein, a surface glycoprotein, is essential for the invasion of the causal agent of COVID-19 into the host system. Several variants have specific mutations in protein S that affect transmission processes, diagnosis, and available therapies. Entry of SARS-CoV-2 into the host cell promotes immunological dysregulation with increased expression of interferon type 1 and an exaggerated proinflammatory cytokine event called "cytokine storm". This event is often associated with deleterious outcomes such as acute respiratory distress syndrome. In addition, substantial immunological memory can be generated after initial SARS-CoV-2 infection, involving four major cell types, such as anti-spike protein memory B cells (RBD IgG, IgM), T cells (CD4+ and CD8+) and other molecules, such as antibodies. It is important to collect genetic and immunological information related to the SARS-CoV-2 virus to provide a global vision and high quality knowledge about the biology and this disease in order to develop effective control measures and treatments.

Genet. Mol. Res. 2022
DOI: 10.4238/gmr19003
Research Article
Authors:

Cassava Periclinal chimera plants could be synthesized by a very easy grafting method. Thanks to this technique we can produce vigorous plants during a very short period. This can be achieved by grafting two types that have high combining ability. The most striking feature is that we can obtain enormous roots up to five times the common ones. It is suggested this vigor is due to gene action of overdominance and there is DNA movement from epidermis (one cell layer tissue) to internal tissues. Previous results are explained in view of this present one.

Genet. Mol. Res. 2022
DOI: 10.4238/gmr19079
Research Article

Complex chromosomal rearrangements are extremely rare in humans. Most apparently balanced complex chromosomal rearrangements are de novo; they usually are detected in phenotypically normal subjects. Nevertheless, in some cases they are found in patients with multiple congenital abnormalities and neurodevelopmental disorders, which may be due to cryptic genomic imbalance. We report on a case of complex chromosomal rearrangement in a patient with an abnormal phenotype and neurodevelopmental delay. The conventional karyotyping of a child showed an apparently balanced three-way translocation t(4;7;5)(q31;p21;q31)dn. FISH and chromosomal microarray revealed that the rearrangement was far more complex than originally diagnosed, with more breakpoints involving chromosomes and four cryptic microdeletions on chromosomes 4 and 5. One copy number variant indicated microdeletion 5q31.3 syndrome associated with deletion/mutation of the gene PURA. A combination of several different approaches, including GTG, FISH and chromosomal microarrays, was sufficient to determine an unexpected level of complexity and to resolve the nature of the complex chromosomal rearrangement.

Genet. Mol. Res. 2022
DOI: 10.4238/gmr19065
Research Article

The Amazon harbors numerous bitter cassava genotypes, of which only a few have been studied agronomically. We evaluated the genotype x environment interaction (GxE) displayed by seven traditional varieties found in the Brazilian municipalities of Lábrea-AM, 07°14’83.5”S, 64°44’70”W, (Cobiçada, Minerva, and Flecha-Amarela) and Manaus-AM, 02º59’00”S, 60º01'00”W, (Mana, Trairinha, Nanica, and Jurará), to determine the landraces best adapted to both sites. A randomized block design, with seven treatments and four replications with eight plants per plot, was adopted at each site. We evaluated commercial root number, length, diameter, length/diameter ratio, mass, dry matter, peel thickness, pulp coloring, plant height, stem diameter, and aerial part mass. GxE interaction analysis revealed GxE interaction for plant height and root diameter and number, and yield. Jurará was the most adapted variety at both sites for the main agronomical characteristics. It showed 43.7 and 26.5 t ha-1 root yield; 39.8 and 43.7 t ha-1 aerial mass; 10.8 and 4.8 roots per plant and 331.7 and 316.6 cm plant height, respectively in Lábrea and Manaus, respectively. Therefore, Lábrea and Manaus are suitable sites for making studies of GxE interaction. Jurará can be recommended for the Amazon region as well and should be tested in other tropical and subtropical regions.

Genet. Mol. Res. 2022
DOI: 10.4238/gmr19049
Research Article

Staphylococcus aureus is a contagious pathogen frequently associated with bovine subclinical mastitis (SCM) cases in Brazil. Molecular characterization of S. aureus allows monitoring of specific features at the strain level, such as transmission routes and antimicrobial resistance, and it can be a helpful tool for implementation of prevention measures among and within herds. We evaluated molecular typing and antimicrobial resistance profiles of S. aureus isolates from lactating cows with SCM. A total of 79 S. aureus isolates recovered from bovine SCM were submitted to pulsed-field gel electrophoresis (PFGE) analysis and tested for antimicrobial susceptibility against 13 antimicrobials, based on minimum inhibitory concentrations. Based on the band patterns generated by PFGE, dendrograms were constructed to compare S. aureus pulsotypes (n = 17). Resistance was observed for amoxicillin (100% of the isolates), erythromycin (96%) and for ampicillin and penicillin (77%). All S. aureus isolates were susceptible to gentamicin, enrofloxacin, ciprofloxacin and tetracycline. One methicillin-resistant S. aureus strain was identified based on resistance to cefoxitin. We found a wide genotypic diversity of S. aureus causing SCM among the isolates. In general, S. aureus was sensitive to quinolones and aminoglycosides, while we observed β-lactams resistance in most of the isolates. Our findings are similar to those of previous results that reported high resistance of S. aureus mainly to β-lactams. Consequently, control measures for this bacterium need to be implemented in order to control the spread of the disease and establish more assertive treatment protocols.

Genet. Mol. Res. 2022
DOI: 10.4238/gmr19009
Research Article

Spontaneous abortions, which occur in 15-20% of all pregnancies, constitute the most common human genetic disease, since most miscarriages are caused by chromosomal anomalies. In our laboratory, we devised a protocol for sequential use of quantitative fluorescent PCR (QF-PCR), homologous gene quantitative PCR (HGQ-PCR) and SNP-arrays that allows examination of numerical and structural analyses of all chromosomes in spontaneous abortions at low cost. We describe our results with 1,295 samples of fetal tissues collected consecutively after pregnancy losses. Positive signals with QF-PCR and HGQ-PCR were always confirmed using microsatellite amplification of the specific chromosome involved.  Among the exams, 64.6% were abnormal. The most common anomalies were trisomies (69.5%), triploidy (13.5%) and monosomy X (9.1%). The most frequent trisomies involved the following chromosomes: 16 (23.5%), 22 (16.0%), 21 (14.1%) and 15 (10.1%). SNP array analysis permitted the diagnoses of all trisomies. Additionally, deletions and/or duplications and chromosomal mosaicism were detected by SNP-array in 23 cases. In conclusion, our sequential analysis of fetal tissues is a new, highly useful, rapid, and cost-effective approach for the diagnosis of chromosomal alterations in spontaneous abortions.

Genet. Mol. Res. 2022
DOI: 10.4238/gmr19082
Research Article

The dehydration responsive element (DRE)-binding proteins (DREB) play a role in the signaling network that activates many abiotic stress-responsive genes. We isolated and molecularly characterized the DREB gene from ancestral diploid wheat species growing in Azerbaijan and native to this region. This territory is included in a region that is considered the center of origin of cultivated wheat. One-week-old seedlings of Triticum urartu (Au), Aegilops speltoides (B) and Ae. tauschii (D) were used for genomic DNA extraction. Gene-specific primer pairs were applied forisolation of the DREB gene. The amplification products were purified using a gel extraction kit and sequenced. Data analysis was performed using FGENESH, BLAST, INTERPROSCAN, SMART, MAFFT, ExPASy, ProteinPredict, and PSIPRED tools. Ensembl Plants and NCBI were used as integrative resources. Numerous SNPs and nine microindels were detected in the partial target sequence of the DREB gene in Ae. speltoides. Nonsynonymous SNPs were determined in T. urartu (1 transition and 5 transversions), and Ae. tauschii (2 transitions and 2 transversions). Analysis of amino acid sequences encoded by the putative DREB genes revealed a conserved AP2/ERF domain, with two conserved functional amino acids (14th valine and 19th glutamic acid) that play crucial roles in the recognition of the DNA-binding sequence and two tryptophan rings that determine the geometry of the GCC-box binding domain. Nuclear localization signal and conserved Ser/Thr-rich region were observed in the corresponding amino acid sequences. One α-helix and three β-sheets were detected in the secondary structure of the AP2 domain. The isolated sequences of DREB gene from T. urartu and Ae. tauschii were confirmed and registered in NCBI with Accession Numbers MZ935739 and MZ935740. Identification of the DREB gene in wheat progenitors and its characterization is important for evaluating their genomic material for possible use to enhance the diversity of wheat cultivated under stress conditions.

Genet. Mol. Res. 2022
DOI: 10.4238/gmr19035
Research Article

We developed a new and simple feeding device for Drosophila melanogaster. In addition, we tested three negative geotaxis methods (measuring the percentage of the flies able to climb 8 cm in 8 s, measuring the distance climbed in 3 s, and measuring the distance climbed in 8 s). The flies were exposed to chlorpyrifos (CPF) using the new feeding device. Our results demonstrated that the three methods for measuring negative geotaxis could be used interchangeably with respect to the needs and conditions of the experiments; however, we recommend the 8 s method with PAST software because the other two methods were carried out using manual measurements. The use of this free software makes the process more accurate with no additional cost. We found that CPF caused impairment in locomotor activity, reduction in AChE activity, and disturbance of the dopaminergic pathways in D. melanogaster, suggesting that CPF toxicity is not confined to the cholinergic system. This study provides a new system to study neurodegenerative damage using a user-friendly and no-cost software for measuring climbing activity in D. melanogaster.

Genet. Mol. Res. 2022
DOI: 10.4238/gmr19056
Research Article

Research on genes affecting phenotypic variation in milk production and composition from indicine (Bos indicus) cattle is imperative, since these breeds are important tropical genetic resources, and there have been few studies investigating the genetic basis of these traits. We identified polymorphisms in k-casein (CSN3), b-lactoglobulin (LGB), thyroglobulin (TG) and prolactin (PRL) and examined their effect on milk and composition traits in the Guzerá breed. DNA samples of 260 Guzerá  cattle selected for dual purpose use were genotyped. Allele frequencies observed for the A allele were 0.83, 0.18 and 0.25 respectively for CSN3, LGB and PRL genes, while for the TG gene T allele had an allele frequency of 0.09. For all polymorphisms evaluated, observed genotypic frequencies were in agreement with those expected according to the Hardy-Weinberg Equilibrium hypothesis. A polymorphism association study evaluated breeding values (BV) for 305-day milk (BV-M), fat (BV-F), and protein (BV-P) production, employing the allele substitution model using a sample of 139 cows belonged to 27 full and half-sib families of a MOET (multiple ovulation and embryo transfer) selection nucleus. Association was found between the LGB polymorphism and BV-M, BV-F and BV-P. Animals with LGB AA genotype have, on average, higher BV when compared to animals with LGB AB and BB genotypes (277.85 kg for BV-M, 12.09 kg for BV-F and 9.33 kg for BV-P).  These findings contribute to a better understanding on the influence of these polymorphisms on milk production traits in Guzerá cattle.

Genet. Mol. Res. 2022
DOI: 10.4238/gmr19046
Research Article

The Brazilian Testudinidae family is widespread across South America. It includes Chelonoidis denticulatus, the largest tortoise in South America and Chelonoidis carbonarius, found mostly in the north and northwestern part of the continent. Using hemoglobin to identify species is cheaper than other methods such as DNA sequencing and can offer useful information, since the hemoglobin molecule is a well-preserved protein chain during the evolution of species. Thus, in order to establish a hemoglobin profile for the Brazilian Testudinidae C. denticulatus, C. carbonarius and morphotype 1, hemoglobin electrophoresis was performed at acid pH in phosphate agar and at alkaline pH in cellulose acetate, in order to visualize the specific fractions of each species. High performance liquid chromatography was used for the quantification of fractions. For an in-depth analysis and better detailing of the hemoglobin profile of the species, polypeptide chain electrophoresis was performed at acid and alkaline pH. We observed differences in the hemoglobin profiles of C. denticulatus in relation to C. carbonarius and morphotype 1, which suggests that this methodology, not common in taxonomic studies, can help determine relationships between species, since hemoglobins are proteins with well-preserved genes. We found differences in hemoglobin mobility between C. denticulatus, C. carbonarius and morphotype 1 in electrophoresis at alkaline pH, however, the behavior of globin chains was similar between the three groups. High performance liquid chromatography showed different retention times in the globin fractions of C. denticulatus and C. carbonarius, but not between C. carbonarius and morphotype 1, indicating that, possibly, the divergence time between C. carbonarius and morphotype 1 is more recent than the divergence between C. denticulatus and C. carbonarius, due to the highly conserved character of this functional protein. Thus, considering the high degree of conservation of hemoglobins in vertebrates, and the differences observed in electrophoresis at alkaline pH and HPLC, we infer that C. carbonarius and morphotype 1 present a common branch.

Genet. Mol. Res. 2022
DOI: 10.4238/gmr18977
Research Article

Quantitative PCR puts great demands on DNA quality and relies on a comparison of fragment amplification between two chromosomes using different primers. The use of a single primer pair capable of reliable relative comparative amplification would be a great advantage.  Using this approach, we developed a rapid, high-throughput, semi-automated and cost-efficient multiplexed method for molecular determination of chromosomal sex called MQS-PCR – multiplex quantitative sexing PCR. DNA sequences located on different chromosomes and differing in length can be amplified and fluorescently labelled with a common fluorescent primer and conveniently separated and detected using capillary electrophoresis. In this method, the intensity of amplification of each of the fragments is compared to determine DNA dosage. MQS-PCR achieves 100% analytical sensitivity and specificity in detecting normal and abnormal sex chromosomal complements (45,X, 46,X,i(X)(q10), 46,X,i(X)(p10), 46,X,X(p-), 46,X,X(q-), 47,XXX, 47,XXY and 47,XYY). It is a reliable, low cost, and rapid detection method for the determination of chromosomal sex and sex chromosomal abnormalities in human samples.

Genet. Mol. Res. 2022
DOI: 10.4238/gmr19067
Research Article

Wheat is considered a basic cereal for civilization with great economic importance for world agriculture. Currently, wheat is planted in the south, southeast and midwest regions of Brazil. Brazilian consumption of wheat will grow in the coming years due to population increase, which will require developing new cultivars for non-tradtional regions. We investigated commercial wheat genotypes grown at various sowing dates in a region with high temperature conditions. The experiment was conducted during the two summer and two autumn seasons. Sowings were March 10, March 20, April 1 and April 10. The agronomic traits (grain yield, plant height, spike size, total spikelets per spike and fertile spikelets per spike) for four commercial genotypes were evaluated. The experimental design was randomized blocks in a factorial scheme, corresponding to four genotypes, four sowing seasons and two years of cultivation. The second sowing year gave the best performance for the genotypes. Genotypes BR 18 and BRS 404 gave superior agronomic performance, standing out in the third and fourth sowing dates, under these culture conditions.

Genet. Mol. Res. 2022
DOI: 10.4238/gmr18993

Pages