Genomic selection in rubber tree breeding: A comparison of models and methods for managing G×E interactions

Several genomic prediction models combining genotype × environment (G×E) interactions have recently been developed and used for genomic selection (GS) in plant breeding programs. G×E interactions reduce selection accuracy and limit genetic gains in plant breeding. Two data sets were used to compare the prediction abilities of multienvironment G×E genomic models and two kernel methods. Specifically, a linear kernel, or GB (genomic best linear unbiased predictor [GBLUP]), and a nonlinear kernel, or Gaussian kernel (GK), were used to compare the prediction accuracies (PAs) of four genomic prediction models: 1) a single-environment, main genotypic effect model (SM); 2) a multienvironment, main genotypic effect model (MM); 3) a multienvironment, single-variance G×E deviation model (MDs); and 4) a multienvironment, environment-specific variance G×E deviation model (MDe). We evaluated the utility of genomic selection (GS) for 435 individual rubber trees at two sites and genotyped the individuals via genotyping-by-sequencing (GBS) of single-nucleotide polymorphisms (SNPs). Prediction models were used to estimate stem circumference (SC) during the first 4 years of tree development in conjunction with a broad-sense heritability (H2) of 0.60. Applying the model (SM, MM, MDs, and MDe) and kernel method (GB and GK) combinations to the rubber tree data revealed that the multienvironment models were superior to the single-environment genomic models, regardless of the kernel (GB or GK) used, suggesting that introducing interactions between markers and environmental conditions increases the proportion of variance explained by the model and, more importantly, the PA. Compared with the classic breeding method (CBM), methods in which GS is incorporated resulted in a 5-fold increase in response to selection for SC with multienvironment GS (MM, MDe, or MDs). Furthermore, GS resulted in a more balanced selection response for SC and contributed to a reduction in selection time when used in conjunction with traditional genetic breeding programs. Given the rapid advances in genotyping methods and their declining costs and given the overall costs of large-scale progeny testing and shortened breeding cycles, we expect GS to be implemented in rubber tree breeding programs

Fatores associados a desfechos desfavoráveis após trauma craniano leve pediátrico em um centro de referência da região norte de Minas Gerais

Study Design: Prospective cohort. Objective: To describe clinical and demographic characteristics of a sample of children with HI referred for acute care in a referral center of the north region of Minas Gerais, Brazil, and assess clinical and radiological markers associated with unfavorable outcomes. Methodology: All children between the ages 0 to 14 years referred with head injury from February to September 2011 were included in this study. Socio-demographic and clinical data were collected at the moment of the initial assessment under informed consent. The patients were also reassessed via telephone calls after 7 and 91 days. Results: A total of 77 patients were included in this study. The mean age was 3.9 years with a standard deviation of 3.76 years. Falls and bicycle collisions were the main mechanisms of trauma. The most relevant clinical marker associated with unfavorable outcomes at 7 days was the parental perception of unusual behavior (Odds Ratio = 11.33; 95% confidence interval: 1.38-93.13; p = 0.02). Computer tomography scan abnormalities were associated with both unfavorable outcomes at 7 days (p=0.03) and at 91 days (p=0.02). Conclusions: The peculiar aspects of head injuries in a Brazilian population were described in this study. It was also found that unusual behavior and abnormalities on CT scan are factors that predict unfavorable outcomes in children with mild HI in this population.Modelo do Estudo: Coorte prospectivo. Objetivo do Estudo: Descrever características clínicas e demográficas de uma amostra de crianças encaminhadas por traumatismo craniano em um centro de referência na região norte de Minas Gerais e avaliar marcadores clínicos e radiológicos associados a desfechos desfavoráveis. Metodologia: Foram incluídas neste estudo todas as crianças entre 0 e 14 anos atendidas com traumatismo craniano de fevereiro a setembro de 2011. Dados sócio demográficos e clínicos foram coletados no momento da avaliação inicial sob consentimento informado. Os pacientes também foram reavaliados por telefone após 7 e 91 dias. Resultados: Um total de 77 pacientes foi incluído neste estudo. A idade média foi de 3,9 anos, com desvio padrão de 3,76 anos. Quedas e colisões de bicicleta foram os principais mecanismos de trauma. O marcador clínico mais relevante associado a desfechos desfavoráveis com 7 dias foi a percepção pelos pais de comportamento anormal (Odds Ratio = 11,3; intervalo de confiança de 95%: 1,38-93,13; p = 0,02). Alterações na Tomografia Computadorizada foram associadas tanto a desfechos desfavoráveis após 7 dias (p=0,03) como após 91 dias (p=0,02). Conclusões: Os aspectos peculiares do traumatismo craniano em uma população brasileira são descritos neste estudo. Encontrou-se, ainda, que um comportamento anormal e alterações na TC são fatores que predizem desfechos desfavoráveis em crianças com traumatismo craniano leve nessa população

Cluster detection analyses for temporal-spatial characterization of bovine tuberculosis in Bahia, Brazil

A tuberculose bovina (BTB) é uma enfermidade causada pela infecção pelo Mycobacterium bovis que acomete o homem e diversas espécies de mamíferos. A BTB tem grande importância por causar prejuízos econômicos nas regiões infectadas e por seu impacto na saúde pública. Foi realizado inquérito epidemiológico no Estado da Bahia, entre 2008 e 2010, com o objetivo de estimar a prevalência e conhecer a distribuição espaço temporal da enfermidade. O Estado foi estratificado em quatro regiões, cada uma com características epidemiológicas e demográficas homogêneas representativas de formas de produção pecuária. Um total de 18.810 cabeças com idade superior a 2 anos foi amostrado em 1350 propriedades. O teste cervical comparativo foi aplicado em cada animal selecionado, sendo considerados positivos os animais reagentes positivos ou duas vezes inconclusivos. Latitude e Longitude foram tomadas para cada propriedade amostrada com o auxilio do aparelho de Global Positioning System (GPS). O teste de Cuzick-and-Edwards e a análise de rastreio espacial (spatial scan statistic) foram utilizados para identificar qualquer agrupamento espacial de BTB. A prevalência de rebanho na Bahia, indicando a proporção de propriedades foco, foi de 1,6% (IC 95%: 1,0% - 2,69% por região). Nenhuma evidência significativa (P<0.05) de aglomeração espacial ou clustering foi detectada, possivelmente devido à baixa prevalência da doença. Estes resultados sugerem que a BTB tem baixa prevalência no estado da Bahia e que, nestas condições epidemiológicas, os focos encontrados não podem ser explicados por fatores espacialmente estruturados.Bovine tuberculosis (BTB) is a disease caused by the infection with Mycobacterium bovis that affects humans and several mammalian species. BTB is important, because it inflicts far-reaching economic losses to infected regions, and due to its impact on public health. Epidemiological surveys were conducted in the State of Bahia between 2008 and 2010 with the objective to estimate the prevalence and to assess the spatial distribution of the disease. The State of Bahia has been stratified into four regions, each of them representing a set of homogeneous epidemiological and demographic characteristics, referred to as Production Circuits. A total of 18,810 more than 2-year-old cattle in 1,305 herds, ranging from 320 to 370 ones per region, and 20 to 40 cattle per herd were randomly selected. A cervical comparative test was applied to each selected animal; reactive cattle and cattle with two consecutive inconclusive tests were considered BTB-positive, whereas non-reactive cattle were considered BTB-negative. Positive herds were classified as those with <20 sampled cattle and at least one BTB-positive, as well as those with 40 cattle sampled with <2 BTB-positive animals. Latitude and longitude were recorded for each sampled herd with a generic Global Positioning System (GPS). The Cuzick-and-Edwards' test and the spatial scan statistic were used to assess whether BTB was spatially clustered. Herd-level prevalence, as indicated by the proportion of case-herds, was 1.6% (range 0.3 to 2.9% per region). No significant evidence (P<0.05) of spatial clustering was detected, most likely due to the low disease prevalence in the region. Results here suggest that BTB is low prevalent in the State of Bahia and that under these conditions epidemiological outbreaks found cannot be explained by spatially-structured factors

A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao

<p>Abstract</p> <p>Background</p> <p>The basidiomycete fungus <it>Moniliophthora perniciosa </it>is the causal agent of Witches' Broom Disease (WBD) in cacao (<it>Theobroma cacao</it>). It is a hemibiotrophic pathogen that colonizes the apoplast of cacao's meristematic tissues as a biotrophic pathogen, switching to a saprotrophic lifestyle during later stages of infection. <it>M. perniciosa</it>, together with the related species <it>M. roreri</it>, are pathogens of aerial parts of the plant, an uncommon characteristic in the order Agaricales. A genome survey (1.9× coverage) of <it>M. perniciosa </it>was analyzed to evaluate the overall gene content of this phytopathogen.</p> <p>Results</p> <p>Genes encoding proteins involved in retrotransposition, reactive oxygen species (ROS) resistance, drug efflux transport and cell wall degradation were identified. The great number of genes encoding cytochrome P450 monooxygenases (1.15% of gene models) indicates that <it>M. perniciosa </it>has a great potential for detoxification, production of toxins and hormones; which may confer a high adaptive ability to the fungus. We have also discovered new genes encoding putative secreted polypeptides rich in cysteine, as well as genes related to methylotrophy and plant hormone biosynthesis (gibberellin and auxin). Analysis of gene families indicated that <it>M. perniciosa </it>have similar amounts of carboxylesterases and repertoires of plant cell wall degrading enzymes as other hemibiotrophic fungi. In addition, an approach for normalization of gene family data using incomplete genome data was developed and applied in <it>M. perniciosa </it>genome survey.</p> <p>Conclusion</p> <p>This genome survey gives an overview of the <it>M. perniciosa </it>genome, and reveals that a significant portion is involved in stress adaptation and plant necrosis, two necessary characteristics for a hemibiotrophic fungus to fulfill its infection cycle. Our analysis provides new evidence revealing potential adaptive traits that may play major roles in the mechanisms of pathogenicity in the <it>M. perniciosa</it>/cacao pathosystem.</p

A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing

Background: Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. Results: We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at http://www.corkoakdb.org. Conclusions: This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.Peer Reviewe

CURSO DIÁRIO E SAZONAL DO POTENCIAL HÍDRICO FOLIAR DE MOGNO EM SISTEMAAGROFLORESTAL1

Este trabalho objetivou avaliar o curso diário e sazonal do potencial hídrico foliar de mogno (Swietenia macrophylla King) (Meliaceae) em sistema agroflorestal (SAF). O experimento foi realizado em árvores de S. macrophylla plantadas num sistema agroflorestal instalado no Campo Experimental da Embrapa Amazônia Ocidental, Manaus, AM. Avaliou-se o potencial hídrico foliar (Ψf) dos cursos diário e sazonal nos anos 2004 e 2005, por meio da utilização de bomba de pressão tipo Scholander. Os resultados indicaram que os valores do Ψf de S. macrophylla, de modo geral, foram superiores no início da manhã e no final da tarde, com redução acentuada ao meio-dia, e que, em relação à sazonalidade de precipitação, as menores taxas foram reportadas para a época menos chuvosa, variando de -26 bar em 2004 para -31bar em 2005. Verificou-se que o potencial hídrico de Swietenia macrophylla em sistema agroflorestal sofreu reduções significativas em razão dos baixos índices pluviométricos entre junho e outubro de 2005