Table of Contents | Genet. Mol. Res. 2020 (2)
Advances in biotechnology and molecular biology fields have allowed the sequencing of species genomes to improve the understanding of their genetics. As a consequence of the large number of whole genome sequencing projects, various DNA and protein sequences predicted by bioinformatics still without an identified function and are annotated in data banks as hypothetical proteins (HPs). Approximately 30% of the genome of recently sequenced organisms is composed of HPs, and these proteins are not included in functional studies due to the inexistence of full annotation. The characterization of HPs through bioinformatics is an important step to improve the understanding of genes and proteins and aims to assign some information to these sequences. Here, we used bioinformatics tools to predict the function of a hypothetical protein using as a model a protein from the filamentous fungus Penicillium rubens (XP_002569027.1). This fungus has been extensively studied due its ability to produce a wide range of natural products, many of them with biotechnological and pharmaceutical applications. The first step was to characterize the physicochemical properties of this HP. This protein has a molecular weight of 79.4 kDa and a theoretical pI of 5.06; 44.1% of its sequence is composed of hydrophilic amino acid residues and it was predicted as an extracellular protein. Prediction of 3D structure showed 42.21% of this sequence with an alpha galactosidase from Geobacillus stearothermophilus. In addition, XP_002569027.1 showed the presence of a glycosylase domain and most important amino acids residues in a catalytic site. Thus, we characterized a HP from P. rubens using computational tools and were able to produce useful information for future in vivo and in vitro studies, highlighting the importance of bioinformatics as a preliminary tool for functional studies.
Mucopolysaccharidosis (MPS) related information in Colombia is limited. A descriptive research involving results obtained in the full exome sequencing of 244 patients with different types of pathologies and not clinically diagnosed with MPS was carried out with the purpose of examining the genomic variability of genes associated with the MPS complex in South West Colombia, considering that it is a region where MPS cases are constantly reported. Bioinformatics software was applied with the purpose of analyzing the clinical significance of the different variants. The frequency of each of the variants was calculated, and an interaction network of the genes found within the MPS complex was developed. We found 509 different gene MPS complex variants, of which 262 were not previously reported. The most frequent genes were IDUA, GLB1 and GALNS, involving MPS I and MPS IV A/ B. In the entire MPS complex 9/244 variants were found associated with pathogenesis. Among the 509 variants, we found 27% missense, 2% non-coded 21% synonyms, 1.8% located within the splice region, 3% upstream, and 4.5% in the UTR region. These gene and allelic frequencies of the MPS complex will alert the medical community to the presence of the variants of the genes associated with MPS in the population in order to establish early diagnosis programs. This will allow specific treatment for some of them, associated with transdisciplinary management that minimizes the morbidity and mortality attributed to this disease, including adequate genetic counseling.
The objective of this research was to identify candidate gene markers based on their function related to marbling score and meat quality traits in pigs. A total of 313 commercial pigs with five different Duroc (DR) breed fractions: 1 = 100%DR (n = 227), 2 = 50%DR x 50% Large white (LW)(n = 7), 3 = 50%DR x 50%Landrace (LR)(n = 41), 4 = 75%DR x 25%LW (n = 18), and 5 = 50%DR x 25%LW x 25%LR (n = 20) were measured for marbling score (score 3; MB3 and score 6; MB6), Color (L*), % cooking loss and shear force meat characters. The pigs were slaughtered at around 190 days of age, at an average weight of 122 kg. Five candidate genes (LIPE, LEPR, ADRB3, CAPN1, and CAST) were genotyped by using -RFLP. The genetic parameters were estimated with Bayesian analysis via Gibbs sampling and analyzed by estimated breeding value by BLUP. The breed group had an effect on traits, especially marbling traits, percent cooking loss, and shear force. In Duroc purebreds, the marbling scores were significantly higher than in Duroc crossbreds. Al parameters were significantly higher in 50%DR x 50% Large white (LW) compared with the others. Association analysis showed that the AG genotype of the ADRB3 gene had a higher marbling score than the GG genotype (2.22 vs 1.99 for MB3, 2.92 vs 2.49 for MB6; P < 0.05). The lowest estimated breeding values (EBVs) for color (L*)(3.88) and % cooking loss (2.64) were obtained in the CC genotype of the CAPN1 gene. The GG genotype showed lower shear force and EBVs compared to the AG genotype of CAST gene (4.08 vs 4.85 for shear force (P < 0.05) and -0.03 vs 0.05 for EBV’s, P < 0.01). The AG genotype of ADRB3 could be used in marker assisted selection to improve marbling scores. Also, the GG genotype of CAST is the most appropriate for selection for pork tenderness.
We report the whole ram genome of Jordanian Awassi (Ovis aries), screened using the power of Illumina HiSeq sequencing technology, providing insights into the ram's genomic structure. Generated data will help in the assessment of naturally occurring genetic variation and population structure of this sheep breed using different structure variation markers. Also, it will help in the established marker-trait associations that can be used in marker-assisted breeding for qualitative and quantitative productive traits. A total of 23,812,247 single nucleotide polymorphism (SNPs) were identified, of which 177,117 (0.74%) were in the coding regions, as well as 3.77 million insertions/deletions and 3357 frame-shifting mutations in the coding region. The re-sequencing revealed 38,900 structure variation types distributed along genome, including 45 insertions and 16,643 deletions types. Also, there were 13,689 copy number variations, of which 3743 were up-regulated, and 9946 were down-regulated. These results will help in describing SNPs and the distribution of structural variations types used in genetic mapping and breeding programs of sheep breeds.
Brazil is the fourth largest producer of cassava in the world. In the state of Mato Grosso more than 90% of family farmers grow cassava; therefore, studies that evaluate the genetic resources of this species present in the fields of these farmers can be considered essential. The objective of this study was to evaluate the genetic variability among ethnovarieties of cassava grown in five regions of the state of Mato Grosso, at a phenotypic level using morphoagronomic and molecular characteristics. Forty-five ethno-varieties of cassava were evaluated using 45 morphoagronomic descriptors, 36 qualitative descriptors and nine quantitative descriptors, in addition to 15 microsatellite loci. The data were analyzed with the help of the Past and Genes programs. The descriptors of qualitative nature revealed the existence of morphological divergence, with 97.35% polymorphism and the formation of five genetic groups using the UPGMA method. Forty-four ethno-varieties had more than one desirable root characteristic from an agronomic point of view. Among all the varieties, the Amarela I ethno-variety had the most of these characteristics. With the quantitative variables obtained using the UPGMA method, it was possible to form seven distinct groups, which revealed the Branca Comum and Paraguaia ethno-varieties to be the most dissimilar. The characteristic that most contributed to the distinction of the groups was that of root length (30%). The 15 microsatellite loci amplified 109 alleles, and mean heterozygosity observed was higher than the expected heterozygosity. The UPGMA grouping revealed the formation of four distinct groups, and it was possible to verify duplicity of the Mandioca Batatinha and Pramuquem ethnovarities. By using joint analysis of the data, five genetic groups were observed, without duplicity of material; groups III, IV and V were isolated individuals. Between qualitative and quantitative variables, there was a significant correlation of 31% and between qualitative and molecular data the correlation was 12.4%. The collection of ethno-varieties grown in the fields of family farmers in the state of Mato Grosso present genetic divergence at the phenotypic level, based on morphoagronomic and molecular characteristics, and these ethno-varieties have characteristics of interest for genetic improvement and improved marketability.
The resistance of oat cultivars to fungicide use reduction and supporting longer harvest application interval can reduce or avoid the risk of food contamination and environmental pollution. We compared oat cultivars for resistance to reduction in the number of fungicide applications and with longer intervals from application to harvest, considering favorable and unfavorable crop year conditions and how they affect yield and progress of major leaf diseases. The study was conducted in 2015, 2016 and 2017, in Augusto Pestana, RS, Brazil. The experimental design was a complete randomized block with three replications in a 22 x 4 factorial scheme for 22 oat cultivars recommended for cultivation in Brazil and four conditions of fungicide use: no application; one application 60 days after emergence; two applications at 60 and 75 days after emergence and; three applications at 60, 75 and 90 days after emergence. In the control of leaf diseases, the fungicide FOLICUR® CE was used in 2015 and 2016 and the fungicide PRIMO® in 2017 at dosages of 0.75 and 0.3 liters ha-1, respectively. Most of the oat cultivars had little addtional production with the third application of fungicide at 90 days after emergence. Therefore, we coulold increase the interval between application and harvest with just two applications, at 60 and 75 days after and emergence. FAEM 4 Carlasul, URS Altiva and URS Guria cultivars gave high yields under most fungicide use conditions, allowing a long interval between the last application and grain harvest.
Fusarium wilt is a serious soil disease affecting common bean cultivation, especially crops under a central pivot irrigation system. Our objective was to identify bean lines that combine resistance to Fusarium wilt in the field with other desirable traits. Twenty-eight randomized block trials with three replicates were conducted in the rainy, winter, and dry seasons from 2009 to 2012 in the states of Goiás, Federal District, and Paraná. The trials were composed of six elite lines (one carioca and five black grain type) selected in a previous study as resistant to Fusarium wilt under controlled conditions and five cultivars (three carioca two black grain type). Variance analysis demonstrated variability for reaction to Fusarium wilt and anthracnose, yield, architecture, and lodging tolerance. The interaction among the lines/cultivars and environments was significant for all traits. Five black bean lines were resistant to Fusarium wilt (grades <3.0) in the field; however, none of these lines outperformed the best controls in other traits, especially anthracnose resistance (grades >4.0). The Carioca line (CNFC 15872) was susceptible to fusarium wilt (5.6). Thus, these lines should not be indicated as suitable cultivars. Cultivars BRS Esplendor and BRS Notável exhibited excellent yield (2144 and 2200 kg.ha-1, respectively), high stability, erect architecture (3.4 and 4.1), lodging tolerance (3.3 and 4.0), anthracnose resistance (1.0 and 1.7), and high fusarium wilt resistance (2.0 and 2.6). These cultivars are still excellent options for planting in areas with Fusarium wilt.
Raspberry (Rubus idaeus) is an economically important crop, and its cultivation has expanded recently across temperate and subtropical regions of Brazil. There is no brazilian raspberry cultivar so far. Therefore, the indirect selection can be an useful tool to help during the breeding process. We evaluated linear and canonical correlations in primocane-fruiting raspberry cultivars in 2013 and 2014, in a completely randomized experimental design, with eight replications. The genotypes ‘Alemãzinha’, ‘Heritage’ and ‘Fallgold’ were evaluated during two harvesting seasons, autumn and spring. Canonical groups were established among morphological (Group 1) and yield (Group 2) traits. In Group 1, plant yield and fruit weight were evaluated; in Group 2 the productive period, plant height, stem diameter, dry mass of pruning and plant leaf area were assessed. The linear and canonical correlations among morphological, phenological, and yield traits varied according to harvesting season. The phenological and morphological traits had greater linear correlation with yield traits in autumn than in spring. Based on our findings, to obtain more productive raspberry genotypes, plant leaf area and dry mass of pruning should be prioritized in the indirect selection.
Banana is an importment international economical crop, but drought is the most significant environmental stress in banana intrustry. Previous studies on banana drought tolerance evaluated just a few indicators, such as malondialdehyde (MDA) and plasma membrane permeability (PMP), with little or no systematic morphological and physiological information. We examined the morphological and anatomical structure characters of nine genotypes among 28 banana varieties from the variety resource nursery of China academy of topical agricultural sciences, and combined physiological markers (PMP and MDA) with morphological data. Leaf thickness, upper leaf epidermis and cutin thickness, palisade tissue thickness, spongy tissue thickness, lower leaf epidermis and cutin thickness, cell tense ratio (CTR), PMP and MDA content were significantly different among these varieties. Banana varieties were divided into three groups by cluster analysis based on a CTR index or a MDA content index, and the varieties were divided into two groups by cluster analysis based on the PMP index. Based on discriminant functions, the original classification was confirmed, and the result of discriminant classification was 100% correct. Three discrimination models with superior distinguishing abilities were established.
Ornamental peppers have been attracting great commercial interest in recent years. However, despite the demand, the availability of ornamental pepper cultivars to growers and consumers is still reduced, which should stimulate breeding programs for improved varieties. In this context, the identification and characterization of accessions in ornamental pepper germplasm banks is extremely important. We phenotypically characterized nine pepper accessions and analyzed the genetic divergence between them for the potential development of ornamental pepper cultivars. The experiment was conducted in a greenhouse at the agricultural sciences center of the State University of Montes Claros, Minas Gerais, in a completely randomized design, with nine accessions and eight replications. The plants were morphologically characterized with 34 qualitative and five quantitative descriptors. For taxonomic identification to the species level, a key to identify Capsicum species was used. In the molecular analysis, 32 ISSR primers were used for the detection of polymorphism between individuals. A multivariate analysis was performed by estimating the genetic dissimilarity by the Jaccard coefficient for the molecular variables and by the Gower algorithm for the morphological ones, using the UPGMA method for hierarchical analysis of clusters. The nine accessions that were selected for evaluation were considered as potential parents due to characteristics of ornamental interest. The accessions were all classified as belonging to the species Capsicum annuum and were grouped differently when using morphological versus molecular data. Analysis of molecular data detected greater dissimilarity between accessions, with the formation of a larger number of groups. The joint exploration of the morphological and molecular information allows a more reliable inference of the genetic dissimilarity between accessions and will facilitate planning of crosses.
Fetal sexing from maternal plasma is aimed at early determination of fetal sex, and it is possible to detect in the maternal plasma specific alleles of the fetus, which are inherited paternally. In this case, specific Y chromosome sequences are amplified by PCR. This PCR technique is a useful tool for determining fetal sex, with no risk to the fetus. We determined fetal sex by molecular sexing technique at different gestational stages and compared the results with obstetric ultrasound information, in pregnant women between the 8th and 13th weeks of gestation, who were over 18 years of age. Among the 32 samples collected, 21 were females and 11 were males. Four samples showed false negative results, i.e., the Y chromosome DNA was not detected; however the fetus was male. All results incompatible with true fetal sex were collected from pregnant women at the 8th gestational week. In all four samples, the PCR failed to detect the Y chromosome. The determination of fetal sex from the 9th gestational week on had a satisfactory sensitivity index. The sensitivity and specificity of the tests increase with gestational age, making the test safe and with low probability of false negatives. The maternal cell-free plasma noninvasive test proved accurate for sex detection; it can be considered a practical alternative to traditional invasive diagnostic procedures.
Phenotypic and genotypic correlations of agronomic traits with resistance to phytopathogens can help identify indirect selection criteria for corn yield. The Brazilian corn cultivar NAP5 is resistant to leaf spot and blight disease, while NAP7 is resistant to rust disease. Trials were conducted in two states from February to July 2015. The following traits were evaluated: GY – grain yield, PH - plant height, EH - ear height, MF – days to male flowering, NP - number of plants, NE - number of ears, BP - number of broken plants, LP - number of lodged plants, KW – kernel weight, HT - resistance to the fungus Exserohilum turcicum, WS (white spot) - resistance to Pantoea ananatis, CS - resistance to corn stunt, PP - resistance to Puccinia polysora and CZ - resistance to Cercospora zeae-maydis. The NAP5 population showed high genetic correlations between GY and PH, NP, NE and CS in Jataí, GO. In Uberlândia, MG, NAP5 presented high correlations between GY and PH, NP, NE, WS and CS. For the NAP7 population, genetic correlations were high between GY and CS in Uberlândia and between GY and NE in Jataí. Genetic gains for GY by direct selection ranged from 29 to 31%. The influence of the location was low. NE had the greatest effect on grain yield. For the NAP5 population, indirect selection for yield through selection for NE gave satisfactory genetic gain. The variable NE affected KW, and could be used for indirect selection, though direct selection provides greater gains. The heritability estimate for GY (0.77) in the NAP5 population was higher than for NE (0.61). With direct selection, it is possible to obtain gains of up to 31% in GY. High genetic correlations were also observed in the NAP5 population between NE, GY and CS.
Bees are important pollinating agents and are an integral part of food production and plant maintenance. It is useful to investigate mitochondrial polymorphisms in bees to obtain information that may be relevant to conservation strategies. We examined mitochondrial haplotypes and evaluated genetic diversity and differentiation in the native stingless bees Tetragonisca angustula and Tetragonisca weyrauchi using PCR-restriction fragment length polymorphism. Worker bees were collected from nests in Rondônia state. After isolating DNA, analyses were performed using 10 pairs of heterologous primers for T. weyrauchi, amplifying various regions of mitochondrial DNA (mtDNA). Primers and restriction enzymes were used for the first time for T. weyrauchi but had already been used in other studies with T. angustula. Only four of the tested primers (primer 1 - ND2 and COI; primer 2 - COI; primer 8 - 16S and 12S, and primer 9 - COII) were used for further analyses. For restriction analysis of the amplified regions, 13 enzymes were tested. Primer 1 - (ND2, COI) allowed the identification of a fragment approximately 2,400 bp in size in T. angustula and T. weyrauchi. Fragment cleavage was accomplished using EcoRI and EcoRV enzymes. An approximately 1,850 bp fragment was amplified in the two species using region (COI) primer 2. Using the EcoRV enzyme, cleavage was confirmed only in T. angustula individuals; however, it was observed in both species using the HinfI enzyme. Amplification of the region, using 16S and 12S - primer 8, generated two fragments (1,850 and 350 bp in size), and cleavage was observed in both species using EcoRV, RsaI, and PstI enzymes; however, the XbaI enzyme cleaved in T. weyrauchi alone. Amplification of DNA, using (COII) primer 9, generated a 1,000 bp fragment. The cleavage was performed using ClaI and HinfI enzymes in T. angustula. Bayesian inference analysis showed that mtDNA of T. angustula has a greater genetic variability than that of T. weyrauchi. The variations observed by the analysis of mtDNA using PCR-RFLP showed differences in mtDNA in the two species.
Atherosclerosis is a multifactorial chronic-inflammatory disease related to endothelial aggression to the intima layer of medium and large caliber arteries. Hyperlipidemia and atherosclerosis cause eNOS to lose its function, producing superoxide and leading to endothelial dysfunction. The nitric oxide derived from eNOS is anti-atherogenic. Single nucleotide polymorphisms in the promoter region reduce its activity and predispose individuals to cardiovascular disease. We analyzed the T786C polymorphism of eNOS in atherosclerotic patients under statin treatment, to determine the clinical importance of this type of genetic variation. The study of this polymorphism in atherosclerotic patients with stents could help predict the probability of restenosis. We collected 79 peripheral blood samples from patients diagnosed with atherosclerosis undergoing statin treatment. These included 35 stent patients and 44 patients without stents. The TC genotype was prevalent in stent patients who smoke but there was no significant relation between the T786C polymorphism and restenosis. Based on an in silico approach through molecular modeling and molecular docking, we found that statins stabilize the eNOS protein. Seven amino acid residues in the eNOS binding pocket interact with the statin molecule; this family of drugs acts by stabilizing the eNOS protein. Thus, the use of such drugs may help reduce the risk of restenosis.
Ginger (Zingiber officinale Roscoe) is a self-incompatible plant and has high rates of infertility; its genetic diversity only occurs via processes of mutation and natural selection. Since ginger is important as a condiment and as an herbal medicine, understanding its diversity to a greater degree can contribute both to its conservation and to its use in breeding programs. Considering the importance of the species and the characterization of material from on-farm conservation, this study aimed to evaluate, by means of ISSRs (Inter Simple Sequence Repeats) molecular markers of genetic diversity among individuals obtained in 19 urban and rural backyards in Alta Floresta, Mato Grosso state, Brazil. For the extraction of total DNA, the CTAB method was used and the amplifications were performed using nine ISSR primers. The UPGMA clustering method, when compared with the Ward and Nearest Neighbor methods, best showed genetic diversity, and the Bayesian analysis defined two distinct groups in the Z. officinale germplasm that was evaluated. The ISSR primers amplified a total of 78 fragments and revealed 88% polymorphism. The PIC varied between 0.40 and 0.87, with an average of 0.70, and was classified as median in the detection of polymorphism. The most dissimilar individuals were AF06 and AF12, while the least dissimilar were AF06 and AF04. The Nei (He) and Shannon (I) diversity indices demonstrated genetic variability within the two groups formed from the Bayesian analysis, and AMOVA indicated that the genetic diversity was greater within the groups (53.06%) than among them (46.94%). The absence of duplicates among the individuals analyzed indicates that they can be used to form an active germplasm collection with the aim of conserving and maintaining the genetic diversity of the species.