Research Article

Table of Contents | Genet. Mol. Res. 2018 (3)

Displaying 1 - 15 of 19
Research Article

Heat shock proteins (HSPs) are highly conserved molecules across all plant and animal species. In insects, HSPs are expressed in response to biotic and abiotic stressors and have a well characterized expression pattern in response to heat stress, especially heat shock genes Hsp60, 70 and 90. Temperature affects many aspects of eusocial Hymenoptera, including the stingless bees (Apidae, Meliponini). Consequently, these insects have developed thermal adaptation mechanisms, including thermoregulation. However, this ability decreases when there is deviation from the optimum temperature, compromising colony survival. The study of molecular responses to heat shock stress can be important for the preservation of these pollinizers. We identified and validated in silico the genes encoding HSP60, 70 and 90 in Melipona interrupta, one of the main stingless bees used for honey production in the Amazon region. cDNA fragments of males, workers and queen bees at the white-eyed pupal stage were amplified using degenerate primers. After sequencing, aligning and editing, the sequences were compared with public genomic databases for in silico validation. One fragment of Hsp60, three fragments of Hsp70 and two fragments of Hsp90 were obtained for M. interrupta. These fragments showed 100% similarity with mitochondrial sequences of HSP60 and cytosolic sequences of HSP70 and HSP90 of bees of the genera Apis and Bombus. Therefore, the fragments obtained in this study correspond to parts of HSP60 (mitochondria), HSP70 and HSP90 (cytosol) in white-eyed pupae of M. interrupta. The nucleotide sequences of these fragments did not vary between genders and castes. Our validation in silico of the genes encoding HSPs will be useful for future investigations regarding differential expression of HSPs in response to environmental factors that affect the development, maintenance and survival of stingless bee colonies in the Amazon.

 

Genet. Mol. Res. 17(3): GMR18062
DOI: 10.4238/gmr18062
Research Article

In view of the narrow genetic base of popcorn, probably due to its evolution by selection from flint maize types alone, knowledge about genetic divergence is imperative for the formation of heterotic groups. Thus, our objective was to identify heterotic groups of popcorn lines; we did so by exploiting the representative genotype collection of the Active Popcorn Germplasm Bank of the State University of Northern Rio de Janeiro. Thirty-eight popcorn genotypes from different origins were analyzed by two methodologies to identify divergent groups. In the first method, the genotypic data were processed to determine the number of groups, based on Bayesian clustering algorithms, and two clustering methods (UPGMA and Ward), based on three genetic distance algorithms, weighted index, unweighted index, and an index of genetic distance or dissimilarity, proposed by Smouse and Peakall. The second methodology identified groups based on simultaneous use of morphoagronomic and molecular information and extracting the genetic distance matrix by the Gower algorithm, and later applying UPGMA and Ward clustering methods. The consistency of the clustering methods was evaluated by cophenetic correlation coefficients. The significance of these coefficients was examined by the Mantel test. There was significant genetic variability among corn popcorn accesses at morphological and molecular levels. There also was agreement between multivariate clustering techniques, mainly when using genotypic data provided by microsatellite markers. heterotic groups were identified; these were formed mainly according to the origin of each genotype and/or geographic origin. We found that there is sufficient heterosis to develop new cultivars.

 

Genet. Mol. Res. 17(3): GMR18083
DOI: 10.4238/gmr18083
Research Article

We examined the general and specific combining abilities of common bean cultivars and varieties and tested promising hybrid combinations for the development of productive strains. Two cultivars (IPR Uirapuru and IPR Campos Gerais) and five local varieties (BGU-1, BGU-7, BGU-13, BGU-25 and BGU-36) were planted in a full diallel cross. Treatments were assessed based on a randomized block design, with 10repetitions. The following variables were assessed: mean number of days still emergence, mean number of days till blooming, mean insertion height of the first pod, mean final plant height, mean stem diameter, mean length of the pods, mean number of pods per plant, mean number of seeds per pod, mean number of seeds per plant, mean weight of 50 seeds and grain yield. A Griffing statistical analysis was performed. Cultivar IPR Uirapuru and the local variety BGU-36 were promising for most variables in the general combining ability. Combinations IPR Uirapuru x BGU-7, IPR Uirapuru x BGU-1, BGU-7 x BGU-1, BGU-25 x BGU-13 and BGU-13 x BGU-36 were the most promising in the specific combining ability to generate highly productive strains.

 

Genet. Mol. Res. 17(3): GMR18057
DOI: 10.4238/gmr18057
Thesis Abstract

The chelonians have historically played an important role as a natural resource, the Indians being the first consumers of their meat, eggs, fat and viscera. These animals have been hunted, fished and their eggs harvested for many generations in the Amazon. Currently, 60% of the species are considered threatened by trafficking of wild animals, predatory hunting and loss of natural habitats. Conservation actions by the Riozinho da Liberdade Extractive Reserve in the state of Acre include participative management and environmental education, associated with the management of eggs and hatchlings. Traditional communities maintain a close relationship with nature. However, since chelonians area traditional source of protein, their consumption contributes to population decline of the species in this region. As Amazonians migrate to urban environments, traditional consumption practices are maintained through the acquisition of animals that are illegally captured from the forest. We analyzed the commercialization and consumption of chelonians in the Riozinho da Liberdade Extractive Reserve and developed a conservation program, aiming at reducing predation and maintaining chelonians in the area. To this end, semi-structured questionnaires were applied to 65 residents of the Reserve, in order to obtain information about turtle and tortoise consumption and community perspectives in the group. Subsequently, workshops on biology and management of chelonians were run in five communities, facilitating the effective participation of riparians in participatory management, including egg collection and transfer to hatching trays, thus increasing hatching rates, keeping the young safe when necessary and guidelines for the cleaning and care of the egg laying areas during the Amazonian summer, a period that corresponds to the months of July until the first half of September. In addition, environmental education activities were carried out in the schools of the reserve and conservation centers established with members of the community being responsible for the monitoring of the turtle and tortoise nest areas, avoiding the predation of eggs and females. Five community meetings took place between February and September 2016, with about 64 participants, from eight communities: Esperança (17); Passo da Pátria (14); Oito Praias (9); Guarani (5); Nova Olinda (2); Novo Acre (1); Bom Futuro (1); Itajubá (2); unidentified communities (13); with ages ranging from 5 to 74 years. It was pointed out by participants that, decades ago, the Giant Amazon Turtle (Podocnemis expansa) existed in large numbers in the reserve; however, due to anthropic advance and subsequent predation this number was drastically reduced, reaching local extinction. The yellow-spotted Amazon River Turtle (Podocnemis unifilis) and the yellow-footed tortoise (Chelonoidis denticulatus) are the most popular chelonians for consumption in the reserve, following the same history as the Giant Amazon Turtle. As a result of this study, it was possible to identify that 85% (n = 55) of the community use chelonians for consumption and 45% (n = 29) commercialize these animals. In addition, 15 environmental agents were assigned and 61 participants were trained to monitor the natural egg-laying areas and the transfer of eggs to hatching trays. In addition, environmental education activities were carried out in schools, which promoted the involvement of students in the project. The results helped to sensibilize the local community, making them multipliers of the know-how associated with the conservation of chelonians and favoring sustainable practices in relation to the local fauna. These actions contribute to active citizen training for resolving environmental problems, strengthening the socio-environmental role of the community in solving such problems and enabling a better man-nature relationship.

 

Genet. Mol. Res. 17(3): GMR18102
DOI: 10.4238/gmr18102
Research Article

Soybean stem fly (SSF), Melanagromyza sojae is an important pest in soybean growing regions of the Old World, and recently has been confirmed in soybean areas in Brazil, Paraguay and Bolivia. In the regions where it is endemic, the management of M. sojae is performed by using resistant varieties, chemical insecticides and natural control carried out by parasitoids. One of the main parasitoid species of M. sojae, responsible for high parasitism rates is Syntomopus parisii (Hymenoptera: Pteromalidae). This paper confirms the presence of S. parisii parasitizing pupae of SSF in Brazil and Paraguay, using morphological descriptions. In addition, we provide, for the first time, genetic information on S. parisii specimens, based on the fragment of Cytochrome Oxidase I gene, which indicated low genetic diversity of S. parisii collected in Brazil and Paraguay.

 

Genet. Mol. Res. 17(3): GMR18074
DOI: 10.4238/gmr18074
Research Article

Senefeldera verticillata (Euphorbiaceae) is a species that exclusively occurs in the Atlantic Forest; it is used in the restoration and recovery of degraded areas and has therapeutic uses. Due to the scarcity of information on genetic patterns of this species, genetic diversity was characterized by the use of molecular markers, Inter Simple Sequence Repeats (ISSR). Leaf samples were collected from two populations located in the National Forest (FLONA) of Pacotuba and in the Private Reserve of Natural Patrimony (RPPN) Cafundó. Twelve ISSR primers were used, resulting in 179 amplification products, with 76% polymorphic bands. The genetic diversity values of Nei (H’) and Shannon index (I) were 0.329 and 0.503, respectively. The estimated historical gene flow among the fragments was high (Nm = 13.542). Molecular analysis of variance showed that most of the genetic diversity is within conservation units (95%), with genetic differentiation among populations considered moderate (ΦST = 0.0501). Thus we propose conservation of genetically dissimilar individuals in the two localities, so that the existing variability is preserved. Six groups were identified by the unweighted arithmetic means clustering method, in which 30 matrices of both fragments were collected in a single group. Bayesian analysis indicated that there is a small degree of genetic variation among populations, though organization of groups by locality was not confirmed by the STRUCTURE software. We were able to identify genetic divergence among the trees evaluated in these conservation units, demonstrating the usefulness of the ISSR markers. In addition, this information could help in the adoption of strategies for the selection of respresentative specimens to compose a seed bank of native forest species of the state of Espírito Santo.

 

Genet. Mol. Res. 17(3): GMR18059
DOI: 10.4238/gmr18059
Research Article

The carnauba palm Copernicia prunifera is the third most important non-timber forest species in Brazil; it is mainly known for the production of carnauba wax. We examined intra-population genetic diversity and correlated genotypic and phenotypic traits of 28 trees from a coastal location in Rio Grande do Norte state. Phenotypic variables tree height, diameter at breast height, curvature of the stem, fresh mass of fruits and seeds, and length and diameter of fruits and seeds were evaluated. Genotypic parameters were examined based on inter-simple sequence repeat (ISSR) polymorphisms. The eight ISSR primers detected 79 loci, of which 76% were polymorphic. The polymorphic information content ranged between 0.408 and 0.500, the Nei's diversity index h was 0.327, and Shannon index was 0.470. Although there was no significant association between the matrices of genotypic and phenotypic traits, stepwise multiple regression analysis identified ISSR markers that can be used in a marker-assisted breeding program. The ISSR loci 881(2), 880(1), and M1(4) were significantly and positively associated with plant height. The sMRA also identified a positive association between DBH and 842(5) and a negative association between the curvature of the stem and 857(1). The fresh mass of fruits had a significant negative correlation with ISSR locus 840(1). The other traits showed positive and negative associations when the marker(s) of the previous step(s) were included in the succeeding step in sMRA analyses. These results are relevant for breeding programs, with the perspective of obtaining intra specific hybrids that are superior for desirable characters.

Genet. Mol. Res. 17(3): GMR18018
DOI: 10.4238/gmr18018
Research Article

This work was aimed at determining stability and adaptability through Additive Main Effects and Multiplicative Interaction (AMMI) and Genotype Main Effects and Genotype Environment Interaction (GGE) methodologies, as well as to estimate and predict Restricted Maximum Likelihood/Best Linear Unbiased Prediction (REML/BLUP) parameters and employ them in multivariate models using wheat genotypes grown in the major wheat regions of Brazil. The trials were conducted during the 2017growing seasnon across 12 regions of Brazil, with nine wheat genotypes, arranged in three replicates. When there were significant G x E interactions, the AMMI and GGE methods were applied. The scores were represented in biplot graphs through multivariate methodology of the principal components. REML/BLUP estimates and predictions were employed in the GGE multivariate method to obtain inferences based on genetic effects, which was denominated predicted genetic GGE approach. The predicted genetic approach was superior to a phenotypic comparison to explain the effects of genotypes x environments interaction for wheat seed yield in Brazil. Specific adaptability for seed yield was established through phenotypic and genetic predicted approaches for genotypes BRS 331 and Marfimin the environment Itapeva, SP, as well as the genotype FPS Certerotoin the environment Cascavel. PR, and BRS 327 in the environment Cruz Alta, RS. The use of multivariate biometric methodologies along with the new predicted genetic approach enables reliable positioning of wheat genotypes for seed production across the main wheat regions of Brazil.

 

Genet. Mol. Res. 17(3): GMR18026
DOI: 10.4238/gmr18026
Research Article

We examined the agronomic performance and stability of strawberry cultivars in three environments, using the Annicchiarico and AMMI methods. Thirteen strawberry cultivars were evaluated (Aromas, Oso Grande, Dover, Sweet Charlie, Tudla, Festival, Camarosa, Monterey, Palomar, Portola, Camino Real, San Andreas and Albion), in the towns of Lavras-MG, Guarapuava-PR and Uberlândia-MG. The experimental design was blocks with randomly distributed treatments, with four replications and 18 plants per experimental unit. The total number of fruits (TNF) plant-1, total mass of fruits (TMF) g plant-1, number of commercial fruits (NCF) plant-1 and mass of commercial fruits (MCF) g plant-1 were evaluated. Variance analysis detected a significant effect for cultivar, environment, and cultivar x environment interaction for all the characteristics. The agronomic performance of the Dover cultivar stood out for TNF, TMF and NCF, while the Camarosa cultivar stood out for MCF. When we examined phenotypic stability in terms of yield in different cultivation environments, the Albion cultivar stood out for TMF, and Monterey and San Andreas for NFC.

 

Genet. Mol. Res. 17(3): GMR18041
DOI: 10.4238/gmr18041
Research Article

The main goal of this work was to select resistance sources to common bean anthracnose by field phenotyping and DNA marker-assisted screening. Fifty-five common bean genotypes, including differential varieties, characterized resistance sources, elite lines, cultivars and controls, were evaluated in a field inoculation trial and screened with SCAR markers linked to resistance genes that are important in Brazil. The field trial was carried out in Santo Antônio de Goiás, GO, Brazil, during the fall/winter growing season of 2014, using artificial inoculation with a mixture of six races of Colletotrichum lindemuthianum, selected based on their high virulence and prevalence in Brazil. Amplification reactions with the SCAR markers previously identified as linked to important anthracnose resistance genes on Brazil followed standard procedures. Twenty-eight of the 58 genotypes were resistant to anthracnose (mean severity score ≤ 3.5). Ten of these 28 resistant genotypes stood out because they presented a mean anthracnose severity score of 1.0. Four of the six SCAR markers tested shown to be useful for the assisted selection of their respective target genes (SH18 and SAS13 for Co-42, SAB03 for Co-5, and SAZ20 for Co-6). Two carioca seeded elite lines were highlighted by the phenotypic and molecular screening: K10 (Co-34, Co-42, Co-5 and Co-6) and K13 (Co-4²). The phenotypic and molecular characterization of candidate resistance sources to common bean anthracnose based on their disease reaction in field inoculation trials and on the analysis with molecular markers linked to resistance genes has shown to be a useful strategy. These results aid in the selection of donor parents and resistant lines to be preferably explored by common bean breeding programs in Brazil.

 

Genet. Mol. Res. 17(3): GMR18066
DOI: 10.4238/gmr18066
Research Article

Water stress reduces the yield of agricultural crops severely. The objectives of this study were to investigate genotypic differences between 20 popcorn lines in environments under well-irrigated (WW) and water stressed (WS) conditions to determine phenotypic, genetic and environmental relations among agronomic and root traits. The experiment was arranged in a randomized complete block design with three replications per environment. The following traits were evaluated: volume of expanded popcorn per hectare (PV), grain yield (GY), popping expansion (PE), number of rings of adventitious roots (NRAR), number of adventitious roots (NAR), number of tap roots (NTR), number of crown roots (NCR), adventitious root density (ARD), tap root density (TRD), crown root density (CRD), tap root angle (TRA), and crown root angle (CRA). Under WS, the values of the agronomic traits PV, GY and PE were reduced by 74.03, 67.15 and 28.76%, respectively. Water stress had little influence on NRAR, NAR, DR, NTR, and NCR. Due to an adaptive response to WS, increases were observed in TRA and CRA. In general, the estimates of genetic parameters evaluated under WS were higher. Negative genetic associations between agronomic traits and TRD, and CRD were observed in cultivation under WS; selection for trait PV will produce simultaneous gains in GY and PE under this regime. Under well-watered conditions, the development of genotypes with satisfactory GY and PE is difficult. This reinforces the hypothesis that root phenotypes adapted to particular environments should be identified.

 

Genet. Mol. Res. 17(3): GMR18078
DOI: 10.4238/gmr18078
Research Article

Ankylosing spondylitis (AS) is a potentially disabling form of a systemic chronic inflammatory arthritis affecting mainly the axial skeleton, with or without extraspinal manifestations. The genetic basis of AS is partly known. Moreover, many autoimmunity-related genes have pleiotropic effects. Multiple functional polymorphisms in the genes encoding the tumor necrosis factor (TNF) superfamily of cytokines, their receptors, and signaling proteins, are associated with susceptibility to autoimmune diseases. These arguments prompted us to conduct a study evaluating a possible association of single nucleotide polymorphism (SNP) rs4810485 of the CD40 gene, found previously to be involved in other inflammatory diseases, with susceptibility to AS in the Latvian population; 98 AS patients from the Center of Rheumatology of Pauls Stradins Clinical University Hospital were selected as the case group and 154 ethnically related healthy subjects from the Genome Database of the Latvian Population were included as a control group. CD40 gene rs4810485 polymorphism was tested by a TaqMan Pre-Designed SNP Genotyping Assay. In the case of CD40 gene rs4810485 polymorphism, the minor allele is T. Compared to the control subjects, the case group had a higher frequency of the minor allele T (28.6% vs. 17.5%; p=0.00345).The T allele was the risk allele for disease onset (OR 1.88 (95% CI 1.23-2.88)). The relationship between the disease and genotypes was of moderate significance (V=0.20). As for genotypes, GT and TT were the susceptibility genotypes for AS (respectively OR 2.42 (95% CI 1.38 – 4.25) and 1.94 (95% CI 0.71-5.32)). The GG genotype had a protective feature (OR 0.43 (95% CI 0.25 – 0.73)). A significant difference was not found in the analysis of the SNP alleles and genotype distribution in the peripheral arthritis (p=0.85 and p=0.86, respectively) and uveitis (p=0.47 and p=0.3, respectively) subgroups of AS patients. The study data showed that CD40 gene rs4810485 polymorphism is associated with risk of AS.

Genet. Mol. Res. 17(3): GMR18081
DOI: 10.4238/gmr18081
Research Article

ABSTRACT. In view of the need to obtain genetically superior eucalyptus clones that promote productivity coupled with quality, we used multivariate statistical techniques for the selection and evaluation of Eucalyptus spp. clones for wood production. The experiments were carried out in three environments in the districts of Eldorado do Sul, Butiá and São Gabriel. A clone of the commercial species Eucalyptus saligna was used as a common control in all trials. A total of 84 eucalyptus clones were used belonging to the breeding program in Rio Grande do Sul, Brazil, in a randomized block design, with 20 replicates and one plant per plot, spacing 3.50 x 2.14 m. Silvicultural practices were performed according to the particularities required by each environment. The clones were evaluated at 36 months for diameter at breast height, total height, total individual volume with bark and survival of clones. The datawere submitted to a joint analysis of variance, and the significance was interpreted by the F test at 5% probability. Interaction tests were performed and then multivariate models were used. Selection of clones from their values of genetic divergence and heterogeneity in relation to the others can be used to increase variability in breeding populations. Improvement strategies such as Intrapopulation Recurrent Selection can be "fed" from selections made based on these parameters, but also focusing on increasing productivity and improving wood technology. There wasa great difference in behavior of the clones for each environment, demonstrating the influence of genotype x environment interactions, which can be evaluated later in amplified clonal tests or in the observation plantings of these clones; these will serve for the future indication of genotypes for commercial plantations.

 

Genet. Mol. Res. 17(3): GMR18025
DOI: 10.4238/gmr18025
Research Article

Equine infectious anemia virus (EIAV) infection often results in an initial febrile response, followed by recurrent cycles of the disease and finally, a prolonged asymptomatic period. These variations in clinical signs are due to a number of factors, including virus strain, equid species and differences in susceptibility among animals. As a consequence of the close relation between viral strain and disease, studies about in-vitro replication and fitness of EIAV in macrophages, which are the target cells of the virus, depend on accurate measurement of viral load throughout the infection period. We developed a method to quantify EIAV in-vitro using a one-step RT-qPCR system from a control RNA synthesized for this purpose. Designed primers amplified a 520 base pair fragment from the gag gene region that was inserted into a pGEM-T Easy Vector plasmid and propagated in Escherichia coli DH5-α. The bacteria with the construct were propagated and sufficient quantities of the template DNA were produced. The RNA was synthesized in-vitro from the plasmid linearization product and was used for standardization of a one-step RT-qPCR system with a minimum detection limit of 10 to 15 molecules. The efficiency of the reaction was 101%, with r2 equal to 0.997. This new method can be used for the determination of virus titer in EIAV replication studies in-vitro.

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Genet. Mol. Res. 17(3): GMR18027
DOI: 10.4238/gmr18027
Research Article

The identification of a single statistic that allows selection of superior genotypes for several agronomic traits with high experimental precision would be useful for bean breeding programs. We examined correlations between 12 statistics for agronomic traits to determine which would be useful for the selection of common bean lines that have superior agronomic performance. For this purpose, 21 experiments were carried out between 1998 and 2015, evaluating 156 common bean genotypes and seven agronomic traits. Error mean square presented a positive correlation estimate from intermediate to high magnitude with the coefficient of experimental variation and a significant minimum difference. Thus, these statistics are not adequate to evaluate the experimental precision of traits that confer high agronomic performance in common beans. Genotype mean square showed a positive correlation with the statistics: F-test value for genotype, coefficient of genetic variation, heritability, coefficient of relative variation and selective accuracy; these statistics were correlated with each other for most of the traits. Correlated statistics gave information similar as to the experimental precision of a trait, so they should not be used together. Selective accuracy (SA) is recommended as a classification measure of experimental precision in the selection of  common bean lines that have superior agronomic performance in Value of Cultivation and Use experiments. The SA makes the correct ranking of the common bean genotypes for agronomic performance traits possible, based on genetic superiority; consequently, SA should be implemented in common bean breeding programs.

Genet. Mol. Res. 17(3): GMR18042
DOI: 10.4238/gmr18042

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