Current issues

Table of contents: 2020

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
Research Article

Mucopolysaccharidosis (MPS) related information in Colombia is limited. A descriptive research involving results obtained in the full exome sequencing of 244 patients with different types of pathologies and not clinically diagnosed with MPS was carried out with the purpose of examining the genomic variability of genes associated with the MPS complex in South West Colombia, considering that it is a region where MPS cases are constantly reported. Bioinformatics software was applied with the purpose of analyzing the clinical significance of the different variants. The frequency of each of the variants was calculated, and an interaction network of the genes found within the MPS complex was developed. We found 509 different gene MPS complex variants, of which 262 were not previously reported. The most frequent genes were IDUA, GLB1 and GALNS, involving MPS I and MPS IV A/ B. In the entire MPS complex 9/244 variants were found associated with pathogenesis. Among the 509 variants, we found 27% missense, 2% non-coded 21% synonyms, 1.8% located within the splice region, 3% upstream, and 4.5% in the UTR region. These gene and allelic frequencies of the MPS complex will alert the medical community to the presence of the variants of the genes associated with MPS in the population in order to establish early diagnosis programs. This will allow specific treatment for some of them, associated with transdisciplinary management that minimizes the morbidity and mortality attributed to this disease, including adequate genetic counseling.

Genet. Mol. Res. 19(2): GMR18502
DOI: 10.4238/gmr18502
Research Article

The objective of this research was to identify candidate gene markers based on their function related to marbling score and meat quality traits in pigs. A total of 313 commercial pigs with five different Duroc (DR) breed fractions: 1 = 100%DR (n = 227), 2 = 50%DR x 50% Large white (LW)(n = 7), 3 = 50%DR x 50%Landrace (LR)(n = 41), 4 = 75%DR x 25%LW (n = 18), and 5 = 50%DR x 25%LW x 25%LR (n = 20) were measured for marbling score (score 3; MB3 and score 6; MB6), Color (L*), % cooking loss and shear force meat characters. The pigs were slaughtered at around 190 days of age, at an average weight of 122 kg. Five candidate genes (LIPE, LEPR, ADRB3, CAPN1, and CAST) were genotyped by using -RFLP. The genetic parameters were estimated with Bayesian analysis via Gibbs sampling and analyzed by estimated breeding value by BLUP. The breed group had an effect on traits, especially marbling traits, percent cooking loss, and shear force. In Duroc purebreds, the marbling scores were significantly higher than in Duroc crossbreds. Al parameters were significantly higher in 50%DR x 50% Large white (LW) compared with the others. Association analysis showed that the AG genotype of the ADRB3 gene had a higher marbling score than the GG genotype (2.22 vs 1.99 for MB3, 2.92 vs 2.49 for MB6; P < 0.05). The lowest estimated breeding values (EBVs) for color (L*)(3.88) and  % cooking loss (2.64) were obtained in the CC genotype of the CAPN1 gene. The GG genotype showed lower shear force and EBVs compared to the AG genotype of CAST gene (4.08 vs 4.85 for shear force (P < 0.05) and -0.03 vs 0.05 for EBV’s, P < 0.01). The AG genotype of ADRB3 could be used in marker assisted selection to improve marbling scores. Also, the GG genotype of CAST is the most appropriate for selection for pork tenderness.

Genet. Mol. Res. 19(2): GMR18615
DOI: 10.4238/gmr18615
Research Article

We report the whole ram genome of Jordanian Awassi (Ovis aries), screened using the power of Illumina HiSeq sequencing technology, providing insights into the ram's genomic structure. Generated data will help in the assessment of naturally occurring genetic variation and population structure of this sheep breed using different structure variation markers. Also, it will help in the established marker-trait associations that can be used in marker-assisted breeding for qualitative and quantitative productive traits. A total of 23,812,247 single nucleotide polymorphism (SNPs) were identified, of which 177,117 (0.74%) were in the coding regions, as well as 3.77 million insertions/deletions and 3357 frame-shifting mutations in the coding region. The re-sequencing revealed 38,900 structure variation types distributed along genome, including 45 insertions and 16,643 deletions types. Also, there were 13,689 copy number variations, of which 3743 were up-regulated, and 9946 were down-regulated. These results will help in describing SNPs and the distribution of structural variations types used in genetic mapping and breeding programs of sheep breeds.

Genet. Mol. Res. 19(2): GMR18577
DOI: 10.4238/gmr18577
Research Article

Brazil is the fourth largest producer of cassava in the world. In the state of Mato Grosso more than 90% of family farmers grow cassava; therefore, studies that evaluate the genetic resources of this species present in the fields of these farmers can be considered essential. The objective of this study was to evaluate the genetic variability among ethnovarieties of cassava grown in five regions of the state of Mato Grosso, at a phenotypic level using morphoagronomic and molecular characteristics. Forty-five ethno-varieties of cassava were evaluated using 45 morphoagronomic descriptors, 36 qualitative descriptors and nine quantitative descriptors, in addition to 15 microsatellite loci. The data were analyzed with the help of the Past and Genes programs. The descriptors of qualitative nature revealed the existence of morphological divergence, with 97.35% polymorphism and the formation of five genetic groups using the UPGMA method. Forty-four ethno-varieties had more than one desirable root characteristic from an agronomic point of view. Among all the varieties, the Amarela I ethno-variety had the most of these characteristics. With the quantitative variables obtained using the UPGMA method, it was possible to form seven distinct groups, which revealed the Branca Comum and Paraguaia ethno-varieties to be the most dissimilar. The characteristic that most contributed to the distinction of the groups was that of root length (30%).  The 15 microsatellite loci amplified 109 alleles, and mean heterozygosity observed was higher than the expected heterozygosity. The UPGMA grouping revealed the formation of four distinct groups, and it was possible to verify duplicity of the Mandioca Batatinha and Pramuquem ethnovarities. By using joint analysis of the data, five genetic groups were observed, without duplicity of material; groups III, IV and V were isolated individuals. Between qualitative and quantitative variables, there was a significant correlation of 31% and between qualitative and molecular data the correlation was 12.4%. The collection of ethno-varieties grown in the fields of family farmers in the state of Mato Grosso present genetic divergence at the phenotypic level, based on morphoagronomic and molecular characteristics, and these ethno-varieties have characteristics of interest for genetic improvement and improved marketability.

Genet. Mol. Res. 19(2): GMR18538
DOI: 10.4238/gmr18538
Research Article

The resistance of oat cultivars to fungicide use reduction and supporting longer harvest application interval can reduce or avoid the risk of food contamination and environmental pollution. We compared oat cultivars for resistance to reduction in the number of fungicide applications and with longer intervals from application to harvest, considering favorable and unfavorable crop year conditions and how they affect yield and progress of major leaf diseases. The study was conducted in 2015, 2016 and 2017, in Augusto Pestana, RS, Brazil. The experimental design was a complete randomized block with three replications in a 22 x 4 factorial scheme for 22 oat cultivars recommended for cultivation in Brazil and four conditions of fungicide use: no application; one application 60 days after emergence; two applications at 60 and 75 days after emergence and; three applications at 60, 75 and 90 days after emergence. In the control of leaf diseases, the fungicide FOLICUR® CE was used in 2015 and 2016 and the fungicide PRIMO® in 2017 at dosages of 0.75 and 0.3 liters ha-1, respectively. Most of the oat cultivars had little addtional production with the third application of fungicide at 90 days after emergence. Therefore, we coulold increase the interval between application and harvest with just two applications, at 60 and 75 days after and emergence. FAEM 4 Carlasul, URS Altiva and URS Guria cultivars gave high yields under most fungicide use conditions, allowing a long interval between the last application and grain harvest.

Genet. Mol. Res. 19(2): GMR18542
DOI: 10.4238/gmr18542
Research Article

Fusarium wilt is a serious soil disease affecting common bean cultivation, especially crops under a central pivot irrigation system. Our objective was to identify bean lines that combine resistance to Fusarium wilt in the field with other desirable traits. Twenty-eight randomized block trials with three replicates were conducted  in the rainy, winter, and dry seasons from 2009 to 2012 in the states of Goiás, Federal District, and Paraná. The trials were composed of six elite lines (one carioca and five black grain type) selected in a previous study as resistant to Fusarium wilt under controlled conditions and five cultivars (three carioca two black grain type). Variance analysis demonstrated variability for reaction to Fusarium wilt and anthracnose, yield, architecture, and lodging tolerance. The interaction among the lines/cultivars and environments was significant for all traits. Five black bean lines were resistant to Fusarium wilt (grades <3.0) in the field; however, none of these lines outperformed the best controls in other traits, especially anthracnose resistance (grades >4.0). The Carioca line (CNFC 15872) was susceptible to fusarium wilt (5.6). Thus, these lines should not be indicated as suitable cultivars. Cultivars BRS Esplendor and BRS Notável exhibited excellent yield (2144 and 2200 kg.ha-1, respectively), high stability, erect architecture (3.4 and 4.1), lodging tolerance (3.3 and 4.0), anthracnose resistance (1.0 and 1.7), and high fusarium wilt resistance (2.0 and 2.6). These cultivars are still excellent options for planting in areas with Fusarium wilt.

Genet. Mol. Res. 19(2): GMR18617
DOI: 10.4238/gmr18617
Research Article

Raspberry (Rubus idaeus) is an economically important crop, and its cultivation has expanded recently across temperate and subtropical regions of Brazil. There is no brazilian raspberry cultivar so far. Therefore, the indirect selection can be an useful tool to help during the breeding process. We evaluated linear and canonical correlations in primocane-fruiting raspberry cultivars in 2013 and 2014, in a completely randomized experimental design, with eight replications. The genotypes ‘Alemãzinha’, ‘Heritage’ and ‘Fallgold’ were evaluated during two harvesting seasons, autumn and spring. Canonical groups were established among morphological (Group 1) and yield (Group 2) traits. In Group 1, plant yield and fruit weight were evaluated; in Group 2 the productive period, plant height, stem diameter, dry mass of pruning and plant leaf area were assessed. The linear and canonical correlations among morphological, phenological, and yield traits varied according to harvesting season. The phenological and morphological traits had greater linear correlation with yield traits in autumn than in spring. Based on our findings, to obtain more productive raspberry genotypes, plant leaf area and dry mass of pruning should be prioritized in the indirect selection.

Genet. Mol. Res. 19(2): GMR18500
DOI: 10.4238/gmr18500
Research Article

Advances in biotechnology and molecular biology fields have allowed the sequencing of species genomes to improve the understanding of their genetics. As a consequence of the large number of whole genome sequencing projects, various DNA and protein sequences predicted by bioinformatics still without an identified function and are annotated in data banks as hypothetical proteins (HPs). Approximately 30% of the genome of recently sequenced organisms is composed of HPs, and these proteins are not included in functional studies due to the inexistence of full annotation. The characterization of HPs through bioinformatics is an important step to improve the understanding of genes and proteins and aims to assign some information to these sequences. Here, we used bioinformatics tools to predict the function of a hypothetical protein using as a model a protein from the filamentous fungus Penicillium rubens (XP_002569027.1). This fungus has been extensively studied due its ability to produce a wide range of natural products, many of them with biotechnological and pharmaceutical applications. The first step was to characterize the physicochemical properties of this HP. This protein has a molecular weight of 79.4 kDa and a theoretical pI of 5.06; 44.1% of its sequence is composed of hydrophilic amino acid residues and it was predicted as an extracellular protein. Prediction of 3D structure showed 42.21% of this sequence with an alpha galactosidase from Geobacillus stearothermophilus. In addition, XP_002569027.1 showed the presence of a glycosylase domain and most important amino acids residues in a catalytic site. Thus, we characterized a HP from P. rubens using computational tools and were able to produce useful information for future in vivo and in vitro studies, highlighting the importance of bioinformatics as a preliminary tool for functional studies.

Genet. Mol. Res. 19(2): GMR18574
DOI: 10.4238/gmr18574
Research Article

Banana is an importment international economical crop, but drought is the most significant environmental stress in banana intrustry. Previous studies on banana drought tolerance evaluated just a few indicators, such as malondialdehyde (MDA) and plasma membrane permeability (PMP), with little or no systematic morphological and physiological information. We examined the morphological and anatomical structure characters of nine genotypes among 28 banana varieties from the variety resource nursery of China academy of topical agricultural sciences, and combined physiological markers (PMP and MDA) with morphological data. Leaf thickness, upper leaf epidermis and cutin thickness, palisade tissue thickness, spongy tissue thickness, lower leaf epidermis and cutin thickness, cell tense ratio (CTR), PMP and MDA content were significantly different among these varieties. Banana varieties were divided into three groups by cluster analysis based on a CTR index or a MDA content index, and the varieties were divided into two groups by cluster analysis based on the PMP index. Based on discriminant functions, the original classification was confirmed, and the result of discriminant classification was 100% correct. Three discrimination models with superior distinguishing abilities were established.

Genet. Mol. Res. 19(2): GMR18544
DOI: 10.4238/gmr18544
Research Article

Ornamental peppers have been attracting great commercial interest in recent years. However, despite the demand, the availability of ornamental pepper cultivars to growers and consumers is still reduced, which should stimulate breeding programs for improved varieties. In this context, the identification and characterization of accessions in ornamental pepper germplasm banks is extremely important. We phenotypically characterized nine pepper accessions and analyzed the genetic divergence between them for the potential development of ornamental pepper cultivars. The experiment was conducted in a greenhouse at the agricultural sciences center of the State University of Montes Claros, Minas Gerais, in a completely randomized design, with nine accessions and eight replications. The plants were morphologically characterized with 34 qualitative and five quantitative descriptors. For taxonomic identification to the species level, a key to identify Capsicum species was used. In the molecular analysis, 32 ISSR primers were used for the detection of polymorphism between individuals. A multivariate analysis was performed by estimating the genetic dissimilarity by the Jaccard coefficient for the molecular variables and by the Gower algorithm for the morphological ones, using the UPGMA method for hierarchical analysis of clusters. The nine accessions that were selected for evaluation were considered as potential parents due to characteristics of ornamental interest. The accessions were all classified as belonging to the species Capsicum annuum and were grouped differently when using morphological versus molecular data. Analysis of molecular data detected greater dissimilarity between accessions, with the formation of a larger number of groups. The joint exploration of the morphological and molecular information allows a more reliable inference of the genetic dissimilarity between accessions and will facilitate planning of crosses.

 

Genet. Mol. Res. 19(2): GMR18596
DOI: 10.4238/gmr18596

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