Evaluation of microsatellite allelic patterns to DNA fingerprinting in rubber tree clones

The rubber tree (Hevea brasiliensis) is native to the Amazon region, and it is widely exploited due to natural rubber produced from latex. There are many clonal varieties, without certification tests. In order to determine a genetic certification, 15 clones were genotyped to identify their genetic pattern. Ten microsatellites were used to determine a subset of alleles exclusive for each genetic profile. The genetic estimates obtained were: number of alleles per locus (N), expected (HE) and observed (HO) heterozygosity, Polymorphic Information Content (PIC) and Discriminatory Power (DP). The number of alleles (N) ranged from five to 14, with an average of 9.2. The HE mean (0.80) was higher than HO (0.60), indicating a selection for homozygotes. The locus informativeness was verified with PIC (0.77) and DP (0.90) means showing high polymorphism. The dendrogram represented the formation of three groups related to geographical origin. Clone MDF 180 presented the highest genetic divergence. Two genic pools represented the genetic composition of genotypes. Based on allelic profiles, a set of two microsatellites (A2365 and A2368) was able to distinguish all examined clones. The genetic certification using microsatellite fingerprinting proved to be an alternative to morphological traits.

Identificación molecular y diversidad genética de las especies de nematodos Globodera rostochiensis y G. pallida en regiones productoras de papa de Guatemala / Molecular identification and genetic diversity of the species of nematodesGlobodera rostochiensisandG. pallidain potato growing regions of Guatemala

En Guatemala, la producción del cultivo de papa se ve afectada por los nematodos Globodera rostochiensis y Globo-dera pallida. La capacidad de ambas especies para formar quistes complica su control y provoca el aumento de sus poblaciones. En Guatemala se reporta la presencia de ambas especies de nematodos por identificación morfológica, sin embargo, no se ha realizado una confirmación molecular. Este es el primer estudio para validar la presencia de ambas especies de nematodos por PCR múltiple y la determinación de la diversidad y estructura genética de las poblaciones utilizando marcadores moleculares. Se realizaron muestreos en cuatro departamentos productores de papa del país. La identificación por PCR se realizó con el cebador común ITS5 y los cebadores PITSr3 específico para G. rostochiensisy PITSp4 para G. pallida. La caracterización molecular se realizó con el marcador AFLP. Se confirmó la presencia de las dos especies de nematodos en los cuatro departamentos. Los índices de diversidad Shannon y heterocigosidad esperada revelaron mayor diversidad genética en G. rostochiensis (H = 0.311, He = 0.301) que en G. pallida (H = 0.035, He = 0.223). Los métodos NJ, DAPC y PCA exhibieron una débil estructura entre las poblaciones de ambas especies de nematodos. Los resultados sugieren un patrón de dispersión desde Quetzaltenango hacia el resto del país, atribuido a la comercialización de semilla contaminada con nematodos. Se sugiere promover programas de socialización sobre los beneficios del uso de semilla certificada, además de constantes monitoreos moleculares para un diagnóstico certero de ambas especies de nematodos.

In Guatemala, potato crop production is affected by the nematodes Globodera rostochiensis and Globodera pallida. The ability of both species to form cysts complicates their control and causes an increase in their populations. In Guatemala, both species of nematodes have been reported by morphological identification; however, molecular confirmation has not been carried out. It is the first study to validate the presence of both nematode species by multiplex PCR and determine the diversity and genetic structure of the populations using molecular markers. Sampling was carried out in four pota-to-producing departments of the country. PCR identification was performed with the common primer ITS5 and the primers PITSr3 specific for G. rostochiensis and PITSp4 for G. pallida. We performed molecular characterization with the AFLP marker. We confirmed the presence of the two nematode species in the four departments. Shannon diversity and expected heterozygosity indices revealed higher genetic diversity in G. rostochiensis (H = 0.311, He = 0.301) than in G. pallida (H = 0.035, He = 0.223). The NJ, DAPC, and PCA methods exhibited weak structure among populations of both nematode species. The results suggest a dispersal pattern from Quetzaltenango to the rest of the country, attributed to the commer-cialization of seed contaminated with nematodes. We suggest promoting socialization programs on the benefits of using certified seeds and constant molecular monitoring for an accurate diagnosis of both species of nematodes.

Análisis genético de cinco polimorfismos de nucleótido simple de caseínas lácteas obtenidos con chips genómicos en ganado Holstein de Antioquia, Colombia / Genetic analysis of five single nucleotide polymorphisms of dairy caseins obtained with genomic chips in Holstein cattle from Antioquia, Colombia

RESUMEN Los polimorfismos genéticos asociados con las caseínas de la leche son de gran importancia, ya que pueden ser usados como marcadores genéticos para mejorar el rendimiento productivo en los hatos lecheros. El objetivo de este estudio fue evaluar la diversidad y estructura genética de 5 SNP de caseínas de la leche, obtenidos con chips genómicos en vacas y toros de raza Holstein en Antioquia (Colombia). Fueron muestreados 113 animales de raza Holstein en 3 regiones del departamento de Antioquia (norte, centro y oriente) y un cuarto grupo de sementales comerciales. Los animales fueron genotipificados con chips genómicos de alta densidad (Illumina BovineHD e Illumina SNP50 v2), a partir de los cuales se identificaron 5 SNP (ARS-BFGL-NGS-8140, BTA-77380-no-rs, BTA-32346-no-rs, BTB-00821654 y ARS-BFGL-NGS-15809). Para cada SNP se realizó un análisis genético mediante un análisis de varianza molecular (amova) usando el software GenAIEx 6.501. Los SNP con mayor heterocigosidad total (HT) fueron ARS-BFGL-NGS-8140 y BTA-32346-no-rs, con resultados cercanos al 45%; sin embargo, la Ht para ARS-BFGL-NGS-15809, BTA-77380-no-rs y BTB-00821654 estuvo por debajo del 15%. El SNP con mayor diversidad genética fue BTA-32346-no-rs (Ho-He = 0,06; p < 0,05). En esta investigación se evaluó una subpoblación de toros comerciales extranjeros, en la cual se obtuvieron frecuencias alélicas y genotípicas similares a las obtenidas para las subpoblaciones locales, sugiriendo que los alelos de los toros muy posiblemente están fijados en dichas subpoblaciones, por lo que la estructura y diversidad genética tienden a ser bajas en la muestra de estudio.

ABSTRACT Genetic polymorphisms associated with milk caseins have a great importance since they can be used as genetic markers to improve productive performance in dairy herds. The main goal of the present study was to evaluate the diversity and genetic structure of 5 SNPs of milk caseins, obtained with genomic chip in Holstein cows and bulls from Antioquia (Colombia). 113 Holstein animals were sampled in 3 regions of Antioquia (north, center, and east), and a fourth group of commercial sires. Animals were geno-typed with high-density SNP chips (Illumina BovineHD and Illumina SNP50 v2), from which 5 SNPs were identified (ARS-BFGL-NGS-8140, BTA-77380-no-rs, BTA-32346-no-rs, BTB-00821654 and ARS-BFGL-NGS-15809). For each SNP, a genetic analysis was performed by means of an analysis of molecular variance (AMOVA) using the GenAIEx 6.501 software. The SNPs with the highest total heterozygosity (Ht) were ARS-BFGL-NGS-8140 and BTA-32346-no-rs, with results close to 45%; however, the HT for ARS-BFGL-NGS-15809, BTA-77380-no-rs, and BTB-00821654 were below 15%. The SNP with the highest genetic diversity was BTA-32346-no-rs (Ho-He = 0,06; p < 0,05). In this research a subpopulation of foreign commercial bulls was evaluated, in which similar allelic and genotypic frequencies to those for local subpopulations were obtained, suggesting that the alleles of the bulls are very possibly fixed in these subpopulations, so that the structure and genetic diversity tend to be low in the study sample.

Anthropogenic river fragmentation reduces long-term viability of the migratory fish Salminus brasiliensis (Characiformes: Bryconidae) populations

Life-history, geographical barriers, and damming can shape the genetic diversity of freshwater migratory fish, which are particularly vulnerable to anthropogenic impacts. We investigated the genetic diversity of Salminus brasiliensis, a long-distance migratory species that is recognized as an important provider of ecosystem services. We implemented microsatellite analyses to assess genetic diversity and simulate future scenarios for evaluating the long-term viability of dammed and non-dammed populations from the Uruguay River. High levels of genetic diversity were detected for all sampled populations. However, effective population sizes were lower in the uppermost river stretches, where the landscape is highly fragmented. Population structure analysis indicated two spatial genetic populations. It is suggested that this genetic structure preserves populations partially isolated by an ancient natural barrier, instead of being a result of the presence of dams. The simulated genetic scenarios indicated that genetic variability of S. brasiliensis populations from upstream dams could collapse over the years, mainly due to the reduction in the number of alleles. Therefore, besides helping to better understand issues related to the influence of dams on the genetic diversity of migratory fish, our results are especially relevant for driving local fishery policies and management actions for the species conservation.'

História de vida, barreiras geográficas e barramento dos rios podem moldar a diversidade genética de grandes peixes migratórios de água doce, que são particularmente vulneráveis a impactos antrópicos. Nós investigamos a diversidade genética de Salminus brasiliensis, uma espécie migratória de longa distância que é reconhecida como um importante provedor de serviços ecossistêmicos. Realizamos análises de microssatélites para avaliar a diversidade genética e simular cenários futuros, possibilitando estimar a viabilidade em longo prazo de populações situadas em regiões com e sem represas do rio Uruguai. Altos níveis de diversidade genética foram detectados para todas as populações amostradas. Contudo, os tamanhos populacionais efetivos foram menores nos trechos superiores do rio, onde a paisagem é altamente fragmentada. A análise da estrutura populacional indicou duas populações genéticas espaciais. Sugere-se que esta estrutura genética preserva populações parcialmente isoladas por uma antiga barreira natural, ao invés de ser resultado da presença de barragens. Os cenários genéticos simulados indicaram que a variabilidade genética das populações de S. brasiliensis situadas a montante das barragens entraria em colapso ao longo dos anos, principalmente como resultado da redução do número de alelos. Portanto, além de ajudar a entender melhor questões relacionadas à influência de barragens na diversidade genética de peixes migradores, nossos resultados são especialmente relevantes para a condução de políticas pesqueiras locais e ações de manejo para a conservação das espécies.(AU)

Evidence on the paleodrainage connectivity during Pleistocene: Phylogeography of a hypoptopomatine endemic to southeastern Brazilian coastal drainages

The coastal basins of southeastern Brazil are influenced by climatic changes that caused sea-level oscillations during the Pleistocene. These marine transgressions and regressions can generate isolation and connection among coastal rivers. In this region, freshwater fishes are excellent models for phylogeographic studies because their distributions may have been affected by geographical and ecological changes resulting from these processes. Therefore, the main objective of this study was to evaluate the effects of Pleistocene sea-level changes on the genetic structure of the loricariid Hisonotus leucofrenatus throughout its area of occurrence. Two genes were sequenced: Cytochrome Oxidase subunit 1 (mitochondrial gene) and rpS7 ribosomal protein gene intron 1 (nuclear gene) from specimens representing 14 river drainages. The genetic data corroborate a divide for freshwater fish by the Serra do Tabuleiro mountain in Santa Catarina State. This divide determines two main genetic groups in H. leucofrenatus: one group to the south and one to the north of this mountain range. The genetic structure observed coincide with the limits of estimated paleodrainage systems for the region, supporting that marine transgressions and regressions during the Pleistocene influenced the biogeographical history of H. leucofrenatus.(AU)

As bacias costeiras do sul do Brasil são influenciadas pelas mudanças climáticas que causaram oscilações no nível do mar durante o Pleistoceno. Essas transgressões e regressões marinhas geraram isolamento e conexão entre os rios. Nessa região, as espécies de peixe são excelentes modelos para estudos filogeográficos, pois suas distribuições podem ter sido afetadas por mudanças históricas e ecológicas decorrentes desses processos. Portanto, o objetivo principal deste estudo foi testar os efeitos das alterações do nível do mar durante o Pleistoceno na estrutura genética das populações do loricarídeo Hisonotus leucofrenatus ao longo de sua área de ocorrência. Dois genes foram sequenciados: Citocromo Oxidase subunidade 1 (gene mitocondrial) e o intron 1 da proteína ribossomal rpS7 (gene nuclear) de espécimes representando 14 bacias de drenagens. A estrutura genética observada corrobora uma divisão para peixes de água doce separada pela Serra do Tabuleiro, em Santa Catarina. Essa divisória determina dois grupos principais genéticos em H. leucofrenatus: um grupo ao sul e outro ao norte desse divisor. A estrutura genética também coincide com os limites dos sistemas de paleodrenagens estimados para a região, sustentando que as transgressões e regressões marinhas durante o Pleistoceno influenciaram a história biogeográfica de H. leucofrenatus.(AU)

Genetic diversity in two threatened species of guitarfish (Elasmobranchii: Rhinobatidae) from the Brazilian and Argentinian coasts: an alert for conservation

The guitarfishes Pseudobatos horkelii and Pseudobatos percellens meet the criteria for threatened status as Critically Endangered (CR) and Endangered (EN), respectively. Both species occur in the Southern Atlantic Ocean. Considering the lack of data on the genetic structure of these species, the present study evaluated the genetic variability and population structure of the P. horkelii and P. percellens in the southern region of Brazil and the northern coast of Argentina, based on sequences of mitochondrial DNA, Control Region (D-loop). Samples of P. horkelii (n = 135) were analyzed in six localities situated in Northern Argentina, along the Brazilian states' coast. The mean of nucleotide diversity was 0.0053, the ΦST was 0.4277 and demographic analysis of P. horkelii suggests the existence of stability of the populations, with D = 0.9929, FS = 2.0155, SSD = 0.0817, R = 0.2153. In P. percellens (n = 101) were analyzed from six Brazilian localities along the coast of Santa Catarina, Paraná, and São Paulo. The mean nucleotide diversity was 0.0014 and ΦST value of 0.2921, the demographic analysis indicates a high migration rate of P. percellens among the localities evaluated, with D = 0.5222, FS = 0.3528, SSD = 0.01785, R = 0.3890.(AU)

As raias violas Pseudobatos horkelii e Pseudobatos percellens, são listados como "Criticamente em Perigo" (CR) e "Em Perigo" (EN), respectivamente. Ambas as espécies ocorrem no Sul do Oceano Atlântico. Considerando a falta de dados sobre a estrutura genética dessas espécies, o presente estudo avaliou a variabilidade genética e a estrutura populacional de P. horkelii e P. percellens na região sudeste do Brasil e litoral norte da Argentina, com base em sequências de DNA mitocondrial, região de controle (D-loop). Amostras de 135 indivíduos de P. horkelii analisados em seis localidades, situadas no norte da Argentina e ao longo da costa dos estados brasileiros. A média da diversidade nucleotídica foi de 0.0053, o índice ΦST foi de 0.4277 e a análise demográfica de P. horkelii, indicou a existência de estabilidade das populações, com D = 0.9929, Fus = 2.0155, SSD = 0.0817, R = 0.2153. Em 101 exemplares de P. percellens, foram analisados em seis localidades brasileiras ao longo do litoral de Santa Catarina, Paraná e São Paulo. A diversidade nucleotídica média foi de 0.0014 e o valor ΦST de 0.2921, a análise demográfica indicou uma alta taxa de migração de P. percellens entre as localidades analisadas, com D = 0.5222, FS = 0.3528, SSD = 0.01785, R = 0.3890.(AU)

Metapopulation dynamics of the migratory fish Prochilodus lineatus (Characiformes: Prochilodontidae) in a lotic remnant of the Grande River, Southeastern Brazil

River impoundments for electricity generation lead to environmental changes which severely affect fish migration and species richness. However, little is known about their effect on the genetic structure and population dynamics downstream from the reservoir. Here, we analyzed a set of ten microsatellite loci of Prochilodus lineatus, an important South American migratory fish. Specimens (n = 150) were sampled from five sites in a remnant lotic system that includes sections of the Grande, Pardo and Mogi Guaçu rivers, southeastern Brazil. The data showed that all microsatellites were polymorphic with the allele number per locus ranging from 5 to 32, and genetic diversity (H e ) varied from 0.74 to 0.80. Indices of genetic differentiation and Bayesian analysis showed a significant genetic structure and three genetic clusters inhabiting this river system. An asymmetric gene flow suggests source-sink metapopulation dynamics from tributaries (genetic source) to the main river (genetic sink). A genetic cluster that was not detected in the upper Mogi and Pardo rivers tributaries may indicate there is a "trapped gene pool" downstream from the Porto Colômbia dam. Thus, here we provide new insights into the genetic structure and population dynamics of a migratory fish species in a highly dammed river basin.(AU)

Represamento de rios para geração de eletricidade levam a mudanças ambientais que afetam severamente a migração de peixes e riqueza de espécies. No entanto, pouco se sabe sobre seu efeito na estrutura genética e dinâmica populacional a jusante de reservatórios. Aqui, analisamos um conjunto de dez loci de microssatélites de Prochilodus lineatus, um importante peixe migratório sul-americano. Os espécimes (n = 150) foram amostrados em cinco locais de um sistema lótico remanescente que inclui seções dos rios Grande, Pardo e Mogi Guaçu, sudeste do Brasil. Os dados mostraram que todos microssatélites eram polimórficos com o número de alelos por locus variando de 5 a 32 e diversidade genética (H e ) variou de 0,74 a 0,80. Índices de diferenciação genética e análise de agrupamento baseada em modelo bayesiano indicou a presença de três agrupamentos genéticos habitando este sistema fluvial. Um fluxo gênico assimétrico sugere dinâmica metapopulacional de fonte-sumidouro dos tributários (fonte genética) para o rio principal (sumidouro genético). Um agrupamento genético que não foi detectado nos tributários rio Mogi e rio Pardo parecem indicar que há um "trapped gene pool" a jusante da represa de Porto Colômbia. Assim, nós provemos aqui novos conhecimentos sobre a estrutura genética e dinâmica populacional de uma espécie de peixe migratório em um rio altamente fragmentado por barramentos.(AU)

Transgênicos e o princípio de equivalência substancial / Transgenics and the principle of substantial equivalence

Objetivamos discutir os principais argumentos que estão envolvidos no debate sobre a cientificidade do Princípio de Equivalência Substancial (PES), que afirma serem os OGM quimicamente equivalentes aos organismos selecionados pelas técnicas tradicionais de melhoramento, não requerendo, portanto, estudos toxicológicos adicionais. Problematizamos a cientificidade do PES, especialmente no que diz respeito à questão propriamente química. De fato, o PES estrutura-se conceitualmente na comparação quantitativa entre alguns componentes químico-biológicos da planta transgênica e os da não transgênica. Nesse sentido, as análises químicas propostas não conseguem relacionar sozinhas os possíveis efeitos bioquímicos, toxicológicos e imunológicos dos alimentos transgênicos, pois o princípio restringe as análises à composição química, molecular e analítica dos transgênicos. Emerge assim o problema do locus da incerteza científica, seja como questão epistemológica, seja como questão normativa e moral.

We aim to discuss the main arguments involved in the debate on the scientificity of the Principle of Substantial Equivalence (PSE), which claims that GMOs are chemically equivalent to organisms selected by traditional breeding techniques and therefore do not require additional toxicological studies. We question the scientific character of the PSE, especially with regard to the chemical question itself. Indeed, the PSE is conceptually structured in the quantitative comparison between some chemical--biological components of the transgenic plant and those of the non-transgenic plant. In this sense, the proposed chemical analyses cannot by themselves assess the possi-ble biochemical, toxicological and immunological effects of transgenic foods, since the principle restricts the analysis to the chemical, molecular and analytical composition of transgenics. This gives rise to the problem of the locus of scientific uncertainty, whether as an epistemological question or as a normative and moral issue.

Bases moleculares de la resistencia a meticilina en Staphylococcus aureus / Molecular basis of methicillin-resistance in Staphylococcus aureus

Resumen Desde el inicio de la era antimicrobiana se han ido seleccionando gradualmente cepas de Staphylococcus aureus resistentes a antimicrobianos de amplio uso clínico. Es así como en 1960 se describen en Inglaterra las primeras cepas resistentes a meticilina, y algunos años después son informadas en hospitales de Chile. Actualmente, S. aureus resistente a penicilinas antiestafilocóccicas es endémico en los hospitales de nuestro país y del mundo, siendo responsable de una alta morbimortalidad. La resistencia es mediada habitualmente por la síntesis de una nueva transpeptidasa, denominada PBP2a o PBP2' que posee menos afinidad por el β-lactámico, y es la que mantiene la síntesis de peptidoglicano en presencia del antimicrobiano. Esta nueva enzima se encuentra codificada en el gen mecA, a su vez inserto en un cassette cromosomal con estructura de isla genómica, de los cuales existen varios tipos y subtipos. La resistencia a meticilina se encuentra regulada, principalmente, por un mecanismo de inducción de la expresión del gen en presencia del β-lactámico, a través de un receptor de membrana y un represor de la expresión. Si bien se han descrito mecanismos generadores de resistencia a meticilina mec independientes, son categóricamente menos frecuentes.

Staphylococcus aureus isolates resistant to several antimicrobials have been gradually emerged since the beginning of the antibiotic era. Consequently, the first isolation of methicillin-resistant S. aureus occurred in 1960, which was described a few years later in Chile. Currently, S. aureus resistant to antistaphylococcal penicillins is endemic in Chilean hospitals and worldwide, being responsible for a high burden of morbidity and mortality. This resistance is mediated by the expression of a new transpeptidase, named PBP2a or PBP2', which possesses lower affinity for the β-lactam antibiotics, allowing the synthesis of peptidoglycan even in presence of these antimicrobial agents. This new enzyme is encoded by the mecA gene, itself embedded in a chromosomal cassette displaying a genomic island structure, of which there are several types and subtypes. Methicillin resistance is mainly regulated by an induction mechanism activated in the presence of β-lactams, through a membrane receptor and a repressor of the gene expression. Although mec-independent methicillin resistance mechanisms have been described, they are clearly infrequent.

Quimiotipos, Extracción, Composición y Aplicaciones del Aceite Esencial de Lippia alba / Quimiotipos, extração, composição e uso do óleo essencial de Lippia alba / Chemotypes, extraction, chemical composition and use of lippia alba essential oil

RESUMO Lippia alba é uma planta amplamente distribuída nas zonas tropicais, subtropicais e temperadas das Américas, África e Ásia. O óleo essencial de L. alba tem sido amplamente estudado, entretanto apresenta variações de produção. Portanto este estudo teve como objetivo realizar uma revisão dos principais quimiotipos, métodos de extração, composição e aplicação do óleo essencial de L. alba. Neste estudo são discutidos os principais quimiotipos e sua relação com fatores genéticos e características morfológicas. Também são discutidos os fatores que afetam o rendimento de produção, composição química, métodos de extração e do uso e da atividade biológica do óleo essencial de L. alba. Apesar da vasta literatura sobre os óleos essenciais de L. alba, ainda desenvolvimento de aplicações para a produção de cosméticos, fármacos e alimentos, bem como faltam definições agronomicas sobre o cultivo e melhoramento desta planta.

ABSTRACT Lippia alba is a plant widely distributed in tropical, subtropical and temperate zones of the Americas, Africa and Asia. The essential oil of L. alba has been widely studied and there are many variations in the production process. Therefore, this study is aimed at conducting a review of the main chemotypes, extraction methods, composition and application of the essential oil of L. alba. In this study, the main chemotypes and its relation to genetic and morphological characteristics are discussed. It also discusses the factors that affect the yield, chemical composition, extraction methods and the use and the biological activity of the essential oil of L. alba. Despite the vast literature on the essential oils of L. alba, there is still a lack of development in its application for the production of cosmetics, pharmaceuticals and food, as well as a lack of agronomic definitions for its cultivation and genetic improvement.

Estimação de parâmetros genéticos para escores visuais e características de desenvolvimento ponderal na raça Nelore / Genetic parameter estimation for visual score and ponderal development traits in Nellore cattle

O objetivo foi avaliar a associação genética entre os escores visuais de estrutura, precocidade e musculosidade, com as características peso aos 18 meses, ganho de peso diário e o perímetro escrotal em machos Nelore. Foram utilizados 7.256 registros de animais participantes de provas de ganho de peso. As estimativas dos componentes de (co)variâncias foram obtidas por meio de Máxima Verossimilhança Restrita, empregando-se um modelo animal. Os efeitos fixos de grupo contemporâneo, idade e peso como covariável linear foram considerados; o único efeito aleatório foi o genético aditivo direto. As estimativas de herdabilidade de estrutura, precocidade e musculosidade foram: 0,30; 0,37; 0,32, respectivamente. As estimativas das correlações genéticas entre os escores variaram de 0,76 a 0,95, indicando que os escores são controlados, em grande parte, pelo mesmo grupo de genes. As estimativas das correlações genéticas dos escores visuais com as características de ganho de peso diário, peso aos 18 meses e o perímetro escrotal apresentaram valores semelhantes entre os escores 0,45 a 0,50; 0,80 a 0,83 e -0,05 a -0,03, respectivamente; indicando que a seleção para os escores trará mudanças genéticas no mesmo sentido para o peso aos 18 meses e em menor medida para o ganho de peso.

The aim of this study was to evaluate the genetic association between visual scores of structure, finishing precocity and muscling with weight at 18 months, daily weight gain and scrotal circumference in male Nellore. A total of 7,256 records of animals participating in weight gain trials were used. The (co)variance components were estimated by restricted maximum likelihood, under an animal model. Contemporary group, age and weight as covariate linears were included as fixed effects. Additive genetic effects were the only random effect. The heritability estimates for structure, precocity and muscling were 0.30; 0.37 and 0.32 respectively. The genetic correlations between visual score were 0.76 to 0.95, indicating that the visual scores are controlled by the same set of genes, a fact making individual selection more complex. The visual scores showed similar genetic correlations with daily weight gain, weight at 18 months and scrotal circumference, ranging from 0.45 to 0.50, from 0.80 to 0.83 and from -0.05 to -0.03, respectively, indicating that individual selection for visual scores will result in genetic changes in the same direction in weight at 18 months and, to a lesser extent, in daily weight gain.

Genetic diversity in two Italian almond collections

Background Sweet-seeded domesticated almonds were brought to the Mediterranean Basin from central Asia about 4000 years ago. In Italy, most of the almonds produced are cultivated in the southern part of the country. Local populations of the tree in Sardinia are largely seed-derived and mostly self-incompatible, so have developed extensive genetic diversity. The need to protect biodiversity has prompted a revived interest in local genetic materials in almond. Two Italian collections have been established, one in Sardinia and the other in Apulia. These collections were the focus of the present evaluation of genetic diversity. Results Eleven SSRs (microsatellites) were used for fingerprinting. The Sardinian germplasm was highly polymorphic, revealing a mean of 14.5 alleles per locus and a mean heterozygosity of 0.71. Using a model-based clustering approach, two genetic clusters were distinguished: one included all the commercial varieties and most of the Sardinian accessions, and the other most of the Apulian accessions. A similar structure was produced using a distance-based cluster analysis. The Sardinian accessions could still be distinguished from the commercial germplasm with few exceptions. Conclusion The extensive genetic variability present in the Sardinian and Apulian almond germplasm indicates that these materials represent an important source of genes for the improvement of the crop.

Diversidade e estrutura genética de populações de Varronia curassavica Jacq. em restingas da Ilha de Santa Catarina / Genetic diversity and structure of Varronia curassavica Jacq. populations in the restinga of Santa Catarina Island

RESUMO Varronia curassavica Jacq. (Boraginaceae) está presente na vegetação de restinga e apresenta relevantes propriedades medicinais. A espécie é explorada especialmente por comunidades locais e pela indústria farmacêutica, porém, carece de informações ecológicas e genéticas a seu respeito. Nesse contexto, o estudo foi conduzido com o objetivo de caracterizar a diversidade genética de três populações de V. curassavica em áreas de restinga na Ilha de Santa Catarina. Foram coletadas folhas de 50 indivíduos adultos em cada uma das três áreas de estudo e as frequências alélicas das populações foram obtidas a partir de 14 locos alozímicos. Foram encontrados 25 alelos distintos nas três populações, sendo dois alelos exclusivos. As populações apresentaram diversidade genética média de 0,111 e índice de fixação médio de -0,060 (-0,273 até 0,222). Os níveis de diversidade são intermediários, semelhantes aos exibidos por espécies da mesma família ou de características ecológicas semelhantes. Os índices de fixação foram todos significativos e discrepantes entre as populações, sendo que duas delas apresentaram excesso de heterozigotos. A divergência genética interpopulacional foi significativa e igual a 0,079, considerada moderada e sugerindo efeitos de subdivisão populacional. Os níveis de diversidade genética encontrados e a redução populacional causada pela redução e fragmentação dos habitats em que a espécie ocorre sugerem medidas de conservação ex situ e demandam maior rigor na proteção legal de áreas de proteção permanente.

ABSTRACT The Varronia curassavica Jacq. (Boraginaceae) is present in restinga vegetation and shows relevant medicinal properties. The species is exploited by local communities and by the pharmaceutical industry; however, it lacks ecological and genetic information. Thus, this study aimed to characterize the genetic diversity of three V. curassavica populations in restinga areas of Santa Catarina Island. Leaves of 50 adult individuals were sampled in each of the three study areas and the allelic frequencies were obtained from 14 allozyme loci. Twenty-five different alleles were found in the three populations, two of them being exclusive. The populations showed, on average, a genetic diversity of 0,111 and a fixation index of -0,060 (-0,273 to 0,222). The diversity levels are intermediary, similar to those ones owned by species of the same family or with similar ecological traits. The fixation indexes were all significant and discrepant among the populations, with two of them showing excess of heterozygotes. The genetic divergence among populations was significant and equal to 0,079, which is considered moderate and suggests effects of population subdivision. The levels of genetic diversity found and the population decrease caused by reduction and fragmentation of habitats in which the species are present implies in ex situ conservation measures and a higher enforcement of the legal preservation of permanent protected areas.

High genetic diversity and small genetic variation among populations of Magnolia wufengensis (Magnoliaceae), revealed by ISSR and SRAP marker

Background Genetic diversity and genetic variation of 10 populations and subpopulations of Magnolia wufengensis, a new and endangered endemic species, were examined by inter simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) molecular markers. Compared with other endangered endemic Magnolia taxa, M. wufengensis holds a relatively high level of genetic variation. Result Total genetic diversity was found to be 87.7% for ISSR and 88.0% for SRAP markers. For polymorphic loci (P), the effective mean number of alleles (Ae) was 1.414 for ISSR markers and 1.458 for SRAP markers, while the mean expected heterozygosity (H) was 0.256 using ISSR and 0.291 for SRAP markers. Within-population variation was estimated for P as 74.9% using ISSR and 74.6% with SRAP markers; the number of alleles Ae was 1.379 with ISSR and 1.397 for SRAP and H 0.235 with ISSR and 0.247 for SRAP markers. Conclusion The analysis of molecular variation of both ISSR and SRAP marker systems indicated that most genetic variation is within populations, with values of 90.64% and 82.92% respectively. Mantel tests indicated a moderate association between the two marker systems and a low correlation between genetic and geographic distances. High levels of genetic diversity and low levels of population divergence suggest that genetic drift is not currently of great concern for this species. Severe habitat loss and fragmentation, predominantly ascribed to anthropogenic pressures, caused in-situ developing restriction of this species. Action for conserving this rare species for its long-term survival should be taken immediately.

Effect of clonal reproduction on genetic structure in Pentaclethra macroloba (Fabaceae: Mimosoideae) / Efecto de la reproducción clonal en la estructura genética de Pentaclethra macroloba (Fabaceae: Mimosoideae)

The existence of monodominant forests on well-drained soils in tropical regions has been widely reported. Such forests most likely result from a combination of both ecological and evolutionary factors. Under conditions of high seed and seedling mortality, vegetative reproduction could create a reproductive advantage leading to forest dominance, and profoundly affect the distribution of genetic variation in a clonal species. We investigated these effects in a low diversity forest site in Northeastern Costa Rica dominated by the species Pentaclethra macroloba, which sprouts from the root mass of fallen trees and from snapped trunks. We examined the population structure of juvenile P. macroloba growing in different soil types and across an elevational gradient. Using seven molecular markers, we genotyped 173 juvenile P. macroloba from 18 plots (six plots in seasonally inundated swamps, and 12 plots in upland non-swamp) spanning 50-300m in elevation at La Selva Biological Station and the adjacent Reserva Ecológica Bijagual in Northeastern Costa Rica. We answered two specific questions: (1) How extensive is clonal reproduction? and (2) what is the distribution of genetic diversity and structure?. We found that clonal reproduction occurred exclusively within inundated swamp areas. However, there was no significant difference between genetic diversity measures in swamp and non-swamp plots, which were both generally low when compared with other tropical forest species. Genetic structure was significant across all plots (F ST=0.109). However, genetic structure among swamp plots (F ST=0.128) was higher than among non-swamp upland plots (F ST=0.093). Additionally, spatial autocorrelation among individuals within non-swamp upland plots was significant from the 25 to 100m spatial scale, but not within swamp plots. The degree of overall genetic structure we found in P. macroloba is high for a tropical forest tree. The incidence of clonal reproduction is a contributing factor in genetic differentiation, but the high structure among plots without clonal reproduction indicates that other factors contribute as well.

La existencia de bosques monodominantes sobre suelos bien drenados en regiones tropicales ha sido ampliamente reportada. Investigaciones recientes han sugerido que tales bosques son probablemente resultado de una combinación de factores ecológicos y evolutivos. Bajo condiciones de alta mortalidad de semillas y plántulas, la reproducción vegetativa podría crear una ventaja reproductiva llevando a la dominancia del bosque, pero también podría afectar profundamente la distribución de la variación genética en especies clonales. Investigamos estos efectos en un sitio de bosque con baja diversidad de especies en el Noreste de Costa Rica que es ampliamente dominado por la especie Pentaclethra macroloba, la cual retoña de la masa de raíces de árboles caídos y de troncos partidos. Examinamos la estructura poblacional de individuos juveniles de P. macroloba creciendo en diferentes tipos de suelo y a través de un gradiente de altitud. Utilizamos siete marcadores moleculares, genotipamos 173 Pentaclethra macroloba de 18 parcelas (seis en ciénagas y 12 en ambientes no cenagosos) ubicados en un gradiente de elevación entre 50-300m en las reservas adyacentes: Reserva Biológica Bijagual y Estación Biológica La Selva, en el centro de Costa Rica. Abordamos dos preguntas específicas: (1) ¿Qué tan extensa es la reproducción clonal? y (2) ¿Cuál es la distribución de diversidad y estructura genética? Encontramos que la reproducción clonal ocurrió exclusivamente dentro de áreas cenagosas inundadas. La estructura genética fue significativa en todas las parcelas (F ST=0.109). Observamos una estructura genética más alta entre poblaciones juveniles dentro de las ciénagas (F ST=0.128) comparada con poblaciones no cenagosas en parcelas a mayor altura (F ST=0.093), con mayor autocorrelación espacial en sitios no cenagosos en el intervalo entre 25 y 100m. La presencia de reproducción clonal no afectó significativamente las medidas de diversidad entre las dos áreas, que fueron generalmente bajas comparadas con otras especies de bosque tropical. El alto grado de estructura genética en general es novedoso para un árbol de bosque tropical. La incidencia de reproducción clonal es un factor que contribuye en la diferenciación genética, pero la alta estructura en parcelas sin reproducción clonal indica que otros factores están contribuyendo también.

The genetic diversity of Sardinian myrtle (Myrtus communis L. ) populations

Background: The myrtle (Myrtus communis) is a common shrub widespread in the Mediterranean Basin. Its fruit and leaves exhibit antioxidant, antibacterial and antifungal properties, and are used for their content of essential oils and for their medicinal properties, but most commonly as an ingredient in locally made liquor. The uncontrolled exploitation of natural stands has reduced both the species' geographical coverage and the size of individual populations. The selection of genotypes for controlled cultivation requires a characterization of the genetic diversity present both within and between populations. Results: Genotypic variation was evaluated using ISSR profiling and genetic diversity characterized using standard population genetics approaches. Two major clusters were identified: one capturing all the candidate cultivars selected from various Sardinian localities, and the other wild individuals collected from Asinara, Corsica and Surigheddu. A moderate level of gene flow between the Sardinian and Corsican populations was identified. Discriminant analysis of principal components revealed a level of separation among the wild populations, confirming the population structure identified by the clustering methods. Conclusions: The wild accessions were well differentiated from the candidate cultivars. The level of genetic variability was high. The genetic data were compatible with the notion that myrtle has a mixed pollination system, including both out-pollination by insects and self-pollination. The candidate cultivars are suggested to represent an appropriate basis for directed breeding.

DNA sequence variation of drought-response candidate genes in Austrocedrus chilensis

Background: Austrocedrus chilensis (D. Don) Pic. Ser. et Bizzarri commonly known as Patagonian cypress is a member of the Cupressaceae family, characterized by a high adaptive potential for growing in marginal areas and good timber quality. The species grows over a wide area and under a wide range of rainfall. This study assessed adaptive genetic variation at SNP level in candidate genes involved in response to drought stress. Results: A total of 18 single nucleotide polymorphisms (SNPs) were found among 1,428 bp. Average nucleotide diversity value (π = 0.00312) was similar to those previously reported in other Cupressaceae. The Fst average among genes and populations was 0.163 and the lowest differentiation was observed in continuous and humid populations. A number of neutrality tests were applied to find evidence of positive selection in our candidate gene set, but only AcAQP2 gene in Pedregoso and San Ramón populations revealed significant departures from neutrality with positive values suggesting balancing selection. Conclusions: In this study we report the levels of nucleotide diversity searched in some drought stress candidate genes in Austrocedrus chilensis and the selective factors that may be acting on this species.

Diversidade genética de populações naturais de pariparoba [Pothomorphe umbellata (L. ) Miq.] por RAPD / Genetic diversity of natural populations of pariparoba [Pothomorphe umbellata (L. ) Miq.] according to RAPD analysis

O objetivo desse trabalho foi analisar a estrutura genética de populações de Pothomorphe umbellata (L.) Miq. com base em polimorfismos moleculares do tipo RAPD. Foram analisadas quatro populações naturais do estado de São Paulo (Jacareí, Jundiaí, Piquete e Ubatuba) e uma população do Paraná (Adrianópolis). Foram identificados 25 locos polimórficos (96,15%). Elevados índices de diversidade genética foram observados dentro das populações (Hs = 0,2220). Verificou-se que 65,33% da variabilidade genética total encontra-se dentro das populações e 34,67% entre as populações; índices estes, obtidos a partir do cálculo da divergência genética (G ST = 0,3467). Os resultados sugerem que essas populações possuem níveis elevados de variabilidade genética, a qual pode ser fortemente impactada pela ação humana.

The aim of this study was to analyze the genetic structure of populations of Pothomorphe umbellata (L.) Miq. based on RAPD molecular polymorphisms. Analysis included four natural populations from São Paulo State (Jacareí, Jundiaí, Piquete, Ubatuba) and one population from Paraná State (Adrianópolis). Twenty-five polymorphic loci (96.15%) were identified. There were high levels of genetic diversity within populations (Hs = 0.2220). Of the total genetic variability, 65.33% is within populations and 34.67% among populations (G ST = 0.3467). Results suggest that these populations have high levels of genetic variability, which can be strongly impacted by human action.

Phylogeography and conservation genetics of the Amazonian freshwater stingray Paratrygon aiereba Müller & Henle, 1841 (Chondrichthyes: Potamotrygonidae)

The family Potamotrygonidae is monophyletic comprising three genera: Paratrygon Duméril, Potamotrygon Garman and Plesiotrygon Rosa, Castello & Thorson. The distribution of most species in this family is restricted to a single basin or fluvial system. Only Potamotrygon motoro, Potamotrygon orbignyi and Paratrygon aiereba are found in more than one river basin. In this study we investigate genetic structuring of Paratrygon aiereba, from five rivers of the Amazon region: Negro, Solimões-Amazon-Estuary system, Tapajós, Xingu and Araguaia. Sixty-three individuals were sequenced for ATPase 6, and a representative subsample of 27 individuals was sequenced for COI. The COI dataset analysis indicated that Paratrygon is sister to all other potamotrygonid genera and species. Population parameters inferred from the analysis of ATPase 6 sequences revealed that the populations of this species are structured within each river, with no or nearly non-existent gene flow occurring between rivers and a positive correlation between geographic and genetic distances. Paratrygon aiereba is comprised of three geographically restricted clades with K2P interclade distances of at least 2%. Intraspecific divergence within P. aiereba is similar to the interspecific divergence observed in Potamotrygon spp. sampled throughout the same geographic area. Using the premises of COI barcoding and the allopatric distribution of the three P. aiereba clades, the taxon P. aiereba most likely comprises three distinct biological species. Since freshwater stingrays of the family Potamotrygonidae are highly exploited for the aquarium trade, management and conservation strategies need to be implemented at the level of each river basin, rather than at the level of the Amazon basin.

A família Potamotrygonidae forma um clado monofilético com três gêneros: Paratrygon Duméril, Potamotrygon Garman e Plesiotrygon Rosa, Castello & Thorson. A maioria das espécies dessa família possui distribuição restrita a uma única bacia ou sistema fluvial, e somente as espécies Potamotrygon motoro, Potamotrygon orbignyi e Paratrygon aiereba estão presentes em mais de uma bacia hidrográfica. O presente estudo teve como objetivo investigar a estrutura genética de Paratrygon aiereba em alguns rios da região Amazônica: Negro, sistema Solimões-Amazonas, Tapajós, Xingu, e Araguaia. Para tal foram utilizados como marcador molecular os genes de ATPase subunidade 6, e COI. As análises com o fragmento de COI indicaram que o gênero Paratrygon é grupo irmão dos outros gêneros da família potamotrygonidae. Os resultados para o fragmento de ATPase mostraram que essas populações estão estruturadas dentro dos rios, com fluxo gênico restrito, ou mesmo sem fluxo gênico, apresentando uma correlação positiva entre distância genética e distância geográfica. Paratrygon aiereba é composta por três clados com distância genética de pelo menos 2%. A divergência encontrada dentro desse grupo é semelhante à observada entre Potamotrygon spp. Segundo as premissas para barcoding COI e a distribuição alopátrica de três clados em P. aiereba indicam que esse grupo pode ser um complexo de espécies. O rio Negro é conhecido por sua pesca ornamental, e na calha Solimões-Amazonas, esses animais são utilizados como fonte de proteína e sofrem com a pesca comercial. Em vista disso medidas de conservação para esta espécie devem ser tomadas em nível local, considerando cada rio separadamente, ao invés de empregar escalas regionais maiores.

Estudo da função do gene kerV de Pseudomonas aeruginosa / Function of Pseudomonas aeruginosa kerV gene

P. aeruginosa PA14 é uma linhagem isolada de queimadura que apresenta vários fatores de patogenicidade comuns no quadro de infecção de hospedeiros filogeneticamente distintos (plantas, mamíferos ou invertebrados). O gene kerV foi revelado numa busca por mutantes atenuados em virulência em uma biblioteca de mutantes por transposons da linhagem PA14 (Rahme et al., 1997). A caracterização da linhagem D12, mutante em kerV, confirmou sua virulência atenuada (Apidianakis et al., 2005 e An et al., 2009) e resultados do transcriptoma mostraram alteração na expressão de mais de 500 genes, sendo alguns relacionados com o sistema de "quorum sensing" (Rahme et al, dados não publicados). O gene kerV está próximo à montante ao gene gloB, envolvido em detoxificação de metilglioxal, e à jusante aos genes rnhA e dnaQ, que codificam proteínas envolvidas na replicação e reparo do DNA. Este trabalho teve como objetivo estudar a função molecular do produto de kerV e a expressão dos genes do lócus kerV-rnhA-dnaQ. Análises de bioinformática indicam que a proteína KerV é uma metiltransferase dependente de S-adenosil-metionina (SAM), apresentando um domínio conservado de ligação a SAM e uma arquitetura de domínio compatível com a organização em fitas-beta e hélices-alfa alternadas descritas para a família das metiltransferases dependentes de SAM. Ela não apresenta outros domínios conservados que indiquem seu substrato de metilação. A expressão heteróloga desta proteína em E. coli, mostrou que ela é expressa de maneira parcialmente solúvel quando co-expressa com as chaperoninas GroEL/GroES em baixas temperaturas ou quando fusionada a MBP ou GST. A purificação desta proteína mostra que ela é co-eluída com a chaperonina GroEL sugerindo que para atingir sua conformação nativa ela necessita dessas proteínas acessórias. MBP-KerV purificado foi usado para ensaios "in vitro" de atividade de metiltransferase e ligação a SAM, que não foram conclusivos, pois não há certeza do seu ...

P. aeruginosa PA14 is a burn isolate multi-host pathogen strain. The screening for virulence attenuated mutants in a PA14 transposon mutant library revealed the kerV gene (Rahme et al., 1997). The characterization of D12 strain, a kerV mutant, confirmed the attenuated virulence phenotype (Apidianakis et al., 2005 and An et al., 2009) and transcriptome analysis showed the expression of more than 500 genes are affected in D12, some of these genes are related with quorum sensing (Rahme et al, unpublished data). kerV is upstream of the gloB gene, related with methylglioxal detoxification and downstream of the rnhA and dnaQ genes, both related with DNA replication and repair. The purpose of this work was to study the molecular function of KerV product and the expression of kerV-rnhA-dnaQ locus. Bioinformatics analysis indicated that KerV is a SAM dependent methyltransferase that have a conserved SAM binding domain with architecture compatible with classic alternating β-stranded and α-helical regions. KerV does not show any other conserved motif that could indicate its methylation substrate. Heterologous expression in E. coli showed that KerV is partially soluble only when co-expressed with GroeL/GroES chaperones at low temperatures or when KerV is in fusion with MBP or GST tag. During the purification process KerV was copurified with GroEL chaperone suggesting that this association may be required for the correct folding of KerV. Methyltransferase activity and SAM binding assays were done with purified MBPKerV and the results were not conclusive since the proper conformation of MBP-KerV cannot be verified. Yeast two-hybrid assays indicated that RNaseH and DnaQ are not interaction partners of KerV, suggesting that their functions are not directly related. The mutation frequency of D12 strain increased only about four times in relation to PA14, suggesting that KerV is not directly involved with DNA mismatch repair. The assays to detect methylation...