Research Article

Table of Contents | Genet. Mol. Res. 2017 (1)

Displaying 1 - 15 of 158
Research Article

We attempted to identify significant pathway cross-talk in rheumatoid arthritis (RA) by the Monte Carlo cross-validation (MCCV) method. We therefore obtained and preprocessed the gene expression profile of RA. MCCV involves identifying differentially expressed genes (DEGs), identifying differential pathways (DPs), calculating the discriminating score (DS) of the pathway cross-talk, and random forest (RF) classification. We carried out 50 bootstrap iterations of MCCV to identify the key instances of pathway cross-talk involved in RA. We identified a total of 17 significant DEGs and 15 significant DPs by comparing RA samples and normal controls. We found the most significant difference between RA and the normal controls in the eIF4 and p70S6K signaling regulation pathway. Furthermore, we identified 10 instances of pathway cross-talk with the best classification performance for RA and normal controls, using the RF classification model. All of the top 10 pathway pairs involved cross-talk with eIF4 and p70S6K signaling regulation, and the other 10 pathways were immune-related. By MCCV, we identified one critical DP and 10 significant instances of pathway cross-talk in RA. We propose that the eIF4 and p70S6K signaling regulation pathway and the other significant instances of pathway cross-talk play key roles in the occurrence and development of RA, and are potential predictive and prognostic markers for RA.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16029142
Research Article

The aim of this study was to assess the association between the TNFR1 rs2234649 polymorphism and ankylosing spondylitis susceptibility in a Russian Caucasian population. A total of 41 ankylosing spondylitis patients and 43 healthy controls, matched according to age and sex, were enrolled, and polymerase chain reaction-restriction fragment length polymorphism analysis was used to genotype the rs2234649 variant. We evaluated genotype distributions in the patient and control groups with the chi-square test, and assessed the relationship between genotypes and ankylosing spondylitis using the odds ratio. Our analysis showed that the rs2234649 polymorphism does not increase ankylosing spondylitis risk. In conclusion, the TNFR1 gene polymorphism tested does not appear to be useful for assessing predisposition to this disease or for its diagnosis or prognosis.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16019581
Research Article

The sex-linked short tandem repeats (STR), Y-STR and X-STR, are important for autosomal STRs in forensic paternity testing. We evaluated the forensic parameters of 19 Y-STRs and 16 X-STRs in the Han population of Shandong province, China. A Goldeneye 20Y kit (DYS391, DYS389I, DYS390, DYS389II, DYS348, DYS456, Y-GATA-H4, DYS447, DYS19, DYS392, DYS393, DYS388, DYS439, DYS635, DYS448, DYS460, DYS458, DYS437, DYS385 a/b) was used to analyze the forensic parameters of 534 unrelated males. A Goldeneye17X system (DXS6795, DXS9902, DXS8378, HPRTB, GATA165B12, DXS7132, DXS7424, DXS6807, DXS6803, GATA172D05, DXS6800, DXS10134, GATA31E08, DXS10159, DXS6789, DXS6810, amelogenin) was used to analyze 97 unrelated males and 214 females. In addition, we used the kits to examine 5 cases with abnormal amelogenin test results, as well as a male child with agenosomia typed by autosomal STR. We found 203 Y-STR haplotypes with allele frequencies ranging from 0.0019 to 0.7959, and GD ranging from 0.3429 to 0.9667. Expect in DXS6803, the allele frequencies of the other 15 X-STR loci showed no differences between females and males. PD ranged from 0.5504 to 0.9638, while PD ranged from 0.3176 to 0.8377. With the exception of DXS6803 and DXS6810, the allele frequencies of other X-STR loci were in accordance with Hardy-Weinberg equilibrium in females. One amelogenin negative case was characterized as a deletion of Y-DYS458. This paper provided data regarding the genetic polymorphism of Y-STRs and X-STRs in the Han population, and demonstrated the importance of Y-STR and X-STR in forensic autosomal STR analysis.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16019573
Research Article

AKT1, also known as v-akt murine thymoma viral oncogene homolog 1, is involved in the regulation of cell-survival and anti-apoptotic activities, which may affect the pathogenesis of various cancers. However, the association between genetic variants of AKT1 and the risk of developing prostate cancer has not been investigated before. This study investigated the associations between three polymorphisms (rs1130214, rs3730358, and rs2494732) in AKT1 and the risk of development of prostate cancer in the Chinese Han population. Sequenom MassARRAY & iPLEX technology were used to genotype these polymorphisms in 493 Chinese Han patients with prostate cancer and 309 age-matched healthy individuals. Compared to the CC genotype of the rs3730358 polymorphism, the CT genotype of the same polymorphism was strongly associated with a decreased risk of prostate cancer (OR = 0.617, 95%CI = 0.390-0.976, P = 0.037). However, there was no significant difference between the allele frequency of the rs3730358 polymorphism and those of the other two polymorphisms (P > 0.05). Moreover, no significant difference was found in the haplotype analysis (P > 0.05). Our study found that the variant genotype CT of rs3730358 of AKT1 was associated with a decreased risk of prostate cancer, which suggested that this polymorphism could play an important role in the development of the disease.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16019469
Research Article

IL-17 is associated with the occurrence and development of laryngeal cancer. However, no study has reported the association between IL-17 polymorphisms and laryngeal cancer susceptibility. Therefore, we analyzed the association of three polymorphism loci (rs2275913, 197 G/A; rs3748067, 383 A/G; and rs763780, 7488 T/C) of IL-17A and IL-17F with laryngeal cancer in the Chinese population. A case-control study was performed with 325 patients and 325 controls. Polymorphisms were detected by polymerase chain reaction and sequencing methods. SPSS17.0 software was used for statistical analysis. Allele and genotype frequencies of IL-17A rs2275913 were significantly different between patients and controls (P < 0.05). Frequencies of rs2275913 (197 G/A) AA and GA+AA genotypes compared to the GG genotype were significantly higher in patients than in controls, indicating the association of these genes with laryngeal cancer susceptibility; adjusted OR values were 2.54 (1.50-4.23) and 1.62 (1.19-2.17), respectively. Furthermore, individuals with the GA+AA genotype, compared to the GG genotype, aged ≤60 years, with smoking and alcohol consumption habits, and without a family history of cancer showed a higher cancer risk (OR = 2.74, 95%CI = 1.41-5.23; OR = 2.11, 95%CI = 1.21-3.55; OR = 1.91, 95%CI = 1.02-3.70; OR = 1.99, 95%CI = 1.08-3.39, respectively). In conclusion, the rs2275913 IL-17A (197 G/A) is associated with the incidence and development of laryngeal cancer in the Chinese population, and the AA and GA+AA genotypes harbor a high laryngeal cancer risk.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16019076
Research Article

Pak choi is a highly nutritious vegetable that is widely grown in China, Southeast Asia, and other parts of the world. Because it reproduces by seed, it is very important to understand the mechanism of floral organ development. Therefore, using the Chinese cabbage genome as a reference, this study analyzed the expression profiles of shoot apex genes at flower bud differentiation stages 1 and 5, in order to identify genes related to floral organ development. The results showed that the proportion of mapped genes was high, with 84.25 and 83.80% of clean reads from the two sample saligned to the reference genome, respectively. A total of 525 differentially expressed genes (DEGs) were identified, 224 of which were upregulated and 301 were downregulated. The expression levels of genes homologous to Chinese cabbage flowering genes were also analyzed at stages 1 and 5; the expression levels of Bra012997 (ap1), Bra000393 (SOC1), and Bra004928 (SOC1) were significantly upregulated at stage 5, suggesting that these three genes positively regulate floral development in pak choi. DEGs involved in floral organ development were analyzed with homologous genes from Arabidopsis thaliana; the homologous genes Bra029281 (AGL42), Bra026577 (ARPN), Bra022954 (SPL3), Bra029293 (ARF2), Bra007978 (AtRLP12), Bra033221 (SPL8), Bra008037 (LOX4), Bra001598 (IAA19), Bra003892 (PATL1), Bra038778 (AT4G21323), Bra025315 (KLCR2), and Bra013906 (DTX35) are directly related to floral organ development in Arabidopsis, suggesting that these genes have corresponding functions during flower organ development in pak choi, and could be candidates for further genetic research. These results provide a foundation for research on the molecular mechanism of flower organ development in pak choi and other Brassica rapa vegetables.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16019233
Research Article

The Fluorescence Image Analyzer (FLIMA) software was developed for the quantitative analysis of images generated by fluorescence in situ hybridization (FISH). Currently, the images of FISH are examined without a coefficient that enables a comparison between them. Through GD Graphics Library, the FLIMA software calculates the amount of pixels on image and recognizes each present color. The coefficient generated by the algorithm shows the percentage of marks (probes) hybridized on the chromosomes. This software can be used for any type of image generated by a fluorescence microscope and is able to quantify digoxigenin probes exhibiting a red color, biotin probes exhibiting a green color, and double-FISH probes (digoxigenin and biotin used together), where the white color is displayed.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16019658
Research Article

Intramammary infections are one of the main causes of productivity loss in dairy cows. To better understand the immune system response and to avoid the use of live animals, we validated the use of isolated bovine udder as an ex situ model. Six mammary glands were collected from cows ready for culling. Three udders were perfused with Tyrode's solution and three were not-perfused. During six hours, we collected perfusate samples for biochemical analysis. We also collected alveolar and teat canal tissue to evaluate gene expression. The biochemical parameters indicated that the perfused udders remained viable for the entire period of the experiment. A real-time polymerase chain reaction showed an increase in 18S rRNA gene expression in the alveolar tissue at 3 and 4 h after perfusion. There was also an increase in the Ubiquitin gene in the teat canal from not-perfused udders at 1, 3, and 4 h after slaughter. In general, gene expression was stable during the experiment. Our results indicated that the isolated perfused bovine udder model is appropriate for genetic studies, opening a new perspective in animal experimentation methods.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16019637
Research Article

Multiflorous spikelets are found in several grass species of agricultural and economic interest. In oat, this morphological characteristic is associated with the production of naked grains. Although many genetic studies have been performed over the past century, the inheritance of the multiflorous spikelet trait is not fully understood in oat. The objectives of this study were to evaluate environmental effects on the multiflorous spikelet trait, to estimate the number of genes controlling the trait, and to clone and characterize sequences of the AP2 gene in oat. Two genetic populations of recombinant inbreed lines were screened for the multiflorous spikelet trait from different years and sowing dates under field experiments. Normal, multiflorous, and mosaic spikelets were analyzed in the whole panicle for both years and sowing dates. Specific primer pairs for the AP2 gene was utilized to amplify and clone oat sequences. The results demonstrate that under higher temperature and day-length conditions, the variable expressivity of the multiflorous spikelet trait was less pronounced in both populations. Genetic analyses indicated the action of one major gene and two or three modifying genes controlling the expression of the multiflorous spikelet trait in oat, depending on the genetic background. Sequences with similarity to the AP2 gene were isolated from the oat lines UFRGS 017004-2 and URS Taura, and genetic polymorphisms were identified, which are valuable to confirm the action of AP2 on the multiflorous spikelet trait. Our results provide information to assist in the development of future studies of the multiflorous spikelet trait in oat.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16019588
Research Article

Evaluating genetic diversity among genotypes is important for providing parameters for the identification of superior genotypes, because the choice of parents that form segregating populations is crucial. Our objectives were to i) evaluate agronomic performance; ii) compare clustering methods; iii) ascertain the relative contributions of the variables evaluated; and iv) identify the most promising hybrids to produce superior segregating populations. The trial was conducted in 2015 at the State University of Mato Grosso do Sul, Brazil. We used a randomized block design with three replications, and recorded the days to emergence, days to flowering, days to maturity, plant height, number of branches, number of pods, number of seeds per pod, weight of 100 grains, and productivity. The genetic diversity of the genotypes was determined by cluster analysis using two dissimilarity measures: the Euclidean distance and the standardized mean Mahalanobis distance using the Ward hierarchical method. The genotypes 'CNFC 10762', 'IAC Dawn', and 'BRS Style' had the highest grain yields, and clusters that were based on the Euclidean distance differed from those based on the Mahalanobis distance, the second being more precise. The yield grain character has greater relevance to the dispute. Hybrids with a high heterotic effect can be obtained by crossing 'IAC Alvorada' with 'CNFC 10762', 'IAC Alvorada' with 'CNFC 10764', and 'BRS Style' with 'IAC Alvorada'.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16019570
Research Article

The aim of this study was to access the genetic diversity and relatedness between Canindé and British Alpine goat breeds in the States of Piauí and Ceará using microsatellite markers. Genomic DNA was isolated from hair samples of 99 goats belonging to six different flocks. A panel of polymorphic heterologous microsatellite loci was used to genotype individuals. The microsatellite markers resulted in a total number of 145 alleles, with an average of 8.5 alleles per locus. The observed and expected heterozygosities were ≥0.687 and ≥0.627, respectively, for all loci. The polymorphic information content showed that all loci were highly informative with an overall mean of 0.757. Overall F across all populations and loci was 18%, which was consistent with the coefficient of gene differentiation (G = 0.104). AMOVA revealed that 12.8% of the variation was captured between breeds. The Bayesian STRUCTURE clustering detected the maximum likelihood for a model of two genetically distinct groups, in agreement with the number of predefined studied breeds and the two-dimensional plot from the PCoA analysis. The exotic British Alpine breed and the naturalized Brazilian Canindé breed were clearly differentiated by the microsatellite markers, indicating that these two breeds have distant genetic identities, despite the phenotypic similarity.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16019569
Research Article

The objective of this study was to evaluate the effects of multicollinearity under two methods of canonical correlation analysis (with and without elimination of variables) in maize (Zea mays L.) crop. Seventy-six maize genotypes were evaluated in three experiments, conducted in a randomized block design with three replications, during the 2009/2010 crop season. Eleven agronomic variables (number of days from sowing until female flowering, number of days from sowing until male flowering, plant height, ear insertion height, ear placement, number of plants, number of ears, ear index, ear weight, grain yield, and one thousand grain weight), 12 protein-nutritional variables (crude protein, lysine, methionine, cysteine, threonine, tryptophan, valine, isoleucine, leucine, phenylalanine, histidine, and arginine), and 6 energetic-nutritional variables (apparent metabolizable energy, apparent metabolizable energy corrected for nitrogen, ether extract, crude fiber, starch, and amylose) were measured. A phenotypic correlation matrix was first generated among the 29 variables for each of the experiments. A multicollinearity diagnosis was later performed within each group of variables using methodologies such as variance inflation factor and condition number. Canonical correlation analysis was then performed, with and without the elimination of variables, among groups of agronomic and protein-nutritional, and agronomic and energetic-nutritional variables. The canonical correlation analysis in the presence of multicollinearity (without elimination of variables) overestimates the variability of canonical coefficients. The elimination of variables is an efficient method to circumvent multicollinearity in canonical correlation analysis.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16019546
Research Article

The objective of this study was to estimate the direct effects of explanatory variables on the grain yield of corn in the combinations formed by three types of hybrids x two harvests x nine scenarios of explanatory variables x two types of path analyses. Eleven explanatory variables were measured in 361, 373, and 416 single-, triple-, and double-cross hybrid plants from the 2008/2009 harvest, respectively, and in 1777, 1693, and 1720 single-, triple-, and double-cross hybrid plants from the 2009/2010 harvest, respectively: plant height at harvest (PH), ear insertion height (EIH), ear weight (EW), number of grain rows per ear (NR), ear length (EL), ear diameter (ED), cob weight (CW), cob diameter (CD), 100-grain mass (HGM), number of grains per ear (NGE), grain length (GL) and, the main variable, grain yield (YIELD). Before conducting the traditional and ridge path analyses, 0, 1, 2, 3, 4, 5, 6, 7, and 8 explanatory variables were excluded from scenarios 1, 2, 3, 4, 5, 6, 7, 8, and 9, respectively. Next, the direct effects of explanatory variables on YIELD were estimated for each hybrid, harvest, scenario, and type of path analysis. The variables EW, NGE, and HGM had stronger direct effects on YIELD in the first three scenarios and the variables EL and ED had stronger direct effects on YIELD in the other scenarios regardless of hybrid or harvest. The use of the ninth scenario of path analysis is recommended regardless of hybrid and harvest given the ease of explanatory variable measurement (EIH, EL, and ED), the low degree of multicollinearity and the good prediction of the path analysis (R ≥ 0.78).

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16019529
Research Article

The State of Rio Grande do Sul (RS) stands out as the largest wheat producer in Brazil. Wheat is the most emphasized winter cereal in RS, attracting public and private investments directed to wheat genetic breeding. The study of genetic progress should be performed routinely at breeding programs to study the behavior of cultivars developed for homogeneous regions of cultivation. The objectives of this study were: 1) to evaluate the genetic progress of wheat grain yield in RS; 2) to evaluate the influence of cultivar competition trial stratification in homogeneous regions of cultivation on the study of genetic progress. Grain yield data of 122 wheat cultivars evaluated in 137 trials arranged in randomized block design with three or four replications were used. Field trials were carried out in 23 locations in RS divided into two homogeneous regions during the period from 2002 to 2013. Genetic progress for RS and homogeneous regions was studied utilizing the method proposed by Vencovsky. Annual genetic progress for wheat grain yield during the period of 12 years in the State of RS was 2.86%, oscillating between homogeneous regions of cultivation. The difference of annual genetic progress in region 1 (1.82%) in relation to region 2 (4.38%) justifies the study of genetic progress by homogeneous regions of cultivation.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16019517
Research Article

Leptin (LEP), a protein that plays a fundamental role in the metabolism of energy reserves, and the solute carrier family 30 A8 zinc transporter (SLC30A8) have been consistently associated with diabetes. Women with gestational diabetes are at moderate risk of developing diabetes type 1 and 2 after pregnancy, in addition to complications to the fetus. We investigated the association of the polymorphisms rs7799039 (LEP) and rs13266634 (SLC30A8) in a case-control study in Euro-Brazilians with gestational diabetes (GDM, N = 134) and healthy pregnant women (control, N = 180). Real-time PCR with fluorescent probes (TaqMan system) was applied to genotyping. All polymorphisms were in Hardy-Weinberg equilibrium. The minor allele frequencies, for healthy and GDM, respectively, for the A-allele (LEP gene rs7799039) were 40.3% (95%CI = 35-45%) vs 36.6% (95%CI = 31-42%), P = 0.345; and for the T-allele (SLC30A8 gene rs13266634) were 27.8% (95%CI = 23-32%) vs 23.5% (95%CI = 18-29%), P = 0.227. Genotype comparisons for both polymorphisms showed no significant difference (P > 0.05). The polymorphisms rs7799039 and rs13266634 were not associated with GDM in the population studied (P > 0.05). The minor allele frequencies for both polymorphisms were similar to those of other Caucasian populations.

Genet. Mol. Res. 2017
DOI: 10.4238/gmr16019515

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