Research Article

Table of Contents | Genet. Mol. Res. 2020 (3)

Displaying 1 - 15 of 15
Research Article

One of the main global causes of mortality is cerebral ischemia. Studies report that alcohol abuse causes health problems, aggravating the conditions of neurological diseases. The role of microRNAs has been highlighted in the literature as biomarkers in various types of diseases, including neurological disorders. Evidence of dysregulation of serum miRNAs related to apoptosis in experimental brain ischemia associated with alcoholism is scarce. We evaluated the gene expression of miRNA-15b and 16 (apoptotic) and miRNA-21, -221 and -222 (anti-apoptotic) in the blood after experimental induction of temporary focal ischemia (90 minutes) by occlusion of the middle cerebral artery in rats, followed by reperfusion for 48 hours, associated with  a  chronic alcoholism model. Fifty-six rats were randomly divided into seven experimental groups: Control (C); Sham (S); Ischemic (I); Ischemia-reperfusion (IR), Alcoholic (A); Alcoholic and ischemic (I + A); Ischemia-reperfusion and Alcoholic (IR+A). The blood samples were collected for gene expression analysis of some serum miRNAs by PCR in real time. The serum expression of miRNA-16 was higher in the IR group compared to C and S groups (P < 0.05) but no association with chronic alcoholism was found. The serum expressions of miRNA-21, -221 and -222 were low in all groups and were not correlated with ischemic injury and/or chronic alcoholism. The serum expressions of miRNA-15b, -21, -221 and -222 were similar among the experimental groups, with no correlation with ischemia, with or without reperfusion, and/or alcoholism. The overexpression of miRNA-16 in the blood of I and IR groups demonstrated a correlation with the ischemic process, mainly after reperfusion for 48 hours, associated or not with alcoholism.

Genet. Mol. Res. 19(3): GMR18637
DOI: 10.4238/gmr18637
Research Article

Myrica rubra has been cultivated for more than 2000 years it is one of most popular fruits in south China. We compared three M. rubra cultivars, "Muye" (MY), "DongKui" (DK), and "Zao Jia" (ZJ) to determine the causes of the differences in fruit color. We found changes in the anthocyanin and carotenoid contents during the fruit coloring and maturity phases. The anthocyanin contents of the three cultivars increased from the initial fruit coloring phase to the maturity phase. During this period, the total contents of anthocyanin and cyanidin in MY were higher than those in ZJ by 8.57 and 26.45% and higher than those in DK by 80.16 and 129.37%, respectively. RNA-Seq based transcriptome analysis of veraison and mature berries of the three M. rubra cultivars was conducted. The total numbers of genes and N50 lengths were 33,033 and 1,426 for MY, 35,166 and 1,145 for DK, and 31,374 and 476 for ZJ, respectively From the initial color-turning phase to the maturity phase, there were three up-regulated and three down-regulated genes in MY, while there were 3,058 up-regulated and 65 down-regulated genes in DK and 1,484 up-regulated and 1,169 down-regulated genes in ZJ. Based on functional insight of the differentially expressed genes, 3-Amino-1,2,4-triazole (3AT) would be the key gene responsible for color variation in these three cultivars. We concluded that the 3AT gene controls M. rubra berry color. Based on qRT-PCR, we found that expression of 3AT was much higher in MY and ZJ. This result was consistent with our RNA-Seq analysis. In conclusion, cy-3glu and peonidin are pigments that have a significant effect on the color of M. rubra fruit, and 3AT is a functional gene that regulates these pigments. These results could have practical significance for M. rubra selection strategies.

Genet. Mol. Res. 19(3): GMR18371
DOI: 10.4238/gmr18371
Research Article

Understanding the genetic control of internode length is essential to develop more compact winter squash genotypes. Our objective was to elucidate the genetic control of internode length before and after emergence of the first female flower in winter squash, Cucurbita moschata. This was done by estimating the linear and quadratic genetic components and using the maximum likelihood estimation function. The parents used were the long-vined accession BGH 7319 (P1) and the compact cultivar ‘Tronco Verde’ (P2). The F1 plants from this cross were self-fertilized to obtain the F2 generation, and then they were backcrossed with P1 and P2 to obtain generations BC1 and BC2, respectively. By examining the linear and quadratic genetic components of variations in internode length, we found evidence of dominance effects both before and after flowering, with a reversal in dominance after flowering. Using maximum likelihood, we observed that the internode length before flowering was controlled by one major gene with additive and dominance effects, while the internode length after flowering was controlled by multiple genes with additive and dominance effects, plus environmental effects. Based on these results, strategies using backcrosses for introgression of the major gene controlling this trait before flowering and recurrent selection for introgression of the polygenes involved in trait control after flowering are recommended.

Genet. Mol. Res. 19(3): GMR18660
DOI: 10.4238/gmr18660
Research Article

Rice (Oryza sativa) is crop that adapts well to diverse soil and climate conditions; breeding programs have generally been committed to identifying and selecting genotypes that are stable and have high productivity in various environments. In this sense, studies of adaptability and stability are of paramount importance to aid in the recommendation of cultivars, since it allows growers to obtain detailed information about the behavior of the genotypes in each region. We evaluatde the adaptability and stability of irrigated rice genotypes grown with continuous flooding, for the selection and recommendation of cultivars for crops or breeding programs. Eighteen genotypes were evaluated for grain yield in four agricultural years at three sites, covering 12 environments. The adaptability and stability were assessed by the methods of Eberhart and Russell, multiple centroids and GGE biplot. Genotypes behaved differently regarding stability and adaptability in the different environments. Both methodologies identified BRA 02691 and MGI 0607-1 as promising to be released as cultivars; however, classification inconsistencies occurred, such as for the line BRA 031001. Multiple centroid and GGE biplot methods demonstrated greater sensitivity than the Eberhart and Russell method. Using the methods simultaneously provides an innovative approach to the interpretation of GxE interactions and is a viable alternative for genotype classification. The genotype MGI 0607-1 showed promising behavior independent of the methodology used.

Genet. Mol. Res. 19(3): GMR18434
DOI: 10.4238/gmr18434
Research Article

We compared three Pi-efficient (ATF-14B, ATF-53B, 101B) and four Pi-inefficient (ATF-16B, 116R, 136B, 187R) sorghum genotypes under different Pi concentrations. There were no significant differences between the groups in Pi-use efficiency under Pi-deprivation for anthocyanin accumulation, dry-weight matter, acid phosphatase activity (APA), and aerenchyma formation. However, both groups showed anthocyanin accumulation under Pi-deprivation. Under Pi-deficiency, there was a significant reduction of dry weight in both groups, with no significant differences between contrasting genotypes. All genotypes exhibited a significant increase in root/shoot ratios during Pi-deficiency, and these changes were not related to Pi-use efficiency. The total Pi content in roots and shoots in all genotypes was similar and represented less than 0.2 % of the total dry weight. For all genotypes, the Pi content in P+ treatment resulted in a significant variation ranging from 0.45 to 0.85% and 0.41 to 0.66% in roots and shoots, respectively. The genotype 187R had the highest P content in roots and shoots. APA activity showed increased activity only in the roots of both groups. The development of aerenchyma was conspicuous in the basal and in the middle root sections of all genotypes grown under different Pi levels. Two sorghum Pi-transporter genes were strongly overexpressed in the middle part of Pi-deprived roots of 136B genotype. We did not find differences that explain the Pi-use efficiency between efficient and inefficient genotypes. More studies are needed to elucidate the complex mechanism of P-utilization by sorghum plants.

Genet. Mol. Res. 19(3): GMR18469
Research Article

Pyemotidae mites are ectoparasites of a large number of arthropods, and Pyemotes tritici (Acari: Pyemotidae) is often found parasitizing insects in various habitats, including in the laboratory. Here we report widespread infestation of P. tritici in laboratory colonies of various species of stored-products insects. P. tritici infestations were observed in laboratory colonies (MIPGrains/UFV) of Sitophilus zeamais (Coleoptera: Curculionidae), Alphitobius diaperinus (Coleoptera: Tenebrionidae), Lasioderma serricorne (Coleoptera: Anobiidae), Acanthoscelides obtectus (Coleoptera: Bruchidae), Rhyzopertha dominica (Coleoptera: Bostrichidae), Ephestia sp. (Lepidoptera: Pyralidae), and Tribolium castaneum (Coleoptera: Tenebrionidae). The widespread infestation of P. tritici in laboratory colonies of these species is a serious problem. This mite can substantially reduce insect populations or even kill them, making it impossible to rear the insects, as observed in this research. This ectoparasite is not recommended as a biological control agent in integrated pest management of stored-product pests because P. tritici can attack bees, mammals, and other animals and cause dermatitis in humans. In consideration of the above, the widespread infestation of P. tritici in colonies of S. zeamais, A. diaperinus, L. serricorne, A. obtectus, R. dominica, Ephestia sp., and T. castaneum indicates that this mite should be monitored when raising stored-products insects to ensure the development of the insect populations and ensure that the laboratory environment is safe.

Genet. Mol. Res. 19(3): GMR18548
DOI: 10.4238/gmr18548
Research Article

Xanthomonas oryzae pv oryzae (Xoo) is a bacterial pathovar that causes a serious bacterial leaf blight disease of rice. This disease poses significant constraint on food security in Asia, as it causes yield loss in rice. There is an urgent need to control bacterial blight disease through resistance cultivars. However, the genetic potential of Malaysian rice cultivars has not been explored. We screened 10 cultivated Malaysian varieties with high yield performance for resistance genes using three simple sequence repeat and two sequence tagged sites markers coupled with phenotypic screening. All 10 rice genotypes were found to carry xa recessive gene. Four genotypes had two resistance genes tightly linked with the specific markers; Mahsuri Mutant carried the dominant resistance genes, xa4 and xa2 whereas NMR152 and the Tongkat Ali mutant had the dominant genes, xa21 and xa2. However, xa13 and xa5 resistance genes were not detected in this Malaysia rice germplasm group. In a greenhouse assessment, genotypes carrying more than a single resistance gene were found to be resistant against Xoo MXO 1410 isolates. These cultivars have potential as genetic materials for rice quality breeding programs.

Genet. Mol. Res. 19(3): GMR18545
DOI: 10.4238/gmr18545
Research Article

The culture of summer squash (Cucurbita pepo) has great socioeconomic importance worldwide. Characterization of C. pepo germplasm has been predominantly performed by field evaluations, which is very time consuming. Thus, the validation of new techniques capable of optimizing time for the field germplasm selection process would be useful. We evaluated agronomic potential and genetic dissimilarity of C. pepo germplasm and gathered data to determine whether aerial images obtained by drone imaging could assist in the selection of vegetative vigor; this is the first such analysis for this crop. Sixty-five genotypes belonging to the vegetable germplasm bank of the Federal University of Uberlândia were evaluated, with three replications in a randomized block design. The variables evaluated were: production per plant, number of fruits per plant, leaf temperature, precocity, and the indexes SPAD (Soil Plant Analysis Development), LAI (Leaf Area Index), NDVI (Normalized Difference Vegetation Index) and NDRE (Normalized Difference Red Edge Index) the last three variables were obtained using drone imaging. Genetic divergence analysis was performed with multivariate techniques using generalized Mahalanobis distance and UPGMA clustering. Hybrid performance was compared by the Scott-Knott test. UPGMA clustering showed considerable genetic diversity, with the formation of 12 distinct groups. The largest relative contribution was from the leaf area index in the discrimination of the genotypes, demonstrating high efficiency in the validation of the image phenotyping technique. Eight genotypes stood out for yield, fruit number, precocity and high leaf area index, NDVI and NDRE values. The use of image phenotyping using NDVI and NDRE sensors was efficient to identify C. pepo genotypes that differed in plant vigor.

Genet. Mol. Res. 19(3): GMR18598
DOI: 10.4238/gmr18598
Research Article

The cultivation of onion in Brazil has a relevant socioeconomic contribution. Despite the potential, there are few onion breeding programs for tropical conditions. One of the major obstacles is related to the complexity during the selection steps, since in onion, quantitative characters and low heritability predominate. For this reason, the purpose of this study was to assess the dynamics of expression between onion line traits based on phenotypic and genotypic correlations. Four sets of onion genotypes were assessed, comprising both advanced and segregating lines. The traits assessed were plant vigor, diameter of pseudostem, plant architecture, plant cycle, average bulb mass, bulb firmness and bulb postharvest. Phenotypic and genotypic correlations were calculated. Path analysis provided the estimate of the direct and indirect effects based on average bulb mass as the main variable. There was dynamics in trait expression. Coherence was reported for the correlation values of the different traits among the different germplasms (experiment 1 with 109 advanced lines; experiment 2 with 227 segregating lines; experiment 3 with 53 advanced lines; and experiment 4 with110 segregating lines). Correlations were positive for all average bulb mass x plant vigor experiments; plant architecture x plant vigor was also positive in all experiments, except for experiment 1 (109 advanced lines). The correlations which were larger in magnitude were those between bulb postharvest and plant cycle, and between bulb postharvest and average bulb mass. The phenotypic and genotypic correlations showed low association between traits in all experiments, except for experiment 3 (53 advanced lines), in which some pairs of correlations were moderate to high; however, the path analysis confirmed that the cycle (in days) and bulb postharvest showed weak cause-and-effect relationship with the main variable, rendering indirect selection impracticable for onion average bulb mass.

Genet. Mol. Res. 19(3): GMR18636
DOI: 10.4238/gmr18636
Research Article

Bovine brucellosis is a zoonotic disease that has considerable economic impact on the market of products such as meat and milk. As Brazil has one of the largest cattle herds in the world, this disease is a significant agricultural and public health concern. In 2001, Brazil launched the National Program of Control and Eradication of Animal Brucellosis and Tuberculosis. This program included the vaccination of 3-8 month old calves using the smooth and attenuated S19 strain, as well as monitoring with serological tests. There have been reports of excretion and persistence of S19. In this context, the objective of this study was to monitor the persistence of the S19 vaccine strain in blood samples from vaccinated calves. Seroconversion was investigated to evaluate the vaccine immunogenicity. PCR assays of blood and serum were run at at: "day zero" (before vaccination), 1 to 15 days after vaccination and every month until 12 months, totaling 28 collections for each of 10 calves. The vaccine strain was detected throughout the study, even at day zero, before the calves were vaccinated. Sequencing analysis confirmed the presence of the S19 strain. Results from serological tests did not show agglutination in “day zero” samples, meaning the immune response was negative. An immune response was first detected in two samples on the fourth day. One hypothesis that could explain this positivity before vaccination is that the already vaccinated mothers could have transmitted the vaccine to the calves, as the cows presented excretion of the S19 strain in milk and/or urine. This is the first report of the finding of this bovine brucellosis vaccine strain in the blood of calves before vaccination.

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Genet. Mol. Res. 19(3): GMR18659
DOI: 10.4238/gmr18659
Research Article

Rice blast disease is a major threat to rice production worldwide; the causative pathogenic fungus Magnaporthe oryzae induces rice (Oryza sativa) plants to undergo molecular changes that help them to circumvent this fungal attack. Transcriptome studies have demonstrated that many genes are involved in the defense response of rice to M. oryzae, but most of these studies focused on the screening of differentially expressed genes and the studies did not investigate the interactions among genes. We examined the interaction of rice and M. oryzae in a network context. Two near-isogenic lines were profiled at different time-points. Using transcriptome data obtained from an RNA-Seq analysis, a network based on the relationships among genes was developed through weighted gene co-expression network analysis. The analysis of degree centrality identified numerous hub genes and potential key regulators that control the rice response, providing new insights into the molecular network underlying the resistance of rice to M. oryzae infection. Additionally, a protein-protein interaction network was derived to identify complexes that might physically interact. For example, complexes of OsbHLH148/OsJAZ, OsMYB4 and some components of the phenylpropanoid pathway, as well as MYB/bHLH and NB-LRR/OsWRKYs were identified, suggesting possible roles in regulating M. oryzae infection. The combination of in silico data with transcription factor binding indicates that OsbZIP45 may serve as a driver of complex gene expression changes that result in resistance to rice blast disease, and can thus act as an integrator of multiple signals and as a coordinator of diverse cellular pathways to control the defense responses.

Genet. Mol. Res. 19(3): GMR18579
DOI: 10.4238/gmr18579
Research Article

We examined a possible influence of HOX gene mutations, which encode factors controlling anterior-posterior development, on vesicoureteral reflux (VUR). For this purpose, we evaluated the HOX-B7 gene as a promoter of the RET gene. From May 2014-June 2015, 33 pediatric patients diagnosed as having VUR at a university urology clinic were enrolled in the study. Patients with other urological malformations were excluded. The mean age was 69 ± 37 months. We found single genetic polymorphisms in 21 patients on HOX-B7 (exons 1 and 2), and 17 patients had polymorphisms only on exon 1. This variant is in a non-encoding area on the gene locus. Nevertheless, the results showed that these variants could be involved in VUR pathogenesis. Exon 1 mutation was found in six patients who had moderate VUR (grade III) and in seven patients who had severe VUR (grades IV and V). Eight patients with exon 1 variants had renal scarring due to reflux, and seven had homozygote mutations. When we examined the correlation between the duration of VUR and renal scarring, the duration of renal scar development in patients with exon 1 variant clustered at 15 months, but there was no significant difference between groups (P = 0.15), and there was no association between exon 1 variations and renal scarring (P = 0.86). The results showed that these variants could be an important gene for VUR pathogenesis. We concluded that a HOX-B7 variant of exon 1 was associated with moderate to severe VUR.  Our study support the conclusion that HOX-B7 is an important gene for VUR development, but there was no significant association with renal damage.

Genet. Mol. Res. 19(3): GMR18578
DOI: 10.4238/gmr18578
Research Article

Atherosclerosis is an important cardiovascular disease due to its high mortality rate worldwide. Risk factors such as chronic use of cigarettes, poor diet, sedentary lifestyle, diabetes mellitus and genetic factors significantly contribute to the disease. The CYP2C19 gene is a well-studied target for cardiovascular disease treatment. Polymorphisms in the CYP2C19 gene, which encodes cytochrome P450 enzymes, may result in inefficiency of the drug clopidogrel. Identification of CYP2C19 polymorphisms may improve preventive treatment and the prognosis of the disease. We investigated if the CYP2C19*2 polymorphism influences the onset of restenosis in smokers. We analyzed 200 patient blood samples from the Cardiology and Peripheral Vascular Surgery clinics of hospitals in Goiânia, Brazil. The DNA samples were submitted to PCR amplification and the product obtained was submitted to electrophoresis. We found that 34% of the atherosclerotic smokers had stents, and 46% of them developed restenosis. The frequency of the CYP2C19*2 polymorphism showed that 34% of atherosclerotic smokers who had at least one polymorphic allele had a stent and 45% of these patients developed restenosis. These differences were not significant. Although the CYP2C19*2 polymorphism alters the response to clopidogrel, its association with smoking did not influence the development of restenosis.

Genet. Mol. Res. 19(3): GMR18641
DOI: 10.4238/gmr18641
Research Article

Mimosa pigra is a plant commonly used for medicinal purposes in the treatment of several diseases. However, studies regarding its toxicological properties are scarce. We evaluated the toxic, cytotoxic, genotoxic and mutagenic activities of leaf and stem infusions of M. pigra collected in the region of Delta do Parnaíba, Piauí, Brazil, through an in vivo Allium cepa test. Three concentrations of leaf and stem treatments were used (leaf treatment 1 and stem treatment 1 = 0.771 g/L; leaf treatment 2 and stem treatment 2 = 1.542 g/L; leaf treatment 3 and stem treatment 3 = 3.084 g/L), in addition to the negative controls (water) and positive controls (copper sulfate - 1.2 mg/mL - A. cepa test). All the treatments were toxic, causing significant root growth inhibition. Leaf treatment 1, leaf treatment 3 and stem treatment 1 showed significant inhibition of the mitotic index. Leaf treatment 2, stem treatment 1 and stem treatment 3 showed significant genotoxic activity based on the frequency of chromosomal aberrations. The tested concentrations did not provoke significant mutagenic activity when compared to the negative control. We suggest that further studies with other biological systems are needed to evaluate the safetyness of M. pigra infusions for therapeutic purposes.

Genet. Mol. Res. 19(3): GMR18588
DOI: 10.4238/gmr18588
Research Article

Longevity and lifetime production traits are of increasing importance in swine breeding schemes worldwide because these traits influence sow productivity and welfare, as well as affecting farm profitability. The Landrace breed makes up one-half of the F1 Large White x Landrace female, which is the most popular maternal line in the breeding herd of commercial pork production systems in Thailand and throughout the world. The objective of this study was to estimate genetic parameters and detect potential genetic variants associated with age at first farrowing (AFF), length of productive life (LPL), lifetime number of piglets born alive (LNBA), lifetime number of piglets weaned (LNW), lifetime wean to first service interval (LW2S) and lifetime pig efficiency (LTP365) in a Thai Landrace pig population. dData were analyzed for 82,346 litters from 12,843 Landrace pigs housed in three farms; all farms were a part of a large commercial production system. Genetic parameters were estimated using a single-step, genomic-BLUP (ssGBLUP) that utilizes general pedigree and genomic relationships. Landrace sows were genotyped with 60K Illumina PorcineSNP60 BeadChip. The genotypes were analyzed by weighted single-step genome-wide association analyses. Heritability estimates for longevity and length of productive life traits were low and ranged from 0.01 to 0.11. The greatest genetic correlations between LPL with LNBA, LNW, LW2S and LTP365 ranged from 0.44 to 0.91. The greatest genetic correlations between LPL and LNBA, LNW, LW2S and LTP365 ranged from 0.44 to 0.91. Based on these results, genetic selection for LPL was not antagonistic with lifetime production. Twenty-seven candidate genes were identified as being associated with one or more traits evaluated in this Landrace pig population. Highlighted genes related to LPL, LNBA, LNW and LTP365 included TMLHE, PDHX and KCNJ6 on SSC13 in this pig population. This constitutes a list of candidate genes that could be incorporated into selection to improve sow longevity and lifetime production traits in the pig industry.

Genet. Mol. Res. 19(3): GMR18465
DOI: 10.4238/gmr18465