Overview of the use of genomic data in animal breeding / Panorama do uso de dados genômicos no melhoramento genético animal

The use of molecular information in breeding programs contributed to important advances in the improvement of traits of economic interest in livestock production. The advent of single nucleotide polymorphism (SNP) panels applied to genome-wide selection (GWS) and genome-wide association studies (GWAS), along with computational advances (e.g., use of powerful software and robust analyses) allowed a better understanding of the genetic architecture of farm animals and increased the selection efficiency. In this context, the statistic method single-step GBLUP has been frequently used to perform GWS, and more recently GWAS analyses, providing accurate predictions and QTL detection, respectively. Nevertheless, in developing countries, species such as sheep and goats, whose genomic data are more difficult to be obtained, the use of data simulation has been efficient in the study of the major factors involved in the selection process, such as size of training population, density of SNP chips, and genotyping strategies. The effects of these factors are directly associated with the prediction accuracy of genomic breeding values. In this review we showed important aspects of the use of genomics in the genetic improvement of production traits of animals, the main methods currently used for prediction and estimation of molecular marker effects, the importance of data simulation for validation of those methods, as well as the advantages, challenges and limitations of the use of GWS and GWAS in the current scenario of livestock production.

Em programas de melhoramento genético, o uso de informações moleculares garantiu importantes avanços para a melhoria de características de interesse econômico, no âmbito da produção animal. O advento da tecnologia de painéis de SNPs aplicados à seleção genômica ampla (GWS) e associação genômica ampla (GWAS), aliado ao avanço computacional, com o uso de softwares e análises robustas, permitiram melhor compreensão sobre a arquitetura genética dos animais de produção e, consequentemente, maior eficiência na seleção. Nesse contexto, o método estatístico single-step GBLUP tem sido utilizado, frequentemente, na execução da GWS e, mais recentemente, em GWAS, possibilitando predições acuradas e detecção de QTLs, respectivamente. No entanto, em países em desenvolvimento e, em espécies como os ovinos e caprinos, que existe maior dificuldade para a aquisição de dados genômicos, o uso da simulação de dados tem se mostrado eficiente para estudar os principais fatores envolvidos no processo de seleção, como o tamanho da população de treinamento, densidade de chipde SNPs e estratégias de genotipagem, cujos efeitos estão diretamente associados à acurácia da predição de valores genéticos genômicos. Nesta revisão, serão abordados pontos importantes sobre o uso da genômica no melhoramento genético de características produtivas em animais, principais métodos de predição e estimação de efeitos de marcadores moleculares na atualidade, a importância da simulação de dados para a validação desses métodos, bem como as vantagens, os desafios e as limitações no cenário atual da produção animal com o uso da seleção e associação genômica ampla.

Genome-enabled prediction through quantile random forest for complex traits / Predição genômica por meio do random forest quantílitico para características complexas

Quantile Random Forest (QRF) is a non-parametric methodology that combines the advantages of Random Forest (RF) and Quantile Regression (QR). Specifically, this approach can explore non-linear functions, determining the probability distribution of a response variable and extracting information from different quantiles instead of just predicting the mean. This evaluated the performance of the QRF in the genomic prediction for complex traits (epistasis and dominance). In addition, compare the accuracies obtained with those derived from the G-BLUP. The simulation created an F2 population with 1,000 individuals and genotyped for 4,010 SNP markers. Besides, twelve traits were simulated from a model considering additive and non-additive effects, QTL (Quantitative trait loci) numbers ranging from eight to 120, and heritability of 0.3, 0.5, or 0.8. For training and validation, the 5-fold cross-validation approach was used. For each fold, the accuracies of all the proposed models were calculated: QRF in five different quantiles and three G-BLUP models (additive effect, additive and epistatic effects, additive and dominant effects). Finally, the predictive performance of these methodologies was compared. In all scenarios, the QRF accuracies were equal to or greater than the methodologies evaluated and proved to be an alternative tool to predict genetic values in complex traits.

Quantile Random Forest (QRF) é uma metodologia não paramétrica, que combina as vantagens do Random Forest (RF) e da Regressão Quantílica (QR). Especificamente, essa abordagem pode explorar funções não lineares, determinando a distribuição de probabilidade de uma variável resposta e extraindo informações de diferentes quantis em vez de apenas prever a média. O objetivo deste trabalho foi avaliar o desempenho do QRF em predizer o valor genético genômico para características com arquitetura genética não aditiva (epistasia e dominância). Adicionalmente, as acurácias obtidas foram comparadas com aquelas advindas do G-BLUP. A simulação criou uma população F2 com 1.000 indivíduos genotipados para 4.010 marcadores SNP. Além disso, doze características foram simuladas a partir de um modelo considerando efeitos aditivos e não aditivos, com número de QTL (Quantitative trait loci) variando de oito a 120 e herdabilidade de 0,3, 0,5 ou 0,8. Para treinamento e validação foi usada a abordagem da validação cruzada 5-fold. Para cada um dos folds foram calculadas as acurácias de todos os modelos propostos: QRF em cinco quantis diferentes e três modelos do G-BLUP (com efeito aditivo, aditivo e epistático, aditivo e dominante). Por fim, o desempenho preditivo dessas metodologias foi comparado. Em todos os cenários, as acurácias do QRF foram iguais ou superiores às metodologias avaliadas e mostrou ser uma ferramenta alternativa para predizer valores genéticos em características complexas.

The dynamics of genome size and GC contents evolution in genus Nicotiana / A dinâmica do tamanho do genoma e a evolução dos conteúdos de GC no gênero Nicotiana

Hybridization and Polyploidization are most common of the phenomenon observed in plants, especially in the genus Nicotiana leading to the duplication of genome. Although genomic changes associated with these events has been studied at various levels but the genome size and GC content variation is less understood because of absence of sufficient genomic data. In this study the flow cytometry technique was used to uncover the genome size and GC contents of 46 Nicotiana species and we compared the genomic changes associated with the hybridization events along evolutionary time scale. The genome size among Nicotiana species varied between 3.28 pg and 11.88 pg whereas GC contents varied between 37.22% and 51.25%. The tetraploid species in genus Nicotiana including section Polydiclae, Repandae, Nicotiana, Rustica and Sauveolentes revealed both up and downsizing in their genome sizes when compared to the sum of genomes of their ancestral species. The genome sizes of three homoploid hybrids were found near their ancestral species. Loss of large genome sequence was observed in the evolutionary more aged species (>10 Myr) as compared to the recently evolved one’s (<0.2 Myr). The GC contents were found homogenous with a mean difference of 2.46% among the Nicotiana species. It is concluded that genome size change appeared in either direction whereas the GC contents were found more homogenous in genus Nicotiana.

A hibridização e a poliploidização são os fenômenos mais comuns observados em plantas, principalmente no gênero Nicotiana, levando à duplicação do genoma. Embora as mudanças genômicas associadas a esses eventos tenham sido estudadas em vários níveis, o tamanho do genoma e a variação do conteúdo de GC são menos compreendidos devido à ausência de dados genômicos suficientes. Neste estudo, a técnica de citometria de fluxo foi usada para descobrir o tamanho do genoma e o conteúdo de GC de 46 espécies de Nicotiana, e comparamos as mudanças genômicas associadas aos eventos de hibridização ao longo da escala de tempo evolutiva. O tamanho do genoma entre as espécies de Nicotiana variou entre 3,28 pg e 11,88 pg, enquanto os conteúdos de GC variaramentre 37,22% e 51,25%. As espécies tetraploides do gênero Nicotiana, incluindo as seções Polydiclae, Repandae, Nicotiana, Rustica e Sauveolentes, revelaram aumento e redução do tamanho do genoma quando comparados à soma dos genomas de suas espécies ancestrais. Os tamanhos do genoma de três híbridos homoploides foram encontrados perto de suas espécies ancestrais. A perda da grande sequência do genoma foi observada nas espécies evolutivas mais velhas (> 10 Myr) em comparação com as que evoluíram recentemente (< 0,2 Myr). Os teores de GC foram homogêneos com diferença média de 2,46% entre as espécies de Nicotiana. Conclui-se que a mudança no tamanho do genoma apareceu em ambas as direções, enquanto os conteúdos de GC foram encontrados mais homogêneos no gênero Nicotiana.

The dynamics of genome size and GC contents evolution in genus Nicotiana / A dinâmica do tamanho do genoma e a evolução dos conteúdos de GC no gênero Nicotiana

Hybridization and Polyploidization are most common of the phenomenon observed in plants, especially in the genus Nicotiana leading to the duplication of genome. Although genomic changes associated with these events has been studied at various levels but the genome size and GC content variation is less understood because of absence of sufficient genomic data. In this study the flow cytometry technique was used to uncover the genome size and GC contents of 46 Nicotiana species and we compared the genomic changes associated with the hybridization events along evolutionary time scale. The genome size among Nicotiana species varied between 3.28 pg and 11.88 pg whereas GC contents varied between 37.22% and 51.25%. The tetraploid species in genus Nicotiana including section Polydiclae, Repandae, Nicotiana, Rustica and Sauveolentes revealed both up and downsizing in their genome sizes when compared to the sum of genomes of their ancestral species. The genome sizes of three homoploid hybrids were found near their ancestral species. Loss of large genome sequence was observed in the evolutionary more aged species (>10 Myr) as compared to the recently evolved ones (<0.2 Myr). The GC contents were found homogenous with a mean difference of 2.46% among the Nicotiana species. It is concluded that genome size change appeared in either direction whereas the GC contents were found more homogenous in genus Nicotiana.(AU)

A hibridização e a poliploidização são os fenômenos mais comuns observados em plantas, principalmente no gênero Nicotiana, levando à duplicação do genoma. Embora as mudanças genômicas associadas a esses eventos tenham sido estudadas em vários níveis, o tamanho do genoma e a variação do conteúdo de GC são menos compreendidos devido à ausência de dados genômicos suficientes. Neste estudo, a técnica de citometria de fluxo foi usada para descobrir o tamanho do genoma e o conteúdo de GC de 46 espécies de Nicotiana, e comparamos as mudanças genômicas associadas aos eventos de hibridização ao longo da escala de tempo evolutiva. O tamanho do genoma entre as espécies de Nicotiana variou entre 3,28 pg e 11,88 pg, enquanto os conteúdos de GC variaramentre 37,22% e 51,25%. As espécies tetraploides do gênero Nicotiana, incluindo as seções Polydiclae, Repandae, Nicotiana, Rustica e Sauveolentes, revelaram aumento e redução do tamanho do genoma quando comparados à soma dos genomas de suas espécies ancestrais. Os tamanhos do genoma de três híbridos homoploides foram encontrados perto de suas espécies ancestrais. A perda da grande sequência do genoma foi observada nas espécies evolutivas mais velhas (> 10 Myr) em comparação com as que evoluíram recentemente (< 0,2 Myr). Os teores de GC foram homogêneos com diferença média de 2,46% entre as espécies de Nicotiana. Conclui-se que a mudança no tamanho do genoma apareceu em ambas as direções, enquanto os conteúdos de GC foram encontrados mais homogêneos no gênero Nicotiana.(AU)

Genome-Wide Association Study on Two Immune-Related Traits in Jinghai Yellow Chicken

This study was designed to discover molecular marker associated with the interferon INF-γ and avian influenza (AI) antibody titer traits in Jinghai Yellow chicken (Gallus gallus). Serum samples were taken from 400 female chickens and the INF-γ concentrations and AI antibody titer levels were measured. A genome-wide association study was carried out using specific-locus amplified fragment (SLAF) sequencing. Bioinformatics analysis was applied to detect single-nucleotide polymorphisms (SNPs) associated with the two traits. After sequencing and quality control, 103,680 SLAFs and 90,961 SNPs were obtained. The 400 samples were divided into 10 subgroups to reduce the effects of group stratification. The Bonferroni adjusted P-value of genome-wide significance was set at 1.87E−06 according to the number of independent SNP markers and linkage disequilibrium blocks. A SNP that was significantly associated with INF-γ concentration was detected in the myomesin 1 (MYOM1) gene on chromosome 2, and another SNPthat was significantly associated with the AI antibody titer level was detected in an RNA methyltransferase gene (Nsun7), which was found to have an important biological function. We propose that MYOM1 and Nsun7 are valuable candidate genes that influence the disease resistance characters of chicken. However, in-depth investigations are needed to determine the essential roles of these genes in poultry disease resistance and their possible application in breeding disease resistant poultry.(AU)

Tracking the evolutionary pathways among Brazilian Lebiasina species (Teleostei: Lebiasinidae): a chromosomal and genomic comparative investigation

Despite several difficulties in chromosomal analyses of small-sized fishes, the cytogenetics of the Lebiasinidae was largely improved in the last years, showing differential patterns in the chromosomal evolution inside the family. In this context, it has been shown that genus Lebiasina preserves its karyotypic macrostructure, composed of 2n = 36 chromosomes, whereas the other genera generally present higher 2n. This study focused on the comparative cytogenetics of three Lebiasina species, one of them analyzed here for the first time, using conventional and molecular procedures. The results reinforced the differentiated evolutionary path of the genus Lebiasina while, at the same time, highlighted the genomic particularities that have accompanied the evolution of each species. In this sense, the repetitive components of the genome played a significant role in the differentiation of each species. It is also notable that L. minuta and L. melanoguttata, the two species that occur exclusively in the Brazilian territory, show greater chromosomal similarities to each other than to the trans-Andean sister species, L. bimaculata.(AU)

Apesar das dificuldades encontradas em se realizar análises cromossômicas em peixes de pequeno porte, os estudos citogenéticos em Lebiasinidae vêm crescendo nos últimos anos e demonstrando padrões diferenciados na evolução cromossômica entre os membros da família. Nesse contexto, o gênero Lebiasina tem mostrado preservar sua macroestrutura cariotípica, composta por 2n = 36 cromossomos, enquanto os demais gêneros geralmente apresentam 2n maiores. Este estudo tem como foco a citogenética comparativa de três espécies de Lebiasina, sendo uma delas analisada pela primeira vez aqui, através do emprego de técnicas convencionais e moleculares. Os resultados obtidos reforçam a trajetória evolutiva diferenciada do gênero Lebiasina, ao mesmo tempo em que evidenciam as particularidades genômicas que acompanham a evolução de cada uma das espécies. Neste contexto, os componentes repetitivos do genoma tiveram um papel importante na caracterização particular de cada uma das espécies. Também, é notável que L. minuta e L. melanoguttata, duas espécies que ocorrem exclusivamente no território brasileiro, apresentam maior proximidade citogenética entre elas do que com a espécie irmã transandina, L. bimaculata.(AU)

Prospection of putative genes for digestive enzymes based on functional genome of the hepatopancreas of Amazon river prawn

Over recent years, Macrobrachium amazonicum has become a popular species for shrimp farming due to their fast growth, high survival rates, and marketability. Several studies have focused on the development of new technology for the culture of this species, but many aspects of their nutrition and physiology remain unknown. Thus, the goal of the present study was to obtain transcripts of putative genes encoding digestive enzymes, based on a library of the cDNA from the hepatopancreas of M. amazonicum, sequenced in the Ion TorrentTM platform. We identified fragments of nine genes related to digestive enzymes, acting over proteins, carbohydrates and lipids. Endo and exoproteases were also recorded in the hepatopancreas, indicating adaptation to the digestion of protein-richfoods. Nonetheless, the enzymes involved in the carbohydrate metabolism formed the largest functional group in M. amazonicum, including enzymes related to the digestion of starch, chitin, and cellulose. These findings indicate that the species has a genetic apparatus of a well-adapted omnivorous animal. This information may provide important insights for the selection of ingredients for the formulation of a more appropriate diet to the enzymatic repertoire of M. amazonicum.(AU)

Sistema CRISPR/Cas9 e perspectivas de aplicações na cadeia produtiva animal / CRISPR/Cas9 system and perspectives for applications in the animal production chain

O melhoramento genético tem papel fundamental no aumento da eficiência da produção pecuária. Entretanto, programas tradicionais de melhoramento podem levar vários anos para atingir um determinado objetivo. Novas abordagens genômicas permitem acelerar esse processo e recentemente a edição gênica surgiu como nova alternativa, além de ter potencial para induzir outras modificações genéticas de interesse comercial e biomédico. A possibilidade de editar o genoma de diferentes espécies, de maneira simples e eficaz, tornou-se possível com a tecnologia do sistema CRISPR/Cas9. Esse sistema biológico foi identificado em bactérias e funciona como um mecanismo natural de defesa desses organismos. Baseando-se nos princípios biológicos, cientistas adaptaram esse sistema para atuar em células de mamíferos, incluindo humanas. Trabalhos científicos demonstraram a aplicabilidade da técnica, que permite novas abordagens na condução de estudos da função gênica, além de permitir diferentes experimentos de alteração específica da sequência do DNA. Do ponto de vista da produção animal, a utilização do sistema CRISPR traz novos conceitos e possibilidades para o melhoramento genético. O objetivo desta revisão é discutir os princípios da metodologia, associando resultados previamente conhecidos à possíveis aplicações com enfoque na cadeia produtiva animal.(AU)

Genetic improvement has a prominent role in increasing the efficiency of livestock production systems. However, traditional breeding programs may take several years to achieve a specific goal. New genomic approaches could accelerate this process and recently gene editing appeared as an alternative and still holds the potential to induce genetic alterations of commercial and biomedical interest. The possibility of editing the genome of different species, in a simple and effective way, became possible with the technology of the CRISPR / Cas9 system. This biological system was identified in bacteria and works as a natural defense mechanism for these organisms. Based on biological principles, scientists adapted this system to act on mammalian cells, including humans. Scientific studies demonstrated the applicability of the technique, which allows new approaches in conducting studies of gene function, in addition to different experiments of targeted modification of the DNA sequence. From the point of view of animal production, the use of the CRISPR brings new concepts and possibilities for genetic improvement. The purpose of this review is to discuss the principles of the methodology, associating previously known results to possible applications focusing on the animal production chain.(AU)

Sistema CRISPR/Cas9 e perspectivas de aplicações na cadeia produtiva animal / CRISPR/Cas9 system and perspectives for applications in the animal production chain

O melhoramento genético tem papel fundamental no aumento da eficiência da produção pecuária. Entretanto, programas tradicionais de melhoramento podem levar vários anos para atingir um determinado objetivo. Novas abordagens genômicas permitem acelerar esse processo e recentemente a edição gênica surgiu como nova alternativa, além de ter potencial para induzir outras modificações genéticas de interesse comercial e biomédico. A possibilidade de editar o genoma de diferentes espécies, de maneira simples e eficaz, tornou-se possível com a tecnologia do sistema CRISPR/Cas9. Esse sistema biológico foi identificado em bactérias e funciona como um mecanismo natural de defesa desses organismos. Baseando-se nos princípios biológicos, cientistas adaptaram esse sistema para atuar em células de mamíferos, incluindo humanas. Trabalhos científicos demonstraram a aplicabilidade da técnica, que permite novas abordagens na condução de estudos da função gênica, além de permitir diferentes experimentos de alteração específica da sequência do DNA. Do ponto de vista da produção animal, a utilização do sistema CRISPR traz novos conceitos e possibilidades para o melhoramento genético. O objetivo desta revisão é discutir os princípios da metodologia, associando resultados previamente conhecidos à possíveis aplicações com enfoque na cadeia produtiva animal.

Genetic improvement has a prominent role in increasing the efficiency of livestock production systems. However, traditional breeding programs may take several years to achieve a specific goal. New genomic approaches could accelerate this process and recently gene editing appeared as an alternative and still holds the potential to induce genetic alterations of commercial and biomedical interest. The possibility of editing the genome of different species, in a simple and effective way, became possible with the technology of the CRISPR / Cas9 system. This biological system was identified in bacteria and works as a natural defense mechanism for these organisms. Based on biological principles, scientists adapted this system to act on mammalian cells, including humans. Scientific studies demonstrated the applicability of the technique, which allows new approaches in conducting studies of gene function, in addition to different experiments of targeted modification of the DNA sequence. From the point of view of animal production, the use of the CRISPR brings new concepts and possibilities for genetic improvement. The purpose of this review is to discuss the principles of the methodology, associating previously known results to possible applications focusing on the animal production chain.

Genomic characterization of Canine circovirus detected in a dog with intermittent hemorrhagic gastroenteritis in Brazil / Caracterização genômica do Canine circovirus detectado em um cão com gastroenterite hemorrágica intermitente no Brasil

Because Canine circovirus (CanineCV) is a new species of the genus Circovirus, several issues related to its epidemiology, pathogenesis and clinical disease remain unknown. Thus, this study aimed to perform the characterization of the first complete genome sequence of CanineCV detected in a dog with diarrhea in Brazil. A stool sample was collected of a ten-month-old female German Shepherd dog which had signs of intermittent hemorrhagic gastroenteritis, vomiting, and a history of eating raw pork. The complete CanineCV genome was sequenced by Next-Generation Sequencing. The sequence had 2,063 nucleotides, showed a typical genomic organization for circovirus, and was grouped with strain 214 described in the United States by phylogenetic analysis. One amino acid change was found in the replicase protein, and because of that it was considered unique to CanineCV. Therefore, the characterization of the complete genome of Brazilian CanineCV can be used in future studies of molecular epidemiology, pathogenesis and development of diagnostic tools for the prevention and control of this disease.(AU)

Como o Canine circovirus (CanineCV) é uma nova espécie do Gênero Circovirus, várias questões relacionadas com a sua epidemiologia, patogenia e doença clínica permanecem desconhecidas. Assim, este estudo objetivou realizar a caracterização da primeira sequência do genoma completo do CanineCV detectado em um cão com diarreia, no Brasil. Uma amostra de fezes foi coletada de um cão da raça Pastor Alemão, fêmea, 10 meses de idade, o qual tinha sinais de gastroenterite hemorrágica intermitente, vômito e uma história de ingestão de carne crua de porco. O genoma completo do CanineCV foi sequenciado pelo Sequenciamento de Nova Geração. A sequência tinha 2.063 nucleotídeos, apresentou uma organização genômica típica para um circovírus e foi agrupado com a cepa 214, descrita nos Estados Unidos pela análise filogenética. Uma mudança de aminoácido foi encontrada na proteína de replicação e por causa disso ela foi considerada única para o CanineCV. Portanto, a caracterização do genoma completo do CanineCV brasileiro pode ser utilizada em futuros estudos de epidemiologia molecular, patogenia e no desenvolvimento de ferramentas de diagnóstico para prevenção e controle desta doença.(AU)

Improving crops genome through genetic engineering of the key metabolic pathways

Soybean loss due to pests and pathogens is a serious problem worldwide. Soybean producers have few options to manage diseases caused by general pathogens where major genes for full resistance have not been discovered. The innate defense of soybean plants could be enhanced by improving content and composition of lignin by genetic engineering of the phenylpropanoid pathway.We used a novel technique of germ-line genetic transformation of soybean plants via natural pollen tubes as vectors. This technique uses Agrobacterium tumefaciensto mediate transfer of genes of interest to the zygote to introduce the key lignification genes (PtMYB4, PAL5, F5H, CAD1) into soybean genome. We observed 5.6% average transformation efficiency in the first generation of transgenic plants and in the second generation the presence of the transgene constructs was confirmed in more than 50% (for CsVMV/PtMYB4sens, 35SVTM/PAL5, C4H/F5H, CsVMV/CAD1constructs) transgenic soybean lines. We confirmed the expression of the introduced genes at transcriptional level using RT-PCR and Northern blot. Functional analysis using lignin content determination and the activity of PAL5 and CAD1 enzymes demonstrated that the transgenes perform their function in planta. The proposed technique is effectiveand inexpensive and can be used to create novel stress and disease resistant soybean genotypes.

Bacillus cereus group: genetic aspects related to food safety and dairy processing / Grupo do Bacillus cereus: aspectos genéticos relacionados à segurança alimentar e ao processamento de derivados lácteos

Bacillus cereus group includes not pathogenic and high pathogenic species. They are considered as a risk to public health due to foodborne diseases and as an important cause of economic losses to industries due to production of spoilage enzymes. Some researches have been performed in order to assess the possible factors that contribute to put public health into risk because of consumption of food contaminated with viable cells or toxins which have complex mechanisms of production. The control of these bacteria in food is difficult because they are resistant to several processes used in industries. Thus, in this way, this review focused on highlighting the risk due to toxins production by bacteria from B. cereus group in food and the consequences for food safety and dairy industries.(AU)

Diversas espécies fazem parte do grupo de Bacillus cereus, desde algumas apatogênicas até outras com alta patogenicidade. Consistem em risco à saúde pública decorrentes de toxinfecções alimentares, além de causarem importantes perdas econômicas para as indústrias em virtude da produção de enzimas deteriorantes. O controle da contaminação em alimentos por esses micro-organismos é difícil, visto que são resistentes a vários tratamentos utilizados pelas indústrias. Assim, diante do exposto, esta revisão objetivou fornecer informações em relação aos aspectos genéticos desse grupo de bactérias e seus mecanismos de produção de toxinas, além de ressaltar a importância e as novas estratégias de controle para as companhias alimentícias e de laticínios.(AU)

Bacillus cereus group: genetic aspects related to food safety and dairy processing / Grupo do Bacillus cereus: aspectos genéticos relacionados à segurança alimentar e ao processamento de derivados lácteos

Bacillus cereus group includes not pathogenic and high pathogenic species. They are considered as a risk to public health due to foodborne diseases and as an important cause of economic losses to industries due to production of spoilage enzymes. Some researches have been performed in order to assess the possible factors that contribute to put public health into risk because of consumption of food contaminated with viable cells or toxins which have complex mechanisms of production. The control of these bacteria in food is difficult because they are resistant to several processes used in industries. Thus, in this way, this review focused on highlighting the risk due to toxins production by bacteria from B. cereus group in food and the consequences for food safety and dairy industries.(AU)

Diversas espécies fazem parte do grupo de Bacillus cereus, desde algumas apatogênicas até outras com alta patogenicidade. Consistem em risco à saúde pública decorrentes de toxinfecções alimentares, além de causarem importantes perdas econômicas para as indústrias em virtude da produção de enzimas deteriorantes. O controle da contaminação em alimentos por esses micro-organismos é difícil, visto que são resistentes a vários tratamentos utilizados pelas indústrias. Assim, diante do exposto, esta revisão objetivou fornecer informações em relação aos aspectos genéticos desse grupo de bactérias e seus mecanismos de produção de toxinas, além de ressaltar a importância e as novas estratégias de controle para as companhias alimentícias e de laticínios.(AU)

Genome prediction accuracy of common bean via Bayesian models / Acurácia de predição genômica em feijoeiro-comum via modelos Bayesianos

We aimed to apply genomic information based on SNP (single nucleotide polymorphism) markers for the genetic evaluation of the traits stay-green (SG), plant architecture (PA), grain aspect (GA) and grain yield (GY) in common bean through Bayesian models. These models were compared in terms of prediction accuracy and ability for heritability estimation for each one of the mentioned traits. A total of 80 cultivars were genotyped for 377 SNP markers, whose effects were estimated by five different Bayesian models: Bayes A (BA), B (BB), C (BC), LASSO (BL) e Ridge regression (BRR). Although, prediction accuracies calculated by means of cross-validation have been similar within each trait, the BB model stood out for the trait SG, whereas the BRR was indicated for the remaining traits. The heritability estimates for the traits SG, PA, GA and GY were 0.61, 0.28, 0.32 and 0.29, respectively. In summary, the Bayesian methods applied here were effective and ease to be implemented. The used SNP markers can help in the early selection of promising genotypes, since incorporating genomic information increase the prediction accuracy of the estimated genetic merit.(AU)

Objetivou-se incorporar informações genômicas de marcadores SNP (single nucleotide polymorphism) na avaliação genética das características stay-green (SG), arquitetura de planta (AP), aspecto de grãos (AG) e produtividade de grãos (PG) em feijoeiro-comum via modelos Bayesianos. Estes modelos foram comparados quanto a acurácia de predição e habilidade de estimação da herdabilidade para cada característica. Utilizaram-se informações de 80 cultivares genotipadas para 377 marcadores SNP, cujos efeitos de substituição alélica foram estimados por meio de cinco diferentes modelos Bayesianos: Bayes A (BA), B (BB), C (BC), LASSO (BL) e regressão ridge (BRR). Embora as acurácias de predição calculadas por meio de análise de validação cruzada tenham sido similares dentro de cada característica, o modelo BB se destacou para a característica SG, enquanto o modelo BRR foi indicado para as demais. As herdabilidades estimadas para SG, AP, AG e PG foram, respectivamente, 0,61, 0,28, 0,32 e 0,29. Em resumo, os métodos contemplados mostraram-se efetivos e de fácil implementação. O conjunto de marcadores utilizado pode auxiliar na seleção precoce de genótipos promissores, uma vez que a incorporação de informações genômicas aumenta a acurácia de predição do mérito genético estimado.(AU)

Draft genome sequence of Bradyrhizobium manausense strain BR 3351T, an effective symbiont isolated from Amazon rainforest

ABSTRACT The strain BR 3351T (Bradyrhizobium manausense) was obtained from nodules of cowpea (Vigna unguiculata L. Walp) growing in soil collected from Amazon rainforest. Furthermore, it was observed that the strain has high capacity to fix nitrogen symbiotically in symbioses with cowpea. We report here the draft genome sequence of strain BR 3351T. The information presented will be important for comparative analysis of nodulation and nitrogen fixation for diazotrophic bacteria. A draft genome with 9,145,311 bp and 62.9% of GC content was assembled in 127 scaffolds using 100 bp pair-end Illumina MiSeq system. The RAST annotation identified 8603 coding sequences, 51 RNAs genes, classified in 504 subsystems.(AU)

Complete genome sequence of a phthalic acid esters degrading Mycobacterium sp. YC-RL4

ABSTRACT Mycobacterium sp. YC-RL4 is capable of utilizing a broad range of phthalic acid esters (PAEs) as sole source of carbon and energy for growth. The preliminary studies demonstrated its high degrading efficiency and good performance during the bioprocess with environmental samples. Here, we present the complete genome of Mycobacterium sp. YC-RL4, which consists of one circular chromosome (5,801,417 bp) and one plasmid (252,568 bp). The genomic analysis and gene annotation were performed and many potential genes responsible for the biodegradation of PAEs were identified from the genome. These results may advance the investigation of bioremediation of PAEs-contaminated environments by strain YC-RL4.(AU)

Detecção e tratamento de otite por Rhabditis blumi em bovinos da região Norte do Brasil / Detection and treatment of otitis by Rhabditis blumi in cattle of northern Brazil

O presente estudo teve como objetivo descrever a ocorrência de otite parasitária causada por Rhabditis blumi em bovinos leiteiros de raça Gir de uma fazenda da região Norte do Brasil. Foram coletadas amostras de 42 bovinos por swab e lavado dos condutos auditivos externos (CAE). Ao exame clínico, 9,5% (4/42) dos bovinos apresentavam sintomatologia nervosa, como leve a moderada rotação da cabeça, apatia, flacidez dos lábios e ptose palpebral unilateral, alopecia das regiões da cabeça e cupim, causados pelo desconforto e prurido da região auricular, alteração na mastigação e acúmulo de alimento na cavidade oral. Adicionalmente, 71,4% (30/42) dos abovinos mostraram a presença do parasita no cerúmen dos condutos auditivos. À análise microscópica do material do saco conjuntival foi observado presença do parasita em 90% (9/10) dos bovinos avaliados. Os 30 bovinos positivos para Rhabditis spp. foram distribuídos aleatoriamente em três grupos de 10 animais: (G1) Bovinos controle, (G2) Bovinos tratados com ivermectina 1% pour on e (G3) Bovinos submetidos a lavado dos condutos auditivos externos (CAE). Cada tratamento foi repetido três vezes com intervalo de sete dias. No G1 os 10 bovinos mantiveram-se infectados durante todo o estudo. No G2 20% dos bovinos foram negativos após os dois primeiros tratamentos, porém, mostraram-se positivos na terceira avaliação. No G3 todos os bovinos mantiveram-se positivos, sendo observada apenas diminuição da carga parasitária. A identificação por análise molecular por meio de fragmentos amplificados da expansão D2/D3 do 28S rDNA confirmou a presença apenas da espécie Rhabditis blumi nos animais. Baseado nas observações clínicas, morfológicas e moleculares pode-se relatar o primeiro caso de R. blumi em bovinos da raça Gir no Estado do Pará, através da compra de animais oriundos de áreas onde a otite parasitária tem sido diagnosticada, principalmente de Minas Gerais, para formar animais mestiços (Gir x Holandês). Desta forma ressalta-se a importância do exame clínico prévio dos animais a serem transferidos para outras propriedades ou regiões. Este relato também parece ser o primeiro sobre a presença de R. blumi no saco conjuntival de bovinos. O tratamento com ivermectina no G2 não surtiu melhora clínica dos bovinos.(AU)

This study aimed to describe the occurrence of parasitic otitis caused by Rhabditis blumi in dairy cattle of the Gir race from a farm in northern Brazil. Forty-two samples were collected from cattle by swab washed from the external auditory canal (EAC). On clinical examination, in 71.4% (30/42) of the cattle the parasite was found in the cerumen of the ear canal, along with alopecia of head and hump caused by discomfort and itching of the auricular region. At microscopic analysis of material from the conjunctival sac the parasite was found in 90% (9/10) of the evaluated cattle. In addition, 9.5% (4/42) of the cattle showed nervous symptoms, such as mild to moderate rotation of the head, apathy, flaccid lips and unilateral ptosis, change in chewing and food accumulation in the oral cavity. Thirty cattle positive for Rhabditis spp. were randomly divided into three groups of 10 animals each: (G1) Cattle Control, (G2) Cattle treated with ivermectin 1% pour-on, and (G3) Cattle undergoing wash of the external auditory canal (EAC). Each treatment was repeated three times with intervals of seven days. In G1, 10 cattle remained infected throughout the study. In G2, 20% of the cattle were negative after the first two treatments, however were positive at the third evaluation. In G3, all cattle remained positive, but with decrease in parasite load. Identification by molecular analysis of amplified fragments through the expansion D2/D3 28S rDNA confirmed the presence of only Rhabditis blumi. Based on clinical, morphologic and molecular examination, it appears to be the first report of the occurrence of R. blumi infection in Gir cattle in the State of Pará, due to the purchase of cattle from areas where parasitic otitis has been diagnosed, as from Minas Gerais, to produce crossbred animals (Gir x Holstein). This emphasizes the importance of prior clinical examination by the veterinary service in order to transfer only healthy animals to other properties or regions. This appears also to be the first report on R. blumi infection of the conjunctival sac in cattle. Treatment with ivermectin in G2 did not produce clinical improvement.(AU)

Detecção e tratamento de otite por Rhabditis blumi em bovinos da região Norte do Brasil / Detection and treatment of otitis by Rhabditis blumi in cattle of northern Brazil

O presente estudo teve como objetivo descrever a ocorrência de otite parasitária causada por Rhabditis blumi em bovinos leiteiros de raça Gir de uma fazenda da região Norte do Brasil. Foram coletadas amostras de 42 bovinos por swab e lavado dos condutos auditivos externos (CAE). Ao exame clínico, 9,5% (4/42) dos bovinos apresentavam sintomatologia nervosa, como leve a moderada rotação da cabeça, apatia, flacidez dos lábios e ptose palpebral unilateral, alopecia das regiões da cabeça e cupim, causados pelo desconforto e prurido da região auricular, alteração na mastigação e acúmulo de alimento na cavidade oral. Adicionalmente, 71,4% (30/42) dos abovinos mostraram a presença do parasita no cerúmen dos condutos auditivos. À análise microscópica do material do saco conjuntival foi observado presença do parasita em 90% (9/10) dos bovinos avaliados. Os 30 bovinos positivos para Rhabditis spp. foram distribuídos aleatoriamente em três grupos de 10 animais: (G1) Bovinos controle, (G2) Bovinos tratados com ivermectina 1% pour on e (G3) Bovinos submetidos a lavado dos condutos auditivos externos (CAE). Cada tratamento foi repetido três vezes com intervalo de sete dias. No G1 os 10 bovinos mantiveram-se infectados durante todo o estudo. No G2 20% dos bovinos foram negativos após os dois primeiros tratamentos, porém, mostraram-se positivos na terceira avaliação. No G3 todos os bovinos mantiveram-se positivos, sendo observada apenas diminuição da carga parasitária. A identificação por análise molecular por meio de fragmentos amplificados da expansão D2/D3 do 28S rDNA confirmou a presença apenas da espécie Rhabditis blumi nos animais. Baseado nas observações clínicas, morfológicas e moleculares pode-se relatar o primeiro caso de R. blumi em bovinos da raça Gir no Estado do Pará, através da compra de animais oriundos de áreas onde a otite parasitária tem sido diagnosticada, principalmente de Minas Gerais, para formar animais mestiços (Gir x Holandês)[...](AU)

This study aimed to describe the occurrence of parasitic otitis caused by Rhabditis blumi in dairy cattle of the Gir race from a farm in northern Brazil. Forty-two samples were collected from cattle by swab washed from the external auditory canal (EAC). On clinical examination, in 71.4% (30/42) of the cattle the parasite was found in the cerumen of the ear canal, along with alopecia of head and hump caused by discomfort and itching of the auricular region. At microscopic analysis of material from the conjunctival sac the parasite was found in 90% (9/10) of the evaluated cattle. In addition, 9.5% (4/42) of the cattle showed nervous symptoms, such as mild to moderate rotation of the head, apathy, flaccid lips and unilateral ptosis, change in chewing and food accumulation in the oral cavity. Thirty cattle positive for Rhabditis spp. were randomly divided into three groups of 10 animals each: (G1) Cattle Control, (G2) Cattle treated with ivermectin 1% pour-on, and (G3) Cattle undergoing wash of the external auditory canal (EAC). Each treatment was repeated three times with intervals of seven days. In G1, 10 cattle remained infected throughout the study. In G2, 20% of the cattle were negative after the first two treatments, however were positive at the third evaluation. In G3, all cattle remained positive, but with decrease in parasite load. Identification by molecular analysis of amplified fragments through the expansion D2/D3 28S rDNA confirmed the presence of only Rhabditis blumi. Based on clinical, morphologic and molecular examination, it appears to be the first report of the occurrence of R. blumi infection in Gir cattle in the State of Pará, due to the purchase of cattle from areas where parasitic otitis has been diagnosed, as from Minas Gerais, to produce crossbred animals (Gir x Holstein). This emphasizes the importance of prior clinical examination by the veterinary service in order to transfer only healthy animals to other properties or regions[...](AU)

Development and validation of new SSR markers from expressed regions in the garlic genome

Only a limited number of simple sequence repeat (SSR) markers is available for the genome of garlic (Allium sativum L.) despite the fact that SSR markers have become one of the most preferred DNA marker systems. To develop new SSR markers for the garlic genome, garlic expressed sequence tags (ESTs) at the publicly available GarlicEST database were screened for SSR motifs and a total of 132 SSR motifs were identified. Primer pairs were designed for 50 SSR motifs and 24 of these primer pairs were selected as SSR markers based on their consistent amplification patterns and polymorphisms. In addition, two SSR markers were developed from the sequences of garlic cDNA-AFLP fragments. The use of 26 EST-SSR markers for the assessment of genetic relationship was tested using 31 garlic genotypes. Twenty six EST-SSR markers amplified 130 polymorphic DNA fragments and the number of polymorphic alleles per SSR marker ranged from 2 to 13 with an average of 5 alleles. Observed heterozygosity and polymorphism information content (PIC) of the SSR markers were between 0.23 and 0.88, and 0.20 and 0.87, respectively. Twenty one out of the 31 garlic genotypes were analyzed in a previous study using AFLP markers and the garlic genotypes clustered together with AFLP markers were also grouped together with EST-SSR markers demonstrating high concordance between AFLP and EST-SSR marker systems and possible immediate application of EST-SSR markers for fingerprinting of garlic clones. EST-SSR markers could be used in genetic studies such as genetic mapping, association mapping, genetic diversity and comparison of the genomes of Allium species.

Development and validation of new SSR markers from expressed regions in the garlic genome

Only a limited number of simple sequence repeat (SSR) markers is available for the genome of garlic (Allium sativum L.) despite the fact that SSR markers have become one of the most preferred DNA marker systems. To develop new SSR markers for the garlic genome, garlic expressed sequence tags (ESTs) at the publicly available GarlicEST database were screened for SSR motifs and a total of 132 SSR motifs were identified. Primer pairs were designed for 50 SSR motifs and 24 of these primer pairs were selected as SSR markers based on their consistent amplification patterns and polymorphisms. In addition, two SSR markers were developed from the sequences of garlic cDNA-AFLP fragments. The use of 26 EST-SSR markers for the assessment of genetic relationship was tested using 31 garlic genotypes. Twenty six EST-SSR markers amplified 130 polymorphic DNA fragments and the number of polymorphic alleles per SSR marker ranged from 2 to 13 with an average of 5 alleles. Observed heterozygosity and polymorphism information content (PIC) of the SSR markers were between 0.23 and 0.88, and 0.20 and 0.87, respectively. Twenty one out of the 31 garlic genotypes were analyzed in a previous study using AFLP markers and the garlic genotypes clustered together with AFLP markers were also grouped together with EST-SSR markers demonstrating high concordance between AFLP and EST-SSR marker systems and possible immediate application of EST-SSR markers for fingerprinting of garlic clones. EST-SSR markers could be used in genetic studies such as genetic mapping, association mapping, genetic diversity and comparison of the genomes of Allium species.(AU)