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Path analysis allows understanding the direct and indirect effects among traits. Multicollinearity in correlation matrices may cause a bias in path analysis estimates. This study aimed to: a) understand the correlation among soybean traits and estimate their direct and indirect effects on gain oil content; b) verify the efficiency of ridge path analysis and trait culling to overcome colinearity. Three different matrices with different levels of collinearity were obtained by trait culling. Ridge path analysis was performed on matrices with strong collinearity; otherwise, a traditional path analysis was performed. The same analyses were run on a simulated dataset. Trait culling was applied to matrix R originating the matrices R1 and R2. Path analysis for matrices R1 and R2 presented a high determination coefficient (0.856 and 0.832, respectively) and low effect of the residual variable (0.379 and 0.410 respectively). Ridge path analysis presented low determination coefficient (0.657) and no direct effects greater than the effects of the residual variable (0.585). Trait culling was more effective to overcome collinearity. Mass of grains, number of nodes, and number of pods are promising for indirect selection for oil content. [ABSTRACT FROM AUTHOR]

Human cutaneous leishmaniasis (CL) caused by Leishmania braziliensis, presents an exaggerated Th1 response that is associated with ulcer development. Macrophages are the primary cells infected by Leishmania parasites and both reactive oxygen species (ROS) and nitric oxide (NO) are important in the control of Leishmania by these cells. The mechanism involved in the killing of L. braziliensis is not well established. In this study, we evaluate the role of ROS and NO in the control of L. braziliensis infection by monocytes from CL patients. After in vitro infection with L. braziliensis, the oxidative burst by monocytes from CL patients was higher when compared to monocytes from healthy subjects (HS). Inhibition of the ROS pathway caused a significant decrease in the oxidative burst in L. braziliensis infected monocytes from both groups. In addition, we evaluated the intracellular expression of ROS and NO in L. braziliensis-infected monocytes. Monocytes from CL patients presented high expression of ROS after infection with L. braziliensis. The expression of NO was higher in monocytes from CL patients as compared to expression in monocytes from HS. A strong positive correlation between NO production and lesion size of CL patients was observed. The inhibition of ROS production in leishmania-infected monocytes from CL patients allowed the growth of viable promastigotes in culture supernatants. Thus, we demonstrate that while production of ROS is involved in L. braziliensis killing, NO alone is not sufficient to control infection and may contribute to the tissue damage observed in human CL. [ABSTRACT FROM AUTHOR]

Infection with different Leishmania spp. protozoa can lead to a variety of clinical syndromes associated in many cases with inflammatory responses in the skin. Although macrophages harbor the majority of parasites throughout chronic infection, neutrophils are the first inflammatory cells to migrate to the site of infection. Whether neutrophils promote parasite clearance or exacerbate disease in murine models varies depending on the susceptible or resistant status of the host. Based on the hypothesis that neutrophils contribute to a systemic inflammatory state in humans with symptomatic L. braziliensis infection, we evaluated the phenotype of neutrophils from patients with cutaneous leishmaniasis (CL) during the course of L. braziliensis infection. After in vitro infection with L. braziliensis, CL patient neutrophils produced more reactive oxygen species (ROS) and higher levels of CXCL8 and CXCL9, chemokines associated with recruitment of neutrophils and Th1-type cells, than neutrophils from control healthy subjects (HS). Despite this, CL patient and HS neutrophils were equally capable of phagocytosis of L. braziliensis. There was no difference between the degree of activation of neutrophils from CL versus healthy subjects, assessed by CD66b and CD62L expression using flow cytometry. Of interest, these studies revealed that both parasite-infected and bystander neutrophils became activated during incubation with L. braziliensis. The enhanced ROS and chemokine production in neutrophils from CL patients reverted to baseline after treatment of disease. These data suggest that the circulating neutrophils during CL are not necessarily more microbicidal, but they have a more pro-inflammatory profile after parasite restimulation than neutrophils from healthy subjects. [ABSTRACT FROM AUTHOR]

The evaluation of cultivars using multi-environment trials (MET) is an important step in plant breeding programs. One of the objectives of these evaluations is to understand the genotype by environment interaction (GEI). A method of determining the effect of GEI on the performance of cultivars is based on studies of adaptability and stability. Initial studies were based on linear regression; however, these methodologies have limitations, mainly in trials with genetic or statistical unbalanced, heterogeneity of residual variances, and genetic covariance. An alternative would be the use of random regression models (RRM), in which the behavior of the genotypes is characterized as a reaction norm using longitudinal data or repeated measurements and information regarding a covariance function. The objective of this work was the application of RRM in the study of the behavior of common bean cultivars using a MET, based on Legendre polynomials and genotype-ideotype distances. We used a set of 13 trials, which were classified as unfavorable or favorable environments. The results revealed that RRM enables the prediction of the genotypic values of cultivars in environments where they were not evaluated with high accuracy values, thereby circumventing the unbalanced of the experiments. From these values, it was possible to measure the genotypic adaptability according to ideotypes, according to their reaction norms. In addition, the stability of the cultivars can be interpreted as variation in the behavior of the ideotype. The use of ideotypes based on real data allowed a better comparison of the performance of cultivars across environments. The use of RRM in plant breeding is a good alternative to understand the behavior of cultivars in a MET, especially when we want to quantify the adaptability and stability of genotypes. [ABSTRACT FROM AUTHOR]

Persistence may be defined as high sustained yield over multi-harvest. Genetic insights about persistence are essential to ensure the success of breeding programs and any biomass-based project. This paper focuses on assessing the biomass yield persistence for bioenergy purpose of 100 elephantgrass clones measured in six growth seasons in Brazil. To assess the clones' persistence, an index based on random regression models and genotype-ideotype distance was proposed. Results suggested the existence of wide genetic variability between elephantgrass clones, and that the yield trajectories along the harvests generate genetic insights into elephantgrass clones’ persistence and G x E interaction. A gene pool that acts over the biomass yield (regardless of the harvest) was detected, as well as other gene pools, which show differences on genes expression (these genes are the major responsible for clones’ persistence). The lower and higher clones’ persistence was discussed based on genome dosage effect and natural biological nitrogen fixation ability applied to bioenergy industry. The huge potential of energy crops necessarily is associated with genetic insights into persistence, so just this way, breeding programs could breed a new cultivar that fulfills the bioenergy industries. [ABSTRACT FROM AUTHOR]

Flowering is an important agronomic trait. Quantile regression (QR) can be used to fit models for all portions of a probability distribution. In Genome-wide association studies (GWAS), QR can estimate SNP (Single Nucleotide Polymorphism) effects on each quantile of interest. The objectives of this study were to estimate genetic parameters and to use QR to identify genomic regions for phenological traits (Days to first flower—DFF; Days for flowering—DTF; Days to end of flowering—DEF) in common bean. A total of 80 genotypes of common beans, with 3 replicates were raised at 4 locations and seasons. Plants were genotyped for 384 SNPs. Traditional single-SNP and 9 QR models, ranging from equally spaced quantiles (τ) 0.1 to 0.9, were used to associate SNPs to phenotype. Heritabilities were moderate high, ranging from 0.32 to 0.58. Genetic and phenotypic correlations were all high, averaging 0.66 and 0.98, respectively. Traditional single-SNP GWAS model was not able to find any SNP-trait association. On the other hand, when using QR methodology considering one extreme quantile (τ = 0.1) we found, respectively 1 and 7, significant SNPs associated for DFF and DTF. Significant SNPs were found on Pv01, Pv02, Pv03, Pv07, Pv10 and Pv11 chromosomes. We investigated potential candidate genes in the region around these significant SNPs. Three genes involved in the flowering pathways were identified, including Phvul.001G214500, Phvul.007G229300 and Phvul.010G142900.1 on Pv01, Pv07 and Pv10, respectively. These results indicate that GWAS-based QR was able to enhance the understanding on genetic architecture of phenological traits (DFF and DTF) in common bean. [ABSTRACT FROM AUTHOR]

Sweet sorghum [Sorghum bicolor (L.) Moench] is a type of cultivated sorghum characterized by the accumulation of high levels of sugar in the stems and high biomass accumulation, making this crop an important feedstock for bioenergy production. Sweet sorghum breeding programs that focus on bioenergy have two main goals: to improve quantity and quality of sugars in the juicy stem and to increase fresh biomass productivity. Genetic diversity studies are very important for the success of a breeding program, especially in the early stages, where understanding the genetic relationship between accessions is essential to identify superior parents for the development of improved breeding lines. The objectives of this study were: to perform phenotypic and molecular characterization of 100 sweet sorghum accessions from the germplasm bank of the Embrapa Maize and Sorghum breeding program; to examine the relationship between the phenotypic and the molecular diversity matrices; and to infer about the population structure in the sweet sorghum accessions. Morphological and agro-industrial traits related to sugar and biomass production were used for phenotypic characterization, and single nucleotide polymorphisms (SNPs) were used for molecular diversity analysis. Both phenotypic and molecular characterizations revealed the existence of considerable genetic diversity among the 100 sweet sorghum accessions. The correlation between the phenotypic and the molecular diversity matrices was low (0.35), which is in agreement with the inconsistencies observed between the clusters formed by the phenotypic and the molecular diversity analyses. Furthermore, the clusters obtained by the molecular diversity analysis were more consistent with the genealogy and the historic background of the sweet sorghum accessions than the clusters obtained through the phenotypic diversity analysis. The low correlation observed between the molecular and the phenotypic diversity matrices highlights the complementarity between the molecular and the phenotypic characterization to assist a breeding program. [ABSTRACT FROM AUTHOR]