Seleção de genótipos de soja portadores ou não do gene RR por meio de análise multivariada e desempenho agronômico

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Performance of food-type soybean genotypes and their possibility for adaptation to Brazilian latitudes

This work was conducted at the Universidade Estadual de Londrina (UEL), in Londrina, State of Paraná, Brazil, with the goal to study food-type soybean (Glycine max (L.) Merrill) genotypes performance for use in cultivation or crosses. A total of 104 genotypes were analyzed: 88 were food-type with large seeds, eight were food-type with small seeds, and eight-grain types adapted cultivars. The experimental plan was in randomized complete block design with four replications, and 12 traits of agronomic importance were considered. Genetic diversity was observed in the food-type germplasm. There were some genotypes with high yield adapted to a normal period of sowing. Soybean genetic improvement programs for direct human consumption in Brazil, either by means of Asiatic pure lines or by means of the incorporation of genes for late flowering in short-day conditions in this lines is highly viable.

The Impact of Catechol-O-Methyltransferase and Dopamine D4 Receptor Genotypes on Neurophysiological Markers of Performance Monitoring

Dynamic adaptations of one"s behavior by means of performance monitoring are a central function of the human executive system, that underlies considerable interindividual variation. Converging evidence from electrophysiological and neuroimaging studies in both animals and humans hints atthe importance ofthe dopaminergic system forthe regulation of performance monitoring. Here, we studied the impact of two polymorphisms affecting dopaminergic functioning in the prefrontal cortex [catechol-O-methyltransferase (COMT) Val108/158Met and dopamine D4 receptor (DRD4) single-nucleotide polymorphism (SNP)-521] on neurophysiological correlates of performance monitoring. We applied a modified version of a standard flanker task with an embedded stop-signal task to tap into the different functions involved, particularly error monitoring, conflict detection and inhibitory processes. Participants homozygous for the DRD4 T allele produced an increased error-related negativity after both choice errors and failed inhibitions compared with C-homozygotes. This was associated with pronounced compensatory behavior reflected in higher post-error slowing. No group differences were seen in the incompatibility N2, suggesting distinct effects of the DRD4 polymorphism on error monitoring processes. Additionally, participants homozygous for the COMTVal allele, with a thereby diminished prefrontal dopaminergic level, revealed increased prefrontal processing related to inhibitory functions, reflected in the enhanced stop-signal-related components N2 and P3a. The results extend previous findings from mainly behavioral and neuroimaging data on the relationship between dopaminergic genes and executive functions and present possible underlying mechanisms for the previously suggested association between these dopaminergic polymorphisms and psychiatric disorders as schizophrenia or attention deficit hyperactivity disorder.

Performance of different genotypes of vegetable soybeans in Jaboticabal-SP

The study was conducted in the field, in the experimental area of the Section of Crop Production and Aromatic Medicinal Plants, belonging to the Faculty of Agricultural and Veterinary Sciences, Jaboticabal Campus-SP. The aim of the study was to assess the performance of seven genotypes of vegetable soybeans in Jaboticabal-SP. The experiment was carried out in a complete randomized block design with seven treatments (genotypes) and four replications. The genotypes examined were: CNPSOI, JLM003, JLM010, JLM018, JLM019, JLM024 and BRS216. The seeds were obtained from EMBRAPA-Soja and EMBRAPA- Hortaliças, and planted in Styrofoam trays with 128 cells containing Plantmax Hortaliças® as substrate. Transplanting occurred 10 d after seeding when the seedlings showed 2 or 3 definitive leaves and about 12 cm in height, demonstrating that the soil had been properly prepared according to the recommendations for this crop. Pests and diseases were adequately controlled in the event of their occurrence in the experimental area and in accordance with technical recommendations for the chemical products utilized. Collections were carried out based on the maturation of the pods, according to the scale of Fehr and Caviness (1977) adapted by Costa and Marchezan (1982), when the pods reached the reproductive stage R6. The parameters determined were mean precocity, height of the first pod, mean number of pods per plant, mean number of seeds per pod, fresh weight of 100 seeds and total yield of immature grains. Based on the results obtained, the genotypes JLM003 and JLM010 were found to be most indicated for growing vegetable soybeans, because of their capacity to produce immature grains of 1090 and 848 g·m-2, respectively, and fresh weights for 100 seeds of 62.20 and 68.19 g, respectively.

Genome-wide association studies based on sequence-derived genotypes reveal new QTL associated with conformation and performance traits in the Franches-Montagnes horse breed

To identify novel quantitative trait loci (QTL) within horses, we performed genome-wide association studies (GWAS) based on sequence-level genotypes for conformation and performance traits in the Franches-Montagnes (FM) horse breed. Sequence-level genotypes of FM horses were derived by re-sequencing 30 key founders and imputing 50K data of genotyped horses. In total, we included 1077 FM horses genotyped for ~4 million SNPs and their respective de-regressed breeding values of the traits in the analysis. Based on this dataset, we identified a total of 14 QTL associated with 18 conformation traits and one performance trait. Therefore, our results suggest that the application of sequence-derived genotypes increases the power to identify novel QTL which were not identified previously based on 50K SNP chip data.

Water Stress Reveals Differential Antioxidant Responses Of Tolerant And Non-tolerant Sugarcane Genotypes.

The biochemical responses of the enzymatic antioxidant system of a drought-tolerant cultivar (IACSP 94-2094) and a commercial cultivar in Brazil (IACSP 95-5000) grown under two levels of soil water restriction (70% and 30% Soil Available Water Content) were investigated. IACSP 94-2094 exhibited one additional active superoxide dismutase (Cu/Zn-SOD VI) isoenzyme in comparison to IACSP 95-5000, possibly contributing to the heightened response of IACSP 94-2094 to the induced stress. The total glutathione reductase (GR) activity increased substantially in IACSP 94-2094 under conditions of severe water stress; however, the appearance of a new GR isoenzyme and the disappearance of another isoenzyme were found not to be related to the stress response because the cultivars from both treatment groups (control and water restrictions) exhibited identical changes. Catalase (CAT) activity seems to have a more direct role in H2O2 detoxification under water stress condition and the shift in isoenzymes in the tolerant cultivar might have contributed to this response, which may be dependent upon the location where the excessive H2O2 is being produced under stress. The improved performance of IACSP 94-2094 under drought stress was associated with a more efficient antioxidant system response, particularly under conditions of mild stress.

TCF7L2 variant genotypes and type 2 diabetes risk in Brazil: significant association, but not a significant tool for risk stratification in the general population

Background: Genetic polymorphisms of the TCF7L2 gene are strongly associated with large increments in type 2 diabetes risk in different populations worldwide. In this study, we aimed to confirm the effect of the TCF7L2 polymorphism rs7903146 on diabetes risk in a Brazilian population and to assess the use of this genetic marker in improving diabetes risk prediction in the general population. Methods: We genotyped the single nucleotide polymorphisms (SNP) rs7903146 of the TCF7L2 gene in 560 patients with known coronary disease enrolled in the MASS II (Medicine, Angioplasty, or Surgery Study) Trial and in 1,449 residents of Vitoria, in Southeast Brazil. The associations of this gene variant to diabetes risk and metabolic characteristics in these two different populations were analyzed. To access the potential benefit of using this marker for diabetes risk prediction in the general population we analyzed the impact of this genetic variant on a validated diabetes risk prediction tool based on clinical characteristics developed for the Brazilian general population. Results: SNP rs7903146 of the TCF7L2 gene was significantly associated with type 2 diabetes in the MASS-II population (OR = 1.57 per T allele, p = 0.0032), confirming, in the Brazilian population, previous reports of the literature. Addition of this polymorphism to an established clinical risk prediction score did not increased model accuracy (both area under ROC curve equal to 0.776). Conclusion: TCF7L2 rs7903146 T allele is associated with a 1.57 increased risk for type 2 diabetes in a Brazilian cohort of patients with known coronary heart disease. However, the inclusion of this polymorphism in a risk prediction tool developed for the general population resulted in no improvement of performance. This is the first study, to our knowledge, that has confirmed this recent association in a South American population and adds to the great consistency of this finding in studies around the world. Finally, confirming the biological association of a genetic marker does not guarantee improvement on already established screening tools based solely on demographic variables.

Validation of dot blot hybridization and denaturing high performance liquid chromatography as reliable methods for TP53 codon 72 genotyping in molecular epidemiologic studies

Background: Mutations in TP53 are common events during carcinogenesis. In addition to gene mutations, several reports have focused on TP53 polymorphisms as risk factors for malignant disease. Many studies have highlighted that the status of the TP53 codon 72 polymorphism could influence cancer susceptibility. However, the results have been inconsistent and various methodological features can contribute to departures from Hardy-Weinberg equilibrium, a condition that may influence the disease risk estimates. The most widely accepted method of detecting genotyping error is to confirm genotypes by sequencing and/or via a separate method. Results: We developed two new genotyping methods for TP53 codon 72 polymorphism detection: Denaturing High Performance Liquid Chromatography (DHPLC) and Dot Blot hybridization. These methods were compared with Restriction Fragment Length Polymorphism (RFLP) using two different restriction enzymes. We observed high agreement among all methodologies assayed. Dot-blot hybridization and DHPLC results were more highly concordant with each other than when either of these methods was compared with RFLP. Conclusions: Although variations may occur, our results indicate that DHPLC and Dot Blot hybridization can be used as reliable screening methods for TP53 codon 72 polymorphism detection, especially in molecular epidemiologic studies, where high throughput methodologies are required.

Expression of resistance by tetraploid and diploid lucerne genotypes to Phytophthora medicaginis is not influenced by inoculum level or by temperature

Phytophthora-resistant lucerne cultivars do not always perform well under conditions of high disease pressure in the field. To determine whether resistance expression remains stable under different infection intensities, tetraploid and diploid lucerne genotypes, genotypically defined for their reactions to Phytophthora medicaginis, were clonally propagated, and the influence of different reproducible inoculum levels (0 . 5 and 5 . 0 g dry weight mycelium/kg dry weight potting mix), the period of exposure to these levels (10-60 days), and temperature (16/22 degrees C and 24/30 degrees C) on disease expression was determined in controlled environments. Generally, expression of resistance by resistant genotypes, remained stable under these conditions. Biotic (e.g. Aphanomyces eutiches) or abiotic factors other than P. medicaginis may be responsible for the poorer than expected performance under field conditions in some instances, or the percentage of resistant plants in some cultivars currently classified as resistant is insufficient to provide buffering against productivity reductions under severe epidemics. Further research is needed to clarify the situation.

Yield response of rice (Oryza sativa L.) genotypes to different types of drought under rainfed lowlands - Part 1. Grain yield and yield components

Responses of rice genotypes to drought stress may be different when characteristics of the drought stress environments differ. The performance of 128 genotypes was examined under irrigation and four different types of drought stress, to determine genotypic consistency in yield and factors determining yields under different drought stress conditions. The different drought conditions were mild drought during grain filling, short and severe drought at flowering, prolonged severe drought during the reproductive to grain filling, and prolonged mild drought during vegetative and grain filling. Genotypic grain yield under mild stress conditions was associated with yield under irrigated conditions, indicating the importance of potential yield in environments where the yield reduction was less than 50%. However, yields under irrigated conditions differed over time and locations. Under prolonged or severe drought conditions, flowering time was an important determinant of grain yield. Earlier flowering genotypes escaped the severe stress and had higher grain yields indicating large genotype by environment (G x E) interactions which have implications for plant breeding even for mild stress. It is suggested that variations in flowering time, potential yields and drought patterns need to be considered for development of drought-resistant cultivars using specific physiological traits. (C) 2002 Elsevier Science B.V. All rights reserved.

UV-visible scanning spectrophotometry and chemometric analysis as tools for carotenoids analysis in cassava genotypes (Manihot esculenta Crantz)

In this study, the metabolomics characterization focusing on the carotenoid composition of ten cassava (Manihot esculenta) genotypes cultivated in southern Brazil by UV-visible scanning spectrophotometry and reverse phase-high performance liquid chromatography was performed. Cassava roots rich in -carotene are an important staple food for populations with risk of vitamin A deficiency. Cassava genotypes with high pro-vitamin A activity have been identified as a strategy to reduce the prevalence of deficiency of this vitamin. The data set was used for the construction of a descriptive model by chemometric analysis. The genotypes of yellow-fleshed roots were clustered by the higher concentrations of cis--carotene and lutein. Inversely, cream-fleshed roots genotypes were grouped precisely due to their lower concentrations of these pigments, as samples rich in lycopene (redfleshed) differed among the studied genotypes. The analytical approach (UV-Vis, HPLC, and chemometrics) used showed to be efficient for understanding the chemodiversity of cassava genotypes, allowing to classify them according to important features for human health and nutrition.

Methods for testing association between uncertain genotypes and quantitative traits.

Interpretability and power of genome-wide association studies can be increased by imputing unobserved genotypes, using a reference panel of individuals genotyped at higher marker density. For many markers, genotypes cannot be imputed with complete certainty, and the uncertainty needs to be taken into account when testing for association with a given phenotype. In this paper, we compare currently available methods for testing association between uncertain genotypes and quantitative traits. We show that some previously described methods offer poor control of the false-positive rate (FPR), and that satisfactory performance of these methods is obtained only by using ad hoc filtering rules or by using a harsh transformation of the trait under study. We propose new methods that are based on exact maximum likelihood estimation and use a mixture model to accommodate nonnormal trait distributions when necessary. The new methods adequately control the FPR and also have equal or better power compared to all previously described methods. We provide a fast software implementation of all the methods studied here; our new method requires computation time of less than one computer-day for a typical genome-wide scan, with 2.5 M single nucleotide polymorphisms and 5000 individuals.

Detection of rifampin-resistant genotypes in Mycobacterium tuberculosis by reverse hybridization assay

We used a colorimetric reverse dot blot hybridization (CRDH) assay to detect the presence of mutations in a specific region of the rpoB gene, associated with rifampin (RIF) resistance, in a panel of 156 DNAs extracted from 103 RIF-sensitive and 53 RIF-resistant cultures of Mycobacterium tuberculosis. When compared with the antimicrobial susceptibility test (AST), the sensitivity and specificity of the CRDH were 92.3% and 98.1%, respectively. When compared with sequencing, the sensitivity and specificity of the CRDH were 90.6% and 100%, respectively. To evaluate the performance of the assay directly in clinical specimens, 30 samples from tuberculosis patients were used. For these samples, the results of the CRDH were 100% consistent with the results of the AST and sequencing. These results indicate that the rate of concordance of the CRDH is high when compared to conventional methods and sequencing data. The CRDH can be successfully applied when a rapid test is required for the identification of RIF resistance in M. tuberculosis.

Morphological, pedigree, and molecular distances and their association with hybrid wheat performance

The objectives of this work were to estimate the genetic distance among wheat genotypes using morphological, pedigree, molecular, and combined morphological and molecular measures, to determine the correlations between these measures, and to evaluate the combining ability of the genotypes. Three generations and two planting designs were studied. Six wheat genotypes were crossed using a diallel design. The F1, F2 and F3generations were evaluated in the field, in the crop seasons of 2003, 2004 and 2005, under spaced plant and full-row planting designs. The estimated general and specific combining abilities of tested hybrids were influenced both by the generation and the planting design. The correlation coefficients among the distance measures and between these measures and genotype performances of different generations for the two planting designs were low to moderate. In order to obtain a more precise estimate of the genetic distance among cultivars and its association with the hybrid performance, more than one generation, planting design, and genetic distance estimation technique should be employed.

Brazilian maize genotypes sensitivity to water deficit estimated through a simple crop yield model

The objective of this work was to determine the sensitivity of maize (Zea mays) genotypes to water deficit, using a simple agrometeorological crop yield model. Crop actual yield and agronomic data of 26 genotypes were obtained from the Maize National Assays carried out in ten locations, in four Brazilian states, from 1998 to 2006. Weather information for each experimental location and period were obtained from the closest weather station. Water deficit sensitivity index (Ky) was determined using the crop yield depletion model. Genotypes can be divided into two groups according to their resistance to water deficit. Normal resistance genotypes had Ky ranging from 0.4 to 0.5 in vegetative period, 1.4 to 1.5 in flowering, 0.3 to 0.6 in fruiting, and 0.1 to 0.3 in maturing period, whereas the higher resistance genotypes had lower values, respectively 0.2-0.4, 0.7-1.2, 0.2-0.4, and 0.1-0.2. The general Ky for the total growing season was 2.15 for sensitive genotypes and 1.56 for the resistant ones. Model performance was acceptable to evaluate crop actual yield, whose average errors estimated for each genotype ranged from -5.7% to +5.8%, and whose general mean absolute error was 960 kg ha-1 (10%).