Inheritance of angular leaf spot resistance in common bean line BAT 332 and identification of RAPD markers linked to the resistance gene

The existence of genetic variability for angular leaf spot (ALS) resistance in the common bean germplasm allows the development of breeding lines resistant to this disease. The BAT 332 line is an important resistance source to common bean ALS. In this work we determined the inheritance pattern and identified RAPD markers linked to a resistance gene present in BAT 332. Populations F₁, F₂,BCs and BCr derived from crosses between BAT 332 and cultivar Rudá were used. Rudá is a commercial cultivar with carioca type grains and susceptible to ALS. The resistance of BAT 332 to race 61.41 of the pathogen was confirmed. Segregation analysis of the plants indicated that a single dominant gene confers resistance. For identification of RAPD markers linked to the resistance gene, bulk segregant analysis (BSA) was used. Two RAPD markers,OPAA07₉₅₀ and OPAO12₉₅₀, linked in coupling phase at 5.10 and 5.83 cM of this gene, respectively, were identified. These molecular markers are important for common bean breeders and geneticists as source of genetic information and for marker assisted selection in breeding programs. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetics components of rice root architecture and carbon isotopic fractionation parameters: a tracer for breeding in a water-saving irrigation management

Journal of Crop Science and Biotechnology - Phenotyping is the major bottleneck in the effort to develop varieties of rice (Oryza sativa L.) suitable for growing under a water-saving irrigation...     

Genetic and functional leaf traits variability of Quercus laurina along an oak diversity gradient in Mexico

The ecological literature has documented the effects of plant hybridization on phenotypic variation, and dominant, intermediate, or novel morphological, chemical and physiological traits in hybrids. It is important to understand the ecological consequences of hybridization by evaluating their impact on phenotypic expression of functional traits. We evaluated the relationship between genetic diversity of Quercus laurina and functional foliar traits along an oak diversity gradient. We selected five study sites that represent an oak diversity gradient where Q. laurina is present. Using chloroplast and nuclear microsatellites, we evaluated genetic diversity, measured functional foliar traits of Q. laurina in each site and assessed the effects of local climate variables on the oak community and functional traits. We found a greater abundance of Q. laurina in all study sites. We did not find a relationship between the number of accompanying red oak species and the population genetic diversity in Q. laurina, but higher genetic diversity was found in all study sites in comparison with European oak species. Sites with more oak species had more variation of foliar functional traits. Our results do not support the hypothesis that predicts higher levels of genetic diversity of Q. laurina in communities with greater oak diversity from the same section, but we demonstrated an increase in the foliar functional traits of Q. laurina associated with oak richness and climate variables. We highlight the need to consider environmental and ecological variables linkages as regulatory mechanisms of the phenotypic plasticity expressed in changes of some functional attributes of oaks.

     

Evaluation of a modified QuEChERS extraction of multiple classes of pesticides from a rice paddy soil by LC-APCI-MS/MS

A new method for the determination of clomazone, fipronil, tebuconazole, propiconazole, and azoxystrobin in samples of rice paddy soil is presented. The extraction of the pesticides from soil samples was performed by using a modified quick, easy, cheap, effective, rugged, and safe (QuEChERS) method. Some extraction conditions such as salt addition, sample acidification, use of buffer, and cleanup step were evaluated. The optimized method dealt with a single extraction of the compounds under study with acidified acetonitrile, followed by the addition of MgSO(4) and NaCl prior to the final determination by liquid chromatography-atmospheric chemical pressure ionization-tandem mass spectrometry. Validation studies were carried out in soil samples. Recoveries of the spiked samples ranged between 70.3 and 120% with relative standard deviation lower than 18.2%. The limits of quantification were between 10 and 50 μg kg(-1). The method was applied to the analysis of real samples of soils where rice is cultivated.     

Spatial Variability in Slash Linear Modeling with Finite Second Moment

This article studies the dependence of spatial linear models using a slash distribution with a finite second moment. The parameters of the model are estimated with maximum likelihood by using the EM algorithm. To avoid identifiability problems, the cross-validation, the Trace and the maximum log-likelihood value are used to choose the parameter for adjusting the kurtosis of the slash distribution and the selection of the model to explain the spatial dependence. We present diagnostic techniques of global and local influences for exploring the sensibility of estimators and the presence of possible influential observations. A simulation study is developed to determine the performance of the methodology. The results showed the effectiveness of the choice criteria of the parameter for adjusting the kurtosis and for the selection of the spatial dependence model. It has also showed that the slash distribution provides an increased robustness to the presence of influential observations. As an illustration, the proposed model and its diagnostics are used to analyze an aquifer data. The spatial prediction with and without the influential observations were compared. The results show that the contours of the interpolation maps and prediction standard error maps showed low changes when we removed the influential observations. Thus, this model is a robust alternative in the spatial linear modeling for dependent random variables. Supplementary materials accompanying this paper appear online.     

Molecular diversity in <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> isolates from common bean fields in Brazil

The common bean (Phaseolus vulgaris L.) is widely cultivated in Brazil and is known as a very important crop for families in this country. Fusarium wilt severely harms common beans and has become a big issue for this crop. In order to assist the breeding programs that target resistance to this disease, the evaluation of genetic diversity of the pathogen and its molecular characterization are crucial. Thus, the present goal was to identify Fusarium isolates obtained from several places in Brazil using molecular tools; select molecular markers for these isolates; and analyze their diversity. All of isolates were molecularly identified as Fusarium oxysporum f. sp. phaseoli (Fop). By using seven selected SSR markers, the results of diversity obtained by the dendrogram and the Bayesian analysis formed four groups where a large diversity of this fungus was found within each state. However, the groups were more homogenous according to the collection source and the pathogenicity test. More specifically, group 2 was composed of the most virulent strains and originated from Minas Gerais State – UFV, and group 3 was mostly composed by isolates from Goias state. Group I was also more diverse in terms of location and virulence. The overall results indicated a positive correlation between Fusarium diversity and its virulence to common bean. Furthermore, the use of these markers was effective in molecular identification and in detecting polymorphism within F. oxysporum f. sp. phaseoli.     

Succession and management of tropical dry forests in the Americas: Review and new perspectives

Understanding tropical forest succession is critical for the development of tropical forest conservation strategies worldwide, given that tropical secondary forests can be considered the forests of the future. Tropical dry forests (TDF) are among the most threatened tropical ecosystems, there are more secondary forests and forest restoration efforts that require a better understanding of successional processes. The main goal of this synthesis for this special issue on the ecology and management of tropical dry forests in the Americas is to present a summarized review of the current knowledge of the ecology and management implications associated to TDF succession. We explore specific issues associated to tropical dry forest succession with emphasis on the use of chronosequences, plant diversity and composition, plant phenology and remote sensing, pollination, and animal–plant interactions; all under the integrating umbrella of ecosystem succession. We also emphasize the need to conduct socio-ecological research to understand changes in land-use history and its effects on succession and forest regeneration of TDF. We close this paper with some thoughts and ideas associated with the strong need for an integrating dimension not considered until today: the role of cyberinfrastructure and eco-informatics as a tool to support sound conservation, management and understanding of TDF in the Americas.     

Manganese (II) Removal from Aqueous Solutions by <Emphasis Type="Italic">Bacillus cereus</Emphasis>: an Optimization Study Using Experimental Design and Response Surface Methodology

The present study was carried out in order to investigate the removal of soluble Mn²⁺ from an aqueous solution using Bacillus cereus. A manganese aqueous solution at 50 mg L^?1 was treated, and the product was less than 1 mg L^?1 of residual concentration, which complied with environmental regulations. Before the optimization, B. cereus was able to remove Mn²⁺ ions from an aqueous solution; however, the residual content was around 2.5 mg L^?1. Screening experiments aiming at defining the effects of the growth medium composition indicated that both casamino acid-peptone and yeast extract contributed to manganese removal. These experiments also showed the interaction between these two components of the culture media, nevertheless the use of glucose did not prove significant. Considering these observations, the Doehlert design was used to generate a response surface. The model was significant with the p value lower than 0.05 and the lack-of-fit not significant (p > 0.05). The optimized composition of the growth medium was defined as 0.5 g L^?1 of casamino acid-peptone and 0.25 g L^?1 of yeast extract, whereas glucose could be removed from the original growth medium. When the optimized condition of the growth medium was used, the time required for manganese removal was reduced from 21 to 8 days. After optimization, B. cereus was capable of producing high manganese removal, reducing the residual concentration to levels below 1.0 mg L^?1.     

Molecular marker-assisted selection for development of common bean lines resistant to angular leaf spot

The objective of this work was to develop homozygous common bean lines carrying angular leaf spot resistance genes derived from the cultivars ‘Mexico 54’, ‘MAR 2’ and ‘BAT 332’ through marker‐assisted selection. Molecular markers SCAR OPN02₈₉₀, RAPD OPE04₅₀₀ and OPAO12₉₅₀ linked to the resistance genes of ‘Mexico 54’, ‘MAR 2’ and ‘BAT 332’, respectively, were used in segregating backcross‐derived populations to selection. DNA fingerprinting was used to select homozygous BC₂F₃ and BC₁F₃ resistant plants genetically closer to the recurrent parent. Two homozygous BC₂F_2:3 and two and five BC₁F_2:3 families derived from ‘Ruda’ vs. ‘Mexico 54’ (RM), ‘MAR 2’ (RMA) and ‘BAT 332’ (RB) crosses were selected, respectively. After only one (RMA, RB) or two backcrosses (RM), five and eight BC₁F₃ lines derived from RMA and RB, respectively, and seven BC₂F₃ lines derived from RM, with 14.9–16.6, 16.9–18.6 and 9.3–11.1% of relative genetic distances to the recurrent parent were selected. This is the first report of lines resistant to angular leaf spot carrying genes of the cultivars ‘Mexico 54’, ‘MAR 2’ and ‘BAT 332’ developed with the aid of molecular markers.     

Performance and intestinal microbiota of chickens receiving probiotic in the feed and submitted to antibiotic therapy

The purpose of this study was to verify the ability of a probiotic in the feed to maintain the stability of the gut microbiota in chickens after antibiotic therapy and its association with growth performance. One thousand six hundred twenty 1‐day‐old Cobb male were housed in floor pens (36 pens, 45 birds/pen) and were fed corn‐/soya bean meal‐based diets supplemented with or without probiotic (Bacillus subtilis) during the entire rearing phase. From 21 to 24 days of age (three consecutive days), the chickens were submitted to antibiotic therapy via drinking water (bacitracin and neomycin) in order to mimic a field treatment and induce dysbiosis. Growth performance was monitored until 42 days of age. At 2, 4 and 6 days after antibiotic therapy, three chickens from each pen were euthanized and the contents of the small intestine and caeca were collected and pooled. The trial was conducted with four treatments and nine replicates in a 2 × 2 factorial arrangement for performance characteristics (with and without probiotic × with and without antibiotic therapy); for the intestinal microbiota, it was in a 2 × 2 × 3 factorial arrangement (with and without probiotic × with and without antibiotic therapy × 2, 4 and 6 days after the antibiotic therapy) with three replicates per treatment. Terminal restriction length polymorphism (T‐RFLP) analysis showed that the structure of gut bacterial community was shaped by the intestinal segment and by the time after the antibiotic therapy. The number of 16S rDNAs copies in caecum contents decreased with time after the therapeutic treatment. The antibiotic therapy and dietary probiotic supplementation decreased richness and diversity indexes in the caecal contents. The improved performance observed in birds supplemented with probiotic may be related to changes promoted by the feed additive in the structure of the intestinal bacterial communities and phylogenetic groups. Antibiotic therapy modified the bacterial structure, but did not cause loss of broiler performance.