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Table of contents: 2019

Research Article

The efficiency of a selection index generally depends on the quality of the variance matrixes, which demands controlled experiments. Using Artificial Neural Networks (ANNs) trained from a selection index is advantageous for selecting genotypes since an ANN has the capacity to classify genotypes in an automated way. We propose the use of ANNs for the selection of alfalfa genotypes, based on a selection index. Data were collected from 77 alfalfa genotypes evaluated based on nine traits from four cuttings. The traits were divided into forage yield and nutritive value groups. In order for the ANNs to learn the classification pattern, the Tai index was used, which allows secondary traits to be included in the index to improve the gains of the main traits. An index was established for each group of traits, and based on the index scores the genotypes were subdivided into four classes (optimal, good, medium, and bad). After testing different topologies, ANNs were established for each index, according to the apparent error rates. The chosen ANNs were efficient in classifying the genotypes since the highest apparent error rate reached 15%, meaning that the ANNs efficiently captured the data pattern. Considering the ANN classification for both groups of traits, there was a high degree of agreement with the classification obtained from the Tai index, as expected. Even in the cuttings where the ANNs presented the worst performance, their potential to classify alfalfa genotypes was clear, because the wrong classifications were placed in groups close to the correct ones. This ensured that the best genotypes did not run the risk of being discarded, since they would not be classified in the group of bad genotypes. The ANNs that were developed have good potential for use in alfalfa breeding programs.


Genet. Mol. Res. 18(2): GMR18221
DOI: 10.4238/gmr18221
Research Article

Endometriosis is a chronic disease with adverse implications for fertility. We investigated the G894T polymorphism in the endothelial nitric oxide synthase gene in fertile and infertile women with endometriosis. This prospective study included a group of 52 women with a laparoscopic diagnosis of endometriosis. DNA was extracted from blood obtained from 47 patients and analyzed by PCR. The overall cohort was divided into infertile (n = 24) and fertile (n = 23) subgroups and compared in terms of genotypic and allelic frequencies. The genotypic distribution followed Hardy-Weinberg equilibrium (c2 = 2.21, P = 0.137) and included the GG genotype in 28/47 GT in 14/47, and TT in 5/47 of the samples. Genotypic and allelic frequencies between fertile and infertile women with endometriosis showed that absence of the TT genotype was associated with fertility in endometriosis patients (P = 0.0623). The T allele was present in 17 patients of the infertile group and 7 patients of the fertile group (P = 0.025). This allele was significantly associated with infertility (relative risk = 2.21, 95% confidence interval 1.56 - 3.08) for the recessive model of inheritance. Our findings suggest that women with endometriosis and the G894T polymorphism in the endothelial nitric oxide synthase gene are at increased risk of infertility.


Genet. Mol. Res. 18(2): GMR18201
DOI: 10.4238/gmr18201
Research Article

Corn is considered one of the most important crops in the world agricultural scenario. In order to improve production, it is crucial to understand and quantify the genetic variation involved in the phenotypic manifestation of this species. We characterized corn genotypes using a multivariate approach and examined canonical interrelations between characters of agronomic importance. The study was carried out in the 2016/2017 crop year in the southernmost state of Brazil, in the northwest region of Rio Grande do Sul. The treatments were composed of six open-pollinated corn genotypes (PL 712, PL 725, PL 796, PL 804 and PL 861). The experimental design was a randomized block with four replications. Analysis of variance revealed a significant difference at 5% of probability by the F test for the attributes plant height, ear insertion height, stem diameter, ear length, number of seed rows per ear, number of seeds per row of ear, thousand seed weight, seed yield, percentage of germination, first germination count, emergency percentage and cold test. Genetic variability analysis showed genotype PL 712 to have superior seed productivity. The physiological quality of the seeds produced was variable among the genotypes, but it followed the trend of superiority for PL 712. Linear associations revealed a tendency for tall stature plants to increase seed yield of open pollinated corn. The most polymorphic characters were plant height and ear insertion, response to cold test, and thousand seed weight. The productivity and seed quality trends that were observed will allow us to plan further research on open pollinated varieties to allow selection and development of superior genotypes for seed productivity and quality in the extreme south of Brazil.


Genet. Mol. Res. 18(2): GMR18123
DOI: 10.4238/gmr18123
Research Article

Several genes have been identified as important in athletic performance. The angiotensin-converting enzyme (ACE) insertion/deletion (I/D) polymorphism has been related to improvements in performance and exercise duration. However, there are large divergences among studies on the influence of ACE I/D polymorphism on physical performance. Other studies have demonstrated that strenuous exercise generally overloads the endogenous antioxidant system’s capacity, leading to oxidative damage to muscles and other tissues in athletes. Few studies have reported significant associations between glutathione S-transferase (GST) deletion polymorphisms and resistance performance in athletes. We examined the effects of ACE I/D and GST deletion polymorphisms in young soccer players in central Brazil. We included 65 soccer players from under-20 (18 to 20 years old) soccer teams and 60 non-athletes in a case-control study. All subjects had their physical performance investigated through the Running-based Anaerobic Sprint Test (RAST). Genotyping was performed using real-time PCR. We found that the I/D genotype was significantly more frequent in athletes compared with the non-athletes. Individuals with the ID and DD genotypes had an approximately 3.13-fold and 4.37-fold increase in strength and power-orientated performance, respectively. The DD genotype in athletes presented RAST-test results considered as excellent to good when compared with non-athletes. When we examined a possible association of the GST deletion polymorphisms and RAST test, we found no influence on athletic performance. We did find association between ACE I/D polymorphism and athletic performance. However, there was no association between GST polymorphisms and risk of oxidative damage in the muscles. Our findings may help to select young players with the most favorable genetic potential to succeed as soccer athletes.


Genet. Mol. Res. 18(2): GMR18192
DOI: 10.4238/gmr18192
Research Article

The search for genetic material of snap beans with desirable yield traits is of utmost importance for yield increase in Brazil. We evaluated 12 snap bean genotypes by diallel crosses that presented characteristics of interest, so as to select the best genitors to generate productive populations in the snap bean breeding program of the Universidade Estadual do Norte Fluminense in Rio de Janeiro state, Brazil. Diallel crosses were performed applying Method 2 of Griffing. The F1 generation, composed of 36 hybrid combinations, was evaluated in a greenhouse, in a completely randomized design with two replicates. The traits evaluated were: pod weight, length, width and thickness, number of seeds and seed weight. There were significant differences among genotypes for most variables, indicating genetic variability between snap bean lines. The following genitor genotypes proved to be the most suitable when the trait to be improved was yield: Top Seed Blue Line, UENF 1445, UENF 7-20-1, and UENF 7-10-1. The hybrids with higher values of combining ability estimates are indicated to generate promising segregating populations. Thus L3 (Top Seed Blue Line) × L18 (UENF 9-24-2), and L12 (UENF 7-14-1) × L1 (UENF 1445) hybrid combinations showed the best estimates of specific combining ability for the traits under evaluation, suggesting a high probability of obtaining superior genotypes. The efficiency of selection for these traits is based on additive genic action and demonstrates progress in the of snap bean breeding program.

Genet. Mol. Res. 18(2): GMR18214
DOI: 10.4238/gmr18214
Research Article

Strawberry (Fragaria x ananassa) stands out among small fruits as the most planted in Brazil, generating considerable income and employment. However, producers are dependent on cultivars originating from international breeding programs and imported seedlings. This entails high costs and plants poorly adapted to the edaphoclimatic conditions of Brazil. In addition, the consumer market demands superior organoleptic and nutritional qualities. We assessed the potential of 194 hybrids for production and physicochemical characteristics from a population of seedlings obtained from intraspecific crosses of the short-day cultivars Dover, Camarosa, Sweet Charlie, Oso Grande, Milsei Tudla, and Festival Florida and the day-neutral cultivar Aromas. The experimental design was an augmented block design that had as control treatments the cultivars Camarosa and Camino Real. Five production and nine physicochemical characteristics were assessed. The mean comparison was performed by the Dunnett test. Among the 14 characteristics analyzed, eight presented significance. The significant production characteristics were the number of commercial fruits, mass of commercial fruits, mass of non-commercial fruits, and the total mass of fruits, with values of 45.03 fruits/plant, 13.17 g, 72.22 g/plant, and 720.77 g/plant, respectively. The physicochemical characteristics that varied significantly were soluble solids to titratable acidity ratio, pectin, ascorbic acid, and anthocyanin, which presented values of 10.23, 2.06 g total pectin/100 g pulp, 71.12 mg ascorbic acid/100 g pulp, and 39.51 mg cyanidin 3-glycoside/100 g pulp, respectively. The crosses that involved Camarosa and Aromas gave a greater number of hybrids with superior positive effects when compared to the controls in terms of production and physicochemical characteristics, respectively. Among the 194 hybrids, 30 were superior to the controls and were selected to advance in the breeding program.


Genet. Mol. Res. 18(2): GMR18156
DOI: 10.4238/gmr18156
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