Research Article

Table of Contents | Genet. Mol. Res. 2017 (2)

Displaying 91 - 105 of 128
Research Article

Fusarium wilt caused by Fusarium oxysporum f. sp lycopersici (Fol) is one of the main diseases affecting tomatoes. The BHRS 2,3 genotype of tomato is, however, resistant to this disease. A proteomic approach was used to understand the defense mechanisms of this genotype using the tomato root, the first tissue that interacts with the fungus, as a target. Protein was extracted and separated by two-dimensional electrophoresis followed by staining with Coomassie brilliant blue. The proteins were identified by MALDI-TOF/TOF mass spectrometry. A total of 22 proteins were identified, 21 of which showed differential expression with 12 proteins being upregulated and nine being downregulated. Plants responded to the pathogen with increased expression of pathogenesis-related proteins. We noted the induction of proteins involved in hypersensitivity reaction and other defense mechanisms. The expression of proteins of primary metabolism related to energy production, however, decreased, as did the expression of two proteins related to defense against abiotic stress. These results demonstrate the presence of important mechanisms for defense against Fol in the tomato genotype BHRS 2,3.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16027209
Research Article

Sugarcane (Saccharum sp) is one of the most promising crops and researchers have sought for renewable alternative energy sources to reduce CO emission. The study of strategies, which allow breeders in the selection of superior genotypes for many traits simultaneously, is important. Therefore, the objectives of this study were: i) to apply path analysis to better understand the relationship between the lignocellulosic traits and technological quality traits with total recoverable sugars (TRS) and ii) to use several multivariate selection indexes to predict the genetic gain and to select superior genotypes in the sugarcane breeding. A total of 40 sugarcane genotypes were evaluated in an experimental design using incomplete blocks with two replicates. The follow traits were evaluated: dry matter (DM), total soluble solids (BRIX), apparent sucrose content in the juice (POL), apparent sucrose content in sugarcane (POLS), fiber content (FIB), purity (PUR), TRS, lignin content (LC), cellulose content (CC), hemicellulose content (HC), and ash content (AC). These traits were analyzed by analysis of variance, phenotypic correlation network, path analysis, and selection index. The highest direct effect on TRS was obtained by POLS (0.337), POL (0.299), BRIX (0.227), and FIB (-0.146). The estimates of phenotypic correlation between these characters and TRS were in the same direction, which demonstrated a cause-and-effect relationship. The highest indirect effect was of POL via POLS (0.331) followed by POLS via POL (0.294). BRIX presented high indirect effects via POLS (0.266) and via POL (0.246). On the other hand, FIB presented negative indirect effects via POLS (-0.169) and POL (-0.103). In conclusion, path analysis and index selection are useful strategies to help breeders in the selection of superior genotypes in sugarcane.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16029678
Research Article

The aims of this study were to assess the linear relationships between agronomic and nutritional traits and to identify promising traits for indirect selection in early and super-early maturing maize genotypes. Two trials were run in the 2009/2010 agricultural year, each consisting of a randomized block design with three replications. One trial was run on 36 early maturing maize genotypes and the other on 22 super-early maturing genotypes. Six agronomic traits, 11 protein-nutritional traits, and four energetic-nutritional traits were measured. Error normality assumptions were verified using the Kolmogorov-Smirnov test and residual variance homogeneity assumptions using the Levene test. Analysis of variance and the F-test were run for each of the 21 traits. Next, the genotype correlation coefficient matrix was estimated for the 21 traits and each trial. Ridge path analysis was based on values of k = 0.00 and k = 0.10 on the diagonal of X'X correlation matrix, taking the nutritional traits as principal variables and agronomic traits as explanatory variables. The number of days from sowing to male flowering, the number of days from sowing to female flowering, plant height, ear insertion height, ear weight and grain yield can be used in indirect selection as indicators of grain nutritional quality.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16029671
Research Article

Selecting and validating reference genes are the first steps in studying gene expression by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR). The present study aimed to evaluate the stability of five reference genes for the purpose of normalization when studying gene expression in various cultivars of Prunus persica with different chilling requirements. Flower bud tissues of nine peach genotypes from Embrapa's peach breeding program with different chilling requirements were used, and five candidate reference genes based on the RT-qPCR that were useful for studying the relative quantitative gene expression and stability were evaluated using geNorm, NormFinder, and bestKeeper software packages. The results indicated that among the genes tested, the most stable genes to be used as reference genes are Act and UBQ10. This study is the first survey of the stability of reference genes in peaches under chilling stress and provides guidelines for more accurate RT-qPCR results.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16029666
Research Article

This study aimed to evaluate the genetic variability of the teak germplasm bank, using morphological traits and inter-simple sequence repeat molecular markers. Thirty clones were evaluated in a randomized complete block design with three replicates, and each plot was composed of three plants. A joint analysis of quantitative and qualitative variables was performed using the Gower algorithm. Quantitative, qualitative, and molecular variables were analyzed simultaneously using the Ward-MLM procedure. There is genetic variability among the 30 teak genotypes studied, considering the quantitative, qualitative, and molecular variables by the Ward-MLM statistical procedure. Morphological traits used proved to be efficient for the study of genetic variability; however, it was not possible to compose a descriptor table for clonal teak genotypes based on the traits evaluated. The Gower method was efficient in discriminating the groups, demonstrating that the simultaneous analysis of qualitative and quantitative data is feasible and can allow greater efficiency in the knowledge of the variability among teak genotypes. The genotype 22 showed to be the most divergent compared to the other genotypes, except for the cluster of genotypes by the UPGMA method based on the Gower distance obtained by the Ward-MLM procedure, which formed a group with genotypes 9 and 30, in the morphological and molecular analyses and was grouped alone.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16029665
Research Article

Drought, in conjunction with high temperature, is an important environmental constraint to cotton production. Development of cotton varieties with increased tolerance against adverse environmental conditions has been proposed as effective strategy for ensuring reliable yields. In the present study, 30 simple sequence repeat (SSR) primers were used to estimate genetic divergence among 22 cotton genotypes for drought stress tolerance. Genetic diversity is a prerequisite for developing drought resistant cotton genotypes. Eleven SSR primers out of 30 were able to discriminate among the cotton genotypes, implying that 37% of the primers were informative. In total, 41 alleles were detected, with an average of 3.72 alleles per primer. The number of alleles per locus ranged from one (JESPR-284) to six (JESSPR-302), and the allelic diversity in the experimental material was 0.40. Genetic similarity coefficients ranged from 0.87-1.00. The result of principal component analysis confirmed the clustering of 21 cotton genotypes in two groups leaving one genotype (CIM-109) ungrouped. Overall, genetic diversity among the 22 cotton genotypes was low. More polymorphic SSR markers are needed to explore the workable genetic variation among the screened cotton genotypes in future studies.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16029664
Research Article

We assessed the impact of genetic divergence and the ability to combine corn hybrids used for the production of silage on the agronomic and bromatological traits of silage quality. We evaluated 18 corn hybrids used as genitors in a circulant diallel scheme in which each genitor hybrid participated in 9 hybrid combinations, and evaluated 100 treatments [18 genitor hybrids, 81 diallelic hybrids, and a commercial check hybrid (DKB330)] in a triple lattice 10 x 10 experimental design in two environments in Brazil. Genetic variability was adequate among the corn silage hybrids, and we can recommend the use of genitors 2B688 and P30B39 for the formation of a base population for intrapopulational breeding. The P30P34 hybrid is the best for intrapopulational breeding when aiming for silage with high protein content, low fiber content, and higher in vitro digestibility. Interpopulational breeding directed at improving silage digestibility can use a combination of genitors P30P34 and AS1572, but AS1572 and P30K64 are the most recommended. Hybrids 2B688, P30P34, and SG6015 are considered the most genetically distant of the others hybrids, and have desirable combining potential; therefore, they are important genitors for the formation of new segregated populations for improving corn silage.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16029643
Research Article

The recent advent of exome sequencing has allowed for the identification of pathogenic gene variants responsible for a variety of diseases that were previously clinically diagnosed, with no underlying molecular etiology. Among these conditions, intellectual disability is a prevalent heterogeneous condition, presenting itself in a large spectrum of intensity, in some cases associated with congenital malformations, behavioral and various other intellectual development alterations. Here we report on a 36-year-old male patient, with a mild intellectual disability that remained undiagnosed at the molecular level for all his life. Using Nextera Exome Sequencing, a Chr3:9.517.294 A>AC (c.3848_3849insC) SETD5 gene insertion was found. This rare variant was classified as likely pathogenic due to its frameshift nature in the gene, in which loss-of-function mutations have been previously reported to cause intellectual disability, as well as a 3p25.3 microdeletion phenotype. It is possible that this variant shows partial activity, due to its gene localization, which would explain the patient's mild phenotype when compared with other reports.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16029615
Research Article

Buffalo production is spreading globally because of its economic advantage. Then, it has become necessary to improve the reproductive and productive efficiency of these animals, as well as to look for genetic factors that increase this efficiency. The objectives of this study were to characterize the promoter region of the melatonin 1A receptor gene (MTRN1A), to detect possible SNPs and associate them with fertility characteristics, and identify binding sites of transcription factors involved in the regulation of genetic expression in buffaloes in the Amazon. The conventional PCR method was carried out using the two primers designed from the reference sequence deposited in the GenBank AY52466.1. The products of the PCRs were purified, sequenced, and subsequently edited and aligned. Twenty-six SNPs were found, where 73% presented allele frequencies of wild nucleotides above 0.5, and 73% presented deviations from the Hardy-Weinberg equilibrium (P < 0.05) and F varying between 0.06 and 1.00, characterizing high degrees of inbreeding within the population. A block of ACAA deletion (position -1483) was observed in 25% of samples. The associations between these SNPs and reproductive characteristics were observed for calving interval and 5 SNPs: -1289, -1139, -911, -724, and -656 (P < 0.05), and three other SNPs: -1395, -724, and -94 (P < 0.05) were associated significantly with age at first calving, and were not associated with calving concentration. The promoter region was characterized by the different types of binding factors, where only 11 sites are significantly strong enough for transcription factor bindings. The ACAA deletion also exhibited a strong association with transcription factors. As a result, it would be necessary to test the SNPs above with other reproductive characteristics of economic relevance to approve the gene as a strong candidate for the selection of buffaloes in the Amazon.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16029610
Research Article

Several human health problems have been related to the allergenic constitution of bovine milk due to the body's immune reaction to milk proteins. It is necessary find solutions to minimize the occurrence of such reactions, given the importance of milk as a source of animal protein. The aim of this study was to evaluate the allelic frequency of the CSN2 gene and to evaluate differences in the characteristics of Gir and Guzerá bovine milk. One hundred and fifty-six cows were used (68 Gir and 88 Guzerá) from the Felipe Camarão Experimental Station herd of the Agricultural Research Corporation of RN (EMPARN). DNA extractions were carried out from hair follicles of the animals; the gene was then amplified and sequenced in an ABI 3100 automatic sequencer. The obtained sequences were submitted to analysis using the Geneious 5.6.5 program. Data were submitted to analysis of variance and to the Tukey-Kramer test at 5% probability and cluster analyses by main components were performed. Allele frequencies were 98 and 97% for the A2 allele and 0.96 and 0.93% for the genotype A2A2 for Gir and Guzerá, respectively. Gir and Guzerá animals showed differences in protein, lactose, and non-fat dry extract levels. Although correlations between milk yield and the production and some milk components are moderate, increases in milk yield are always greater than the increase in constituent yield. In addition, even though Guzerá animals have a higher percentage of protein, lactose, and non-fat dry extract, milk from Zebu breeds is an alternative for individuals sensitive to β-casein protein.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16029592
Research Article

This study searched a rare and aggressive type of cancer in dogs and humans, the breast carcinosarcoma. Both clinical and pathological traits of mammary carcinosarcomas in dogs are similar to humans, such as infrequent occurrence, fast tumor growth, and unfavorable prognosis when compared to carcinomas. Other possible alterations include chromosomal abnormalities that can be useful for the identification of tumoral cells and diagnosis. The aim of this study was to compare the chromosomal features of peripheral lymphocytes and tumor cells in a mammary carcinosarcoma of a 14-year-old female Poodle. Chromosomes were analyzed from 210 metaphases by conventional Giemsa staining, C-banding, and base-specific fluorochrome staining with chromomycin A3 (CMA) and DAPI. Of the 105 blood cells, 56.3% followed the standard karyotype of dogs (2n = 78). In contrast, the carcinosarcoma cells showed high chromosomal numbers (104 to 153), divided into 80% hypertriploid (118 to 136 chromosomes), 10.5% hypotetraploid (137 to 153 chromosomes), 5.7% hypotriploid (104 to 116 chromosomes), and 3.8% triploid cells (117 chromosomes). Among the aneuploid cells identified, we highlighted the trisomy of pair 1 and X chromosome once these elements were easily recognized in karyotype because of their size (pair 1) or differential morphology. Heterochromatin in normal cells was restricted to the pericentromeric region of all chromosomes while few C-bands were observed in tumor cells. This apparent loss of heterochromatin in neoplastic cells was supposed to favor centric fusion among formerly acrocentric chromosomes. Fluorochrome staining reinforced this hypothesis once GC-rich segments (CMA) were identified on 10 chromosomes from normal cells (2n = 78) whereas carcinosarcoma metaphases had up to 11 chromosomes bearing CMA signals in spite of their remarkable high chromosomal numbers. We concluded that, like in humans, the carcinosarcoma in dogs caused genome instability that eventually led to structural and numerical chromosomal aberrations. Besides, this study reinforced the importance of cytogenetic studies in dogs as a reference material for human cancer studies, especially in rare cases, since it is possible to increase knowledge about the characteristics of breast neoplasms in which there is a little availability of similar cases for comparative studies.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16029433
Research Article

Cell death-inducing DFF45-like effector (CIDE) B is a member of the CIDE family of apoptosis-inducing factors. In the present study, we detected a single nucleotide polymorphism (SNP), c.414G>A, which corresponds to the synonymous SNP 414Arg, in CIDE-B in the Berkshire pigs. We also analyzed the relationships between the CIDE-B SNP and various meat quality traits. The SNP was significantly associated with post-mortem pH, water-holding capacity (WHC), fat content, protein content, drip loss, post-mortem temperature at 12 h (T12) and 24 h (T24) in a co-dominant model (P < 0.05). A significant association was detected between the SNP and post-mortem pH, fat content, protein content, drip loss, shear force, and T24 in gilts; and color parameter b*, WHC, and T24 in barrows (P < 0.05). The SNP was significantly correlated with the fat content, and CIDE-B mRNA expression was significantly upregulated during the early stage of adipogenesis, suggesting that CIDE-B may contribute towards initiation of adipogenesis (P < 0.05). Furthermore, CIDE-B mRNA was strongly expressed in the liver, kidney, large intestine, and small intestine, and weakly expressed in the stomach, lung, spleen, and white adipose tissue. These results indicate that the CIDE-B SNP is closely associated with meat quality traits and may be a useful DNA marker for improving pork quality.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16029408
Research Article

Previous studies have found that 1,25-dihydroxyvitamin D [1,25(OH)D or VD] exerts many biological effects, including the inhibition of cell proliferation and induction of apoptosis, but its mechanism of action remains unclear. The goal of our investigation was to explore the effects of 1,25(OH)D on the proliferation of cultured human mesangial cells and their expression of Ki67 in vitro, and to establish its mechanism of action. Cultured human mesangial cells were randomly divided into the following four groups: normal control (N group; administered Dulbecco's modified Eagle's medium containing 5% fetal bovine serum), proliferation [epidermal growth factor (EGF) group; administered 10 μg/L EGF], VD intervention [administered 10 M 1,25(OH)D], and proliferation and intervention [EGF+VD group; administered 10 μg/L EGF and 10 M 1,25(OH)D]. Cells were incubated for 48 h with the corresponding treatment, and fluorescence immunocytochemistry and reverse transcription-quantitative polymerase chain reaction were used to detect expression of Ki67 protein and mRNA, respectively. Compared to the N group, Ki67 levels were found to be higher in the EGF group but significantly lower in the VD intervention group. Moreover, expression of Ki67 by cells in the EGF+VD group was significantly lower than that of those in the EGF group. All of these differences were statistically significant (P < 0.05). In conclusion, 1,25(OH)D inhibited Ki67 expression and the proliferation of human mesangial cells; therefore, Ki67 may be regarded as a potent therapeutic target in mesangial proliferative glomerulonephritis.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16029191
Research Article

Sugarcane production is strongly influenced by drought, which is a limiting factor for agricultural productivity in the world. In this study, the gene expression profiles obtained by de novo assembly of the leaf transcriptome of two sugarcane cultivars that differ in their physiological response to water deficit were evaluated by the RNA-Seq method: drought-tolerant cultivar (SP81-3250) and drought-sensitive cultivar (RB855453). For this purpose, plants were grown in a greenhouse for 60 days and were then submitted to three treatments: control (-0.01 to -0.015 MPa), moderate water deficit (-0.05 to -0.055 MPa), and severe water deficit (-0.075 to -0.08 MPa). The plants were evaluated 30, 60, and 90 days after the beginning of treatment. Sequencing on an Illumina platform (RNA-Seq) generated more than one billion sequences, resulting in 177,509 and 185,153 transcripts for the tolerant and sensitive cultivar, respectively. These transcripts were aligned with sequences from Saccharum spp, Sorghum bicolor, Miscanthus giganteus, and Arabidopsis thaliana available in public databases. The differentially expressed genes detected during the prolonged period of water deficit permit to increase our understanding of the molecular patterns involved in the physiological response of the two cultivars. The tolerant cultivar differentially expressed a larger number of genes at 90 days, while in the sensitive cultivar the number of differentially expressed genes was higher in 30 days. Both cultivars perceived the lack of water, but the tolerant cultivar responded more slowly than the sensitive cultivar. The latter requires rapid activation of different water-deficit stress response mechanisms for its survival. This rapid activation of metabolic pathways in response to water stress does not appear to be the key mechanism of drought tolerance in sugarcane. There is still much to clarify on the molecular and physiological pattern of plants in response to drought.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16028845
Research Article

The success of the geographical distribution of goat populations around the world is a consequence of the adaptive potential of these breeds. Several relevant traits to the success of the species in colonizing different ecosystems (and use by man) evolved before domestication. These features were relevant for the selection of different breeds. Each breed represents a genetic heritage that may be unique and essential for maintaining the species. The objective of this study was to catalog the mtDNA haplotypes of the Brazilian autochthonous Canindé goat breed and to characterize the genetic diversity observed in subpopulations by sequencing a 481-bp fragment corresponding to the first portion of the control region in 178 individuals from 10 herds, sampled in six Brazilian states. The global population displays a total of 29 haplotypes and 56 polymorphic sites. About one-third (10) of the haplotypes were common to all subpopulations while the remaining (19) were exclusive to a single subpopulation. The population exhibited high average haplotype diversity (0.82), with maximum and minimum values of 0.90 and 0.56 in individual subpopulations, respectively. In contrast, nucleotide diversity was 0.014, with maximum and minimum values of 0.020 and 0.004, respectively. The spatial analysis of molecular variance did not detect structure within the Canindé goat breed, and analysis of molecular variance revealed that 88.4% of the variation observed in the population was due to differences among individuals in the same subpopulation. Only 11.4% of the genetic variation referred to differences among subpopulations. About one-third (33.1%) of the individuals within population shared the same haplotype, which may be due not only to the breed developing from a small number of matrilines. The Brazilian autochthonous Canindé breed was classified as haplogroup A, a haplotype predominant in the Europe region.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16029656

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