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Table of contents: 2019

Research Article

Inheritance of fertility traits in cattle is complex since they are controlled by multiple loci. Genome-wide association studies are an efficient tool to detect genomic regions that explain the phenotypic variation for a trait of interest. The aim of this study was to identify genomic regions that affect the age at first calving (AFC) and the calving interval (CI) in the Romosinuano (ROMO) and Costeño con Cuernos (CCC) creole cattle breeds and nominate candidate genes that influence these reproductive traits. AFC and CI records were obtained from 4,063 ROMO and 3,922 CCC, and a total of 962 animals were genotyped using the BovineSNP50.  Based on the single-step GBLUP methodology, the effects of 54K single nucleotide polymorphisms (SNPs) were grouped within windows of eight adjacent SNPs to explain the genetic variance. Sixty-six SNP windows were significantly associated with AFC (31 regions) and CI (35 regions). Of these regions, 17 were associated with AFC in ROMO, 14 with AFC in CCC, 17 with CI in ROMO and 18 with CI in CCC. From these, nine candidate genes (CACNA1A, CACNA1D, CACTIN, IARS2, PGRMC2, PTGDR, SYT10, UBE4A, RNF17) were identified as possible candidates involved in molecular mechanism that affect physiological mechanisms, such as hormonal regulation, ovarian cyclicity, growth rate, gametogenesis, acceleration of puberty, regulation of immune system, early embryonic development and the pathways to embryo-maternal recognition and maintenance of pregnancy. Furthermore, some genomic regions located in BTA1, BTA5 and BTA14 showed a pleiotropic effect on both AFC and CI. The polymorphisms identified in this study can help determine gene networks involved in the physiology of reproduction in cattle and to explain the inherent genetic variance of traits that measure reproductive performance in cattle. Some of these polymorphisms might be considered for breeding selection strategies to improve complex traits such as AFC and CI in beef and dairy cattle production systems.

Genet. Mol. Res. 18(2): GMR18258
DOI: 10.4238/gmr18258
Research Article

Several theories have been proposed to explain the etiology of adolescent idiopathic scoliosis (AIS), but none is conclusive. One such theory suggests the primary involvement of muscles due to myopathy, mainly affecting the erector and paravertebral rotator muscles. Studies indicate that there may be an association of AIS with genetic polymorphisms previously associated with physical performance and muscle power through their effects on muscle tissue. One of these is the gene coding for the angiotensin converting enzyme (ACE). We compared the expression of ACE gene polymorphisms in the concave and convex sides of the scoliotic curve in patients with AIS. We evaluated ACE gene expression in the multifidus muscles of the spine of  21 patients operated for AIS correction who had signs of asymmetric myopathy (worse in the concavity). Tissue samples were collected during corrective surgery. There was no significant difference in ACE gene expression in multifidus muscle samples from the two sides of the apex of the thoracic AIS deformity. There were also no differences in the expression of insertion/deletion polymorphisms.

 

Genet. Mol. Res. 18(2): GMR18246
DOI: 10.4238/gmr18246
Research Article

Sickle cell anemia is one of the most common genetic diseases in Brazil. This disease has an autosomal recessive inheritance pattern with a point mutation on chromosome 11, which is the substitution of an adenine by thymine. This mutation leads to the exchange of a glutamic acid for a valine at residue 6 of the beta globin chain, resulting in an abnormal form of hemoglobin, the so-called hemoglobin S (Hb S). The polymerization of Hb S produces reactive oxygen species, oxidizing agents that promote the oxidation of macromolecules, such as lipids, proteins and DNA. GSTs are enzymes that participate in the conjugation reactions of glutathione to a variety of electrolytic compounds that are potentially toxic and carcinogenic. The We analyzed the GSTT1 and GSTM1 gene polymorphisms in a patient with sickle cell anemia in order establish a more efficient clinical approach to treat the patient. The patient under study was 11 years old and sickle cell anemia was confirmed by the Guthrie test. Polymorphism identification was performed by PCR. The genotype identified in the patient was null for GSTT1 and present for GSTM1. In addition, the patient has a recurrent need for blood transfusion.

Genet. Mol. Res. 18(2): GMR18200
DOI: 10.4238/gmr18200
Research Article

Endometriosis is a pathology that affects women in Brazil and around the world. It is characterized by the presence of endometrial cells outside the uterine cavity, leading to chronic pain, infertility and hormonal cycle deregulations. Ectopic endometrial foci may be responsible for changes in anatomy, in hormonal metabolism, immune and inflammatory systems and the pelvic peritoneum, causing pain and infertility. CYP2C19 is an important gene of the cytochrome p450 family that encodes an aromatase associated with estrogen metabolism. The CYP2C19*3 polymorphism is related to a higher susceptibility for endometriosis in women. This gene is overexpressed in chronic inflammation. The CYP2C19 gene is associated with drug metabolism, detoxification of potential carcinogenic agents and steroid metabolism . We analyzed the prevalence of the CYP2C19*3 polymorphism in women with endometriosis. The control group comprised 14 health women and the case group 19 patients with endometriosis. We found that the CYP2C19*3 polymorphism at a significantly higher rate in  endometriosis patients. No individual in the control group presented had this polymorphism and we found no association between this polymorphism and any social habits in patients with endometriosis.

Genet. Mol. Res. 18(2): GMR18199
DOI: 10.4238/gmr18199
Research Article

Human leukocyte antigen-G (HLA-G) has been associated with various immune diseases, including malignancies. The 14-base pair (bp) insertion/deletion (indel) polymorphism (rs16375) in exon 8 of the 3′ untranslated region (3′ UTR) of the HLA-G gene has been reported to influence HLA-G protein expression. We investigated the relationship between the 14-bp indel polymorphism and the occurrence of breast cancer in a Saudi population. The HLA-G 14-bp polymorphism was typed by PCR in 52 patients with breast cancer and 62 healthy control Saudi women. There was a highly significant association between the occurrence of breast cancer and the del allele (OR = 3.75; P < 0.001) and the del/del genotype (OR = 4.96; P < 0.001). Conversely, the 14-bp ins allele and ins/ins genotype exhibited protective effects against breast cancer (P < 0.00001). Remarkably, the genotype 14-bp ins/ins was missing among all patients. This is the first report showing a strong association between HLA-G 14-bp polymorphism and breast cancer in the Saudi population. The results are in agreement with previous reports showing similar association of HLA-G and breast cancer in other populations.

Genet. Mol. Res. 18(2): GMR18263
DOI: 10.4238/gmr18263
Research Article

Brazil nut is a native Amazon species of high commercial value classified as vulnerable in terms of extinction risk due to marked illegal-burning activity and agricultural-frontier expansion processes occurring in the region. This study was undertaken to analyze the genetic diversity within and between two natural Brazil-nut populations occurring spontaneously in the Southern Amazon region spaced 50 km apart, both of which were located in the municipality of Alta Floresta, northern Mato Grosso state, Brazil. These are rural areas and samples were from native forest patches. Leaf samples were collected from 86 plants from distinct areas; 36 were from population AGRO (Agrocondor II Farm, geographic coordinates 55º30’ W and 9º00’ S) and 50 from population CAR (Carolina Farm, geographic coordinates 57º00’ W and 11º00’ S). A molecular-diversity study was conducted using 11 microsatellite loci developed for the species. To determine the level of genetic diversity between and within subpopulations, we applied principal coordinate analysis, analysis of molecular variance, observed and expected heterozygosity, polymorphic information content (PIC), UPGMA-based clustering, and Bayesian inference structuring. Seventy alleles were found with the SSR markers, with an average PIC of 0.72. Average Ho and He were 0.43 and 0.82, respectively. AMOVA revealed that 81% of the variability is within populations, as found in other studies of Brazil-nut in the states of Pará, Acre and Amazonas. The dendrogram obtained by the UPGMA method and the clustering provided by Bayesian inference resulted in two and four groups formed, respectively. All 36 individuals of the AGRO population were allocated in Group I, and the 50 individuals of population CAR were allocated in Groups II, III, and IV. The two subpopulations have sufficient genetic variability for the composition of an in situ germplasm bank that can be used in breeding programs and in programs for the conservation of the species.

 

 

Genet. Mol. Res. 18(2): GMR18174
DOI: 10.4238/gmr18174
Research Article

Extensive use of nitrogen fertilizers in coffee crops increases production costs and environmental pollution. Developing cultivars more efficient in nitrogen (N) utilization could contribute to reduce the need for N fertilization and promote sustainable production. We evaluated the variation in production characteristics among 20 coffee cultivars grown in nutrient solution with low N concentration (1.0 mmol.L-1), aiming to identify combinations to compose future populations to be used in breeding programs and obtain cultivars more efficient in N utilization. Morpho-agronomic traits and rooting, absorption, translocation, biomass production, and N utilization efficiencies were evaluated. The clustering methods Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and canonical variables were employed. Cultivars presented differentiated responses at low N concentrations, except for nitrogen absorption efficiency. The UPGMA and canonical variables methods presented similar results, forming five cultivar clusters. Total dry mass contributed the most in the total dissimilarity. Significant genetic variability was detected among coffee cultivars grown at low N availability. Hybrids generated from cultivars Icatu Precoce 3282, Icatu Vermelho IAC 4045, and Acaiá Cerrado MG 1474 were found to be the most promising to obtain a segregating population or heterotic hybrids, aiming at greater N utilization efficiency.

 

Genet. Mol. Res. 18(2): GMR18175
DOI: 10.4238/gmr18175
Research Article

The success of a plant breeding program depends on its ability to develop and release new cultivars with superior performance and capability to withstand biotic and/or abiotic stresses. We evaluated the genotype by environment interaction for grain yield in conventional early maturity soybean genotypes, grown in 15 environments (municipalties) distributed in five Brazilian states, to determine adaptability and stability of the genotypes. The experiments were carried out in the 2009/2010, 2010/2011, 2011/2012, 2012/2013 and 2013/2014 growing seasons. Twenty-eight soybean genotypes of early maturity were evaluated, among them 23 lines developed by the soybean breeding program of the Federal University of Uberlândia-UFU and five checks: M-SOY 6101, M-SOY 8001, Emgopa 316, UFUS Guarani, and UFUS Riqueza. The genotype and environment interaction was significant at 1% probability level by the F test, showing differential behavior among genotypes according to environment. The coefficient of genotypic determination was 79.44%, indicating that genetic variation was superior to environmental influences. The methods Annicchiarico and Lin and Binns modified by Carneiro were similar in the classification of the genotypes that stood out for the broad and specific adaptation to favorable and unfavorable environments; Wricke, Eberhart and Russel and AMMI methods identified UFU 21 and UFU 22 lines as the most stable, both presenting grain yields greater than 3,800 kg.ha-1. UFU 06 line obtained an average of grain yield greater than 4,000 kg.ha-1 and showed wide adaptation by the Annicchiarico, Lin and Binns method, modified by Carneiro, and the Centroid method.

 

Genet. Mol. Res. 18(2): GMR18169
DOI: 10.4238/gmr18169
Research Article

The DNA-binding One Finger (Dof) proteins are a large group of plant-specific transcription factors (TFs) that participate in several biological processes in plants. Although the Dof gene family has been studied in many plant species, detailed information on these genes and their fruit-specific expression during fruit development are not yet available in sweet orange (Citrus sinensis L. Osbeck). Here, we identified and characterized 24 CsDof genes in C. sinensis genome. Phylogenetic analysis showed that orange Dof proteins clustered into four major groups (A, B, C and D) and nine subgroups (A, B1, B2, C1, C2.1, C2.2, C3, D1, D2) based on the established Arabidopsis thaliana classification. The predicted CsDof genes could be mapped on all chromosomes, except for chromosomes 4 and 9. Most of these genes lacked introns or possessed just one intron. Based on freely RNA-seq data, 12 CsDofs with higher transcript abundance in fruits were selected for further analysis by semi-quantitative RT-PCR. This analysis revealed that the CsDof genes exhibit a variety of expression patterns during the early stages of fruit development (up to 90 days after anthesis), making it possible to establish three groups regarding their transcriptional activity. Among them, the CsDof17 showed the highest expression in all sampling stages investigated, indicating that this isoform may play an important role in regulating the early development of sweet orange fruits. Our results provide some useful information for the utilization of the CsDof genes for crop improvement of this important fruit species.

 

Genet. Mol. Res. 18(2): GMR18210
DOI: 10.4238/gmr18210
Research Article

Fig (Ficus carica) is among the 20 main fruits exported by Brazil, which is the eighth largest producer of fresh figs. The characterization of active fig germplasm banks has thus become an important line of research, as it is necessary to gather information to carry out adequate management projects. The objective of this study was to characterize the morphologies of 42 fig tree accessions belonging to the Faculty of Engineering of Ilha Solteira of the University of Sao Paulo State, so that the quality and genetic potential of different accessions of the species could be recognized based on the characteristics of the vegetative parts of the plants. Estimates of variance components were obtained for each variable evaluated using the restricted maximum likelihood/best linear unbiased prediction procedure, available in the genetic-statistical software SELEGEN. Most of the morphological characteristics of fig accessions examined had heritability values ranging from 0.25 to 0.40. However, the number of leaf lobes showed high heritability (0.85), with a genotypic and environmental coefficients of variation ratio higher than 1. This population has medium to high genetic variability; allowing us to identify the materials based on morphological descriptors, among which the number of lobes of the leaves appeared to be the most promising.

 

Genet. Mol. Res. 18(2): GMR18191
DOI: 10.4238/gmr18191
Research Article

Myostatin is a protein involved in the regulation of myogenesis; animal meat quality can be influenced by its expression. Animals with low myostatin levels have increased muscle mass and are relatively stronger. We analyzed the influence of the addition of soybean, used soybean and palm oils to the diet on Myostatin gene expression in the Logissimus dorsi muscle of sheep reared in the Northeast Amazon region. A basic control diet was elaborated and used with the addition of 4% of the different oils. All animals were slaughtered at a weight of 35 kg and 5 g of Logissumus dorsi muscle was collected and RNA extracted, quantified and a RT-PCR was run. The control diet, without added oil, gave the highest Myostatin expression levels among all treatments. When unused soybean oil was added to the diet, it significantly decreased Myostatin expression and induced muscle hyperplasia, generating animals with greater musculature. The other oils did not significantly affect expresson of this gene.

Genet. Mol. Res. 18(2): GMR18149
DOI: 10.4238/gmr18149
Research Article

Progenies from crosses between distinct accessions are potentially exploitable sources of genetic variability, through either evaluation or selection of segregants to obtain promising genotypes. Successful selection can be achieved based on a large number of descriptors that are simultaneously evaluated. Multivariate methods are used initially that fulfill two prerequisites: the estimation of similarity (or dissimilarity) measures between the parents and the use of a clustering technique for group formation. The multivariate method using Ward - Modified Location Model (MLM) allows the determination of the number of groups and their means with high precision, favoring the use of all information on the genotypes. We quantified the genetic diversity in a segregating F2 population of papaya consisting of 92 plants based on morphoagronomic descriptors, using the Ward-MLM strategy. This method clustered the 92 plants into three groups, with the most promising genotypes for selection of plant architecture clustered into group I; the descriptors that contributed the most to the genetic diversity were fruit length, petiole length, first fruit insertion height and fruit mass.

 

Genet. Mol. Res. 18(2): GMR18186
DOI: 10.4238/gmr18186
Research Article

Plant tolerance to abiotic stresses, such as water deficit, is triggered by complex multicomponent signaling pathways. One of the plant responses to stress conditions is expression of a large number of genes whose products are involved in various adaptive functions. Transcription factors (TFs) are important regulators of gene expression, modulating the transcription initiation rate of target genes; they are critical components in signal transduction in response to abiotic stress. Our hypothesis is that genotypes with contrasting tolerance signal water deficit through TFs (10 genes of the DREB family and bZIP) with differing degrees of expression. We believe that these genes will have greater expression in the flooded genotype because drought is an atypical condition in these plants. We tested two rice (Oryza sativa) genotypes: BRS Querência (flooded) and AN Cambará (dryland). When they reached stage V5, the plants were submitted to water deficit, at different levels of soil moisture, 20%, 10% and recovery. In general, we observed that expression varies according to the soil moisture and the genotype. In addition, the coexpression analysis generated seven cluster interactions with several genes. Our hypothesis was confirmed in part; the contrasting genotypes gave different degrees of expression; however, we ca not affirm that the flooded genotype has more significant responses in dry soil because there were variations in expression demonstrating oscillation in metabolism, and the data do not allow us to associate expression with greater drought tolerance.

Genet. Mol. Res. 18(1): GMR18247
DOI: 10.4238/gmr18247
Research Article

Gamma radiation is commonly used to disinfect agricultural products to increase shelf-life. However, this may exert adverse effects on plant growth, development, fertility, and crop production due to oxidative stress and cellular damage. Post irradiation protection using nanoparticles could reduce or reverse deleterious effects after exposure to ionizing radiation. We monitored the effect of zinc oxide nanoparticles (ZnO NPs at 500, 2000, 4000 mg/L) on Vicia faba grown from seeds treated with gamma rays (20, 50, 100 Gy). Phenotypic (seed germination, percentage of inhibition, seedling growth) and cytogenetic markers (chromosomal behavior in mitosis, meiosis and pollen grains) along with ultrastructural changes in the chloroplasts and nuclei (transmission electron microscopy) were assessed. At 20 Gy radiations, ZnO NPs had no effect on the final germination percent; however, at 100 Gy and post-treatment with 4000 mg/L of ZnO NPs, a substantial reduction occurred. While vegetative growth and fruit production increased with 500 and 2000 mg/L ZnO NPs, all three doses of gamma rays induced reduction. ZnO NPs provoked a significant increase in the mitotic index of root meristems compared with the control and gamma radiation. A radioprotective effect of ZnO NPs in the mitotic-meristematic root tips of V. faba was observed. The degree of mutagenic efficiency and pollen grain sterility was dose-dependent. Chloroplasts and nuclei treated with higher concentrations of ZnO NPs (4000 mg/L) and the three doses of gamma rays showed adverse ultrastructural changes. An amelioration or modulation of these changes was observed post irradiation with 500 and 2000 mg/L ZnO NPs. ZnO NPs at 500 and 2000 mg/L concentrations had protective effects through the reduction of adverse effects of all doses of gamma rays at the phenotypic, cytogenetic, and cellular ultrastructure levels. Additional studies are warranted to explore ZnO NPs as potential nano-irradiation protective agents.

Genet. Mol. Res. 18(1): GMR18232
DOI: 10.4238/gmr18232
Research Article

Heterozygosis for the hemoglobin S allele is a relatively common condition that is clinically benign and rarely presents clinical or hematological manifestations. Although rare, symptoms have been reported in these patients. We examined clinical manifestations and laboratory findings in HbAS individuals that could be related to the βS haplotypes: in 31 heterozygotes, with a predominance of females and young adults, and 43 AA homozygotes considered as a control group from samples previously stored in our laboratory. We performed clinical, biochemical and hematological tests, as well as genotyping by PCR-RFLP for the identification of βS haplotypes. Bantu and Benin haplotypes were equally frequent (n= 7, each) and 17 individuals had shown atypical haplotypes. We observed hematological alterations (e.g. mean corpuscular volume levels) that suggest microcytic and hypochromic anemia; however, we did not find iron deficiency anemia or thalassemia. In the clinical examination, the heterozygote individuals reported pain, especially in the upper and lower limbs and joints, as the most frequent complaint. HbS heterozygotes, different from literature reports, had a significantly greater frequency of anemia-related parameters when compared to normal homozygotes.

 

Genet. Mol. Res. 18(1): GMR18109
DOI: 10.4238/gmr18109

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