Current issues

Table of contents: 2021

Research Article

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.

Genet. Mol. Res. 20(2): GMR18772
DOI: 10.4238/gmr18772
Research Article

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.

Genet. Mol. Res. 20(2): GMR18485
DOI: 10.4238/gmr18485
Research Article

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.

Genet. Mol. Res. 20(2): GMR18751
DOI: 10.4238/gmr18751
Research Article

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.

Genet. Mol. Res. 20(2): GMR18802
DOI: 10.4238/gmr18802
Research Article

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.

Genet. Mol. Res. 20(2): GMR18836
DOI: 10.4238/gmr18836
Research Article

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.

Genet. Mol. Res. 20(2): GMR18781
DOI: 10.4238/gmr18781
Research Article

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.

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Genet. Mol. Res. 20(2): GMR18900
DOI: 10.4238/gmr18900
Research Article

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.

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Genet. Mol. Res. 20(2): GMR18778
DOI: 10.4238/gmr18778
Research Article

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.

Genet. Mol. Res. 20(2): GMR18756
DOI: 10.4238/gmr18756
Research Article

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.

Genet. Mol. Res. 20(2): GMR18731
DOI: 10.4238/gmr18731
Research Article

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.

Genet. Mol. Res. 20(2): GMR18899
DOI: 10.4238/gmr18899
Research Article

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.

Genet. Mol. Res. 20(2): GMR18717
DOI: 10.4238/gmr18717
Research Article

The aim of this study was to select Coffea arabica lines with improved adaptability to tropical edaphic conditions. Competitive trials were set up at three locations of the states of Rondônia and Acre. Each trial was composed of 21 lines in the F5 generation and four reference cultivars evaluated as controls. To analyze beverage quality, six liters of coffee fruit at the M3 maturity stage was collected for each line in the environments of Alta Floresta do Oeste, RO (E1), Porto Velho, RO (E2), and Rio Branco, AC (E3). On the same day, after collection, the fruit was washed and placed to dry (natural processing) in full sun over canvas, until the samples reached 11-12% moisture. Sensory analysis of the samples was carried out by three judges/cuppers (Q Grader), according to the sensory analysis method of the Specialty Coffee Association of America. Analysis of variance showed that the effect of the genotype x environment interaction was significant, indicating differentiated performance of the lines grown in the different locations. Environments E2 and E3 were not favorable for beverage quality, whereas environment E1 showed better conditions for production of specialty coffees. In sensory analysis, six lines had higher final beverage quality scores than the controls. Line 2 had a final score of 80, line 11 had a final score of 79, and line 12 had a final score of 77. In addition to good beverage quality, lines 2, 11 and 12 also had yields higher than 30 bags ha-1 in the average of three harvest periods, indicating the possibility of selecting lines with improved adaptation to tropical regions.

Genet. Mol. Res. 20(2): GMR18809
DOI: 10.4238/gmr18809
Research Article

Autism spectrum disorder (ASD)in children is on the rise and is a concern for parents and the community. There has been no research on the epidemiology of autism in children in general and children under six years old in particular in Nghe An, Vietnam. We examined the prevalence of ASD among children under 6 years of age in this region. We retrospectively studied the medical records of perinatal centers and children's outpatient clinics and hospitals. A relationship was found between cases of autism and risk factors, including congenital asphyxia, sepsis during pregnancy, multiple pregnancies, late reproductive age of the mother, children’s watching television time, and parents’ spending less time with children.

Genet. Mol. Res. 20(2): GMR18738
DOI: 10.4238/gmr18738
Short Communication

Genetic polymorphisms involved in carcinogen metabolism contribute to leukemogenesis risk. Epidemiological studies have revealed genetic alterations in chronic lymphocytic leukemia (CLL), including chromosome alterations, noncoding RNA alterations, and genetic polymorphisms. The bioactivation and detoxification of chemical agents is mediated by xenobiotic metabolism enzymes, and genetic polymorphisms may explain interindividual differences in hematological cancer susceptibility. Glutathione S-transferase (GST) enzymes are capable of metabolizing xenobiotics into less toxic and more easily eliminated substances. Some studies have suggested involvement of GSTs polymorphisms in leukemogenesis susceptibility. We investigated possible genetic associations between GSTM1/GSTT1 deletion and GSTP1 rs1695 polymorphisms with CLL risk in a central Brazilian population. For GSTM1/GSTT1 deletion polymorphism, genotyping was performed with multiplex real-time PCR (qPCR), and for GSTP1 rs1695 polymorphism, PCR-RFLP was used. The GSTM1 null genotype presented a trend towards CLL risk. However, GSTT1 deletion polymorphism presented a protective effect for CLL (OR=0.26, p<0.005).The GSTP1 rs1695 was not associated with disease susceptibility. Among confounding factors, male gender and age was associated with a 2.42-fold and 1.06-fold increased risk of CLL, respectively. In conclusion, among the polymorphisms that were evaluated, the GSTM1 deletion polymorphism apparently helpsin the detoxification process and has a protective effect against CLL.

Genet. Mol. Res. 20(2): GMR18754
DOI: 10.4238/gmr18754