A bayesian approach to map QTLs using reversible jump MCMC

A utilização de metodologias bayesianas tem se tornado frequente nas aplicações em Genética, em particular em mapeamento de QTLs usando marcadores moleculares. Mapear um QTL significa identificar sua localização ao longo do genoma, estimar seus efeitos genéticos: aditivo, dominância, epistasia, etc. A abordagem bayesiana permite combinar a verossimilhança dos dados fenotípicos com distribuições a priori atribuídas a todas as quantidades desconhecidas no modelo (número, localização no genoma e efeitos genéticos dos QTLs) de forma a fornecer distribuições a posteriori a respeito dessas quantidades. Métodos de mapeamento bayesiano podem incorporar a incerteza relativa ao número desconhecido de QTLs na análise; essa incerteza, no entanto, resulta em complicações na obtenção da amostra da distribuição conjunta a posteriori, uma vez que a dimensão do espaço do modelo pode variar. O método MCMC com Saltos Reversíveis (MCMC-SR), proposto por Green (1995), é uma excelente ferramenta para explorar a distribuição conjunta a posteriori nesse contexto. Neste trabalho, explora-se o método MCMC-SR, utilizando dados artificiais gerados no software WinQTLCart, atribuindo-se diferentes prioris para o número de QTLs.The use of Bayesian methodology in genetic applications has grown increasingly popular, in particular in the analysis of quantitative trait loci (QTL) for studies using molecular markers. In such analyses the objectives are mapping QTLs, estimating their locations in the genome and their genotypic effects (additive, dominance, and epistatic). The Bayesian approach proceeds by setting up a likelihood function for the phenotype and assigning prior distributions to all unknown quantities in the model (number, chromosome, locus, and genetic effects of QTL). These induce a posterior distribution of the unknown quantities that contains all of the available information for inference of the genetic architecture of the trait. Bayesian mapping methods can treat the unknown number of QTL as a random variable, which has several advantages but results in the complication of varying the dimension of the model space. The reversible jump MCMC algorithm (MCMC-RJ), proposed by Green (1995), offers a powerful and general approach to exploring posterior distributions in this setting. The method was evaluated by analyzing simulated data in WinQTLCart, attributing different priors distributions on the QTL numbers

Effect Of Accessions And Environment Conditions On Coumarin, O-coumaric And Kaurenoic Acids Levels Of Mikania Laevigata

Coumarin, o-coumaric, and kaurenoic acid are bioactive compounds usually found in the leaves of Mikania laevigata. Genetic and environmental variations in the secondary metabolites of plants may have implications for their biological effects. Three different accessions of M. laevigata cultivated in four sites between the Equator and the Tropic of Capricorn in Brazil were evaluated aiming to present potential raw materials and discuss relationships among these three bioactive compounds. The results revealed effects of plant accessions and environmental factors and suggested two contrasting chemical phenotypes of M. laevigata. The first phenotype presented the highest levels of kaurenoic acid (2283 +/- 316 mg/100 g) besides lower levels of coumarin (716 +/- 61 mg/100 g), which was also stimulated by the environment and mild climate at the site nearest to the Tropic of Capricorn. The other phenotype presented the lowest levels of kaurenoic acid (137 +/- 17 mg/100 g) besides higher levels of coumarin (1362 +/- 108 mg/100 g), which was also stimulated by the environment and tropical climate at the site nearest to the Equatorial beach.821614311437EMBRAPA [02.10.06.019.00.03

Identification and phylogeny of Trichoderma species by MALDI-TOF analysis and characterization of antagonistic activities against Sclerotinia scleroti

Common bean (Phaseolus vulgaris L.) is an economically important food commodity in Brazil. However, it can suffer serious damage by white mould disease caused by the pathogen Sclerotinia sclerotiorum. Species of the genus Trichoderma can act as biocontrol agents against of this pathogen. This study describes the identification based on morphological, MALDI-TOF MS and molecular analysis of these 29 Trichoderma sp. isolates and their in vitro antagonistic behaviour against S. sclerotiorum. In order to evaluate the disease incidence greenhouse experiments were also performed using bean seedling. According to the results obtained, MALDI-TOF MS technique was appropriate for all Trichoderma species identification confirming the morphological and molecular-based identifications through analysis of rDNA ITS sequence data. In vitro inhibition experiments showed that 38% of Trichoderma isolates colonised the entire surface of the medium (grade 1 evaluation score) in dual cultures against S. sclerotiorum. Pathogen exposition to non-volatile metabolites produced by Trichoderma resulted in the inhibition of their mycelia growth between c.a. 83 and 100%. Moreover, 19 Trichoderma isolates enabled a total suppression of disease in bean seedlings when evaluated in greenhouse experiments. Two Trichoderma isolates identified as Trichoderma asperellum (CEN201 and CEN162) were responsible to the highest rates of growth promotion in bean plants, which ranged from 26 to 34%. The MALDI-TOF technique was appropriate for species designation for the majority of Trichoderma species, confirming most molecular-based identifications through analysis of rDNA ITS sequence data

Evaluation of inhibitory effects of Trichoderma asperellum metabolites on mycelial growth of Sclerotinia sclerotiorum

Common bean (Phaseolus vulgaris L.) is an economically important food commodity in Brazil. However, it can suffer serious damage by white mould disease caused by the pathogen Sclerotinia sclerotiorum. Species of the genus Trichoderma can act as biocontrol agents against of this pathogen. This study describes the identification based on morphological, MALDI-TOF MS and molecular analysis of these 29 Trichoderma sp. isolates and their in vitro antagonistic behaviour against S. sclerotiorum. In order to evaluate the disease incidence greenhouse experiments were also performed using bean seedling. According to the results obtained, MALDI-TOF MS technique was appropriate for all Trichoderma species identification confirming the morphological and molecular-based identifications through analysis of rDNA ITS sequence data. In vitro inhibition experiments showed that 38% of Trichoderma isolates colonised the entire surface of the medium (grade 1 evaluation score) in dual cultures against S. sclerotiorum. Pathogen exposition to non-volatile metabolites produced by Trichoderma resulted in the inhibition of their mycelia growth between c.a. 83 and 100%. Moreover, 19 Trichoderma isolates enabled a total suppression of disease in bean seedlings when evaluated in greenhouse experiments. Two Trichoderma isolates identified as Trichoderma asperellum (CEN201 and CEN162) were responsible to the highest rates of growth promotion in bean plants, which ranged from 26 to 34%. The MALDI-TOF technique was appropriate for species designation for the majority of Trichoderma species, confirming most molecular-based identifications through analysis of rDNA ITS sequence data

Novos isolados de Trichoderma antagônicos a Sclerotinia sclerotiorum

Quarenta e nove isolados de Trichoderma obtidos no centro-oeste do Brasil foram avaliados quanto a sua atividade antagônica in vitro contra Sclerotinia sclerotiorum (agente causal do mofo branco) e identificados com base nas sequências ITS do DNA ribossômico nuclear. Os testes de cultivo pareado mostram que todos os isolados exibiram algum antagonismo, com um máximo de 77% de inibiação micelial e inibição total da produção de escleródios. Dois isolados se destacaram como os mais promissores, considerando ambos os parâmetros avaliados (CEN1253 - T. koningiopsis e CEN1265 - T. brevicompactum). Cinco espécies diferentes foram identificadas: T. harzianum (23), T. spirale (9), T. koningiopsis (8), T. brevicompactum (7) and T. asperellum (2). Estes isolados estão armazenados na Coleção de Fungos para Controle Biológico da Embrapa e as informações obtidas nos experimentos serão incorporadas na base de dados de ativos biológicos, no sistema de informações de recursos genéticos, e disponibilizados para estudos futuros.Forty-nine isolates of Trichoderma from the Brazilian Midwest were evaluated for their antagonistic activity in vitro against Sclerotinia sclerotiorum (causal agent of white mold), which were then identified based on their nuclear ribosomal ITS sequences. Paired culture tests showed that all isolates exhibited some antagonism, with a maximum of 77% mycelial inhibition and complete inhibition of sclerotia production. Two isolates were found to be the most promising biocontrol agents, considering both antagonistic parameters (CEN1253 - T. koningiopsis and CEN1265 - T. brevicompactum). Five different species were identified: T. harzianum (23), T. spirale (9), T. koningiopsis (8), T. brevicompactum (7) and T. asperellum (2). These isolates are stored in the Embrapa Fungi Collection for Biological Control and the information obtained in the experiments will be incorporated into the database of biological assets within the genetic resources information system (Allele) and be made available for further studies

Growth curve of locally adapted pantaneiro cows raised under natural conditions

The objective of this study was to use morphometric and ultrasound evaluations to estimate the growth curve of the Pantaneiro cattle breed, raised in its natural habitat, aiming at the re-insertion of this breed in production systems. One hundred and three females, aging from months to 11 years, and raised on native pastures, were evaluated. The animals belonged to the Conservation Nucleus of Embrapa Pantanal, located in the Pantanal of Mato Grosso do Sul (Brazil). Weight, thoracic perimeter (TP), body length (BL), rump height (RH), height at withers (HW), hip height (HH), depth (DP), distance between the ilia (DI) (cm) and rib-eye area (REA) were measured. To relate the measurements with the age of the animals, the univariate regression model was used, assigning the variable response to gamma distribution. The Pearson correlation between variables was also estimated. The inflection point of the growth curve was 37 months for HH; between 38 and 39 months for TP and HW; between 40 and 41 months for DI, HH and DP; and 45 months for BL. The REA results could not fit in a statistical model. The majority of the variables presented a correlation above 60% among themselves, except for REA × Age, of 15.81%; REA × HW, of 34.44%; HH × Age, of 46.19; HH × DI, of 58.07%; REA × HH, of 24.57%; and REA × TP, of 39.9%. The cows showed maturity age at 40 months, which may have occurred because they were raised in natural farming conditions. In Pantaneiro cows reared in extensive systems only on natural pastures, the use of ultrasound is not effective to estimate the curve of muscular development, perhaps because this breed was not selected for weight gain

Seleção de espécies de abelhas para avaliação de risco ambiental de algodoeiro GM no Cerrado brasileiro

The objective of this work was to list potential candidate bee species for environmental risk assessment (ERA) of genetically modified (GM) cotton and to identify the most suited bee species for this task, according to their abundance and geographical distribution. Field inventories of bee on cotton flowers were performed in the states of Bahia and Mato Grosso, and in Distrito Federal, Brazil. During a 344 hour sampling, 3,470 bees from 74 species were recovered, at eight sites. Apis mellifera dominated the bee assemblages at all sites. Sampling at two sites that received no insecticide application was sufficient to identify the three most common and geographically widespread wild species: Paratrigona lineata, Melissoptila cnecomola, and Trigona spinipes, which could be useful indicators of pollination services in the ERA. Indirect ordination of common wild species revealed that insecticides reduced the number of native bee species and that interannual variation in bee assemblages may be low. Accumulation curves of rare bee species did not saturate, as expected in tropical and megadiverse regions. Species‑based approaches are limited to analyze negative impacts of GM cotton on pollinator biological diversity. The accumulation rate of rare bee species, however, may be useful for evaluating possible negative effects of GM cotton on bee diversity. O objetivo deste trabalho foi listar espécies de abelhas candidatas potenciais para análise de risco ambiental (ARA) de algodoeiros geneticamente modificados (GM) e identificar as espécies de abelhas mais adequadas para essa finalidade, de acordo com sua abundância e distribuição geográfica. Inventários de abelhas em flores de algodoeiro foram realizados nos estados da Bahia e do Mato Grosso, e no Distrito Federal. Durante 344 horas de amostragem, foram coletadas 3.470 abelhas de 74 espécies, em oito locais. Apis mellifera dominou as assembleias de abelhas em todos os locais. A amostragem em dois locais que não receberam aplicação de inseticidas foi suficiente para identificar as três species de abelhas silvestres mais comuns e de distribuição geográfica mais ampla: Paratrigona lineata, Melissoptila cnecomola e Trigona spinipes, as quais poderiam ser usadas como indicadoras de serviços de polinização na ARA. A ordenação indireta de espécies silvestres comuns revelou que os inseticidas reduziram o número de espécies de abelhas nativas e que a variação interanual nas assembleias de abelhas pode ser baixa. As curvas de acumulação de espécies raras de abelhas não saturaram, conforme esperado em regiões tropicais e megadiversas. As abordagens baseadas em espécies são limitadas para avaliar os impactos negativos de algodoeiros GM sobre a diversidade biológica de polinizadores. A taxa de acumulação de espécies raras de abelhas, no entanto, pode ser útil para avaliar os possíveis efeitos negativos de algodoeiros GM sobre a diversidade de abelhas