Evaluation of six single nucleotide polymorphisms for bovine traceability in the context of the argentine-chinese beef trade

Genetic traceability refers to methods associated with the identification of animals and their products through DNA characterization of individuals, breeds or species. To trace breeds, it is necessary to define the breed groups to analyze, and the most appropriate molecular marker set. The selection of genetic markers depends on the gene frequency distribution, the genetic distance among breeds and the presence of private alleles. In this study, we assessed six single nucleotide polymorphisms (SNPs) located in the DGAT1, TG, LEP, GH, FABP4 and GnRHR genes, as potential genetic markers to be included into a panel for genetic traceability for the identification of breed origin associated with the bovine beef trade. The results of the genetic characterization of four of the main Chinese cattle populations and of the principal breeds raised in Argentina and in the world (five Bos taurus and two B. indicus) suggest that these SNP markers can be successfully used as a part of an effective traceability system for the identification of cattle breed origin in the context of the Chinese meat imports, and in particular in the Argentine-Chinese beef trade.La trazabilidad genética, la cual se basa en la identificación de animales y sus productos, permite la identificación individual, racial o de especie. Esta metodología es útil para detectar fraudes y valorizar producciones locales. Para llevar a cabo la trazabilidad es necesario definir los grupos raciales a analizar y el panel de marcadores más apropiados a utilizar. La selección de marcadores depende de la distribución de las frecuencias génicas, de la distancia genética entre las razas y de la presencia de alelos privativos. El objetivo de este trabajo consistió en evaluar seis polimorfismos de nucleótido simple (SNPs) ubicados en los genes DGAT1, TG, LEP, GH, FABP4 y GnRHR como posibles marcadores genéticos apropiados para ser incluidos en un panel de trazabilidad para la identificación de la raza de origen en el contexto de la comercialización de carne bovina. Los resultados de la caracterización genética de cuatro de las principales poblaciones bovinas chinas y de las razas más importantes de nuestro país (cinco Bos taurus y dos B. indicus) sugieren que los marcadores estudiados pueden ser utilizados exitosamente como parte de un sistema de trazabilidad efectivo para identificar el origen de la carne bovina en el contexto de la importación de carne en el mercado chino y en particular en el comercio entre Argentina y China.Fil: Ripoli, María Verónica. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico La Plata. Instituto de Genética Veterinaria "Ingeniero Fernando Noel Dulout"; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias; ArgentinaFil: Wei, S.. Chinese Academy of Agricultural Sciences; ChinaFil: Rogberg Muñoz, Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico La Plata. Instituto de Genética Veterinaria "Ingeniero Fernando Noel Dulout"; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias; ArgentinaFil: Guo, B. L.. Chinese Academy of Agricultural Sciences; ChinaFil: Goszczynski, Daniel Estanislao. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico La Plata. Instituto de Genética Veterinaria "Ingeniero Fernando Noel Dulout"; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias; ArgentinaFil: Fernandez, María Elena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico La Plata. Instituto de Genética Veterinaria "Ingeniero Fernando Noel Dulout"; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias; ArgentinaFil: Melucci, L.. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires. Estación Experimental Agropecuaria Balcarce; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; ArgentinaFil: Liron, Juan Pedro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico La Plata. Instituto de Genética Veterinaria "Ingeniero Fernando Noel Dulout"; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias; ArgentinaFil: Villarreal, E.. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires. Estación Experimental Agropecuaria Balcarce; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; ArgentinaFil: Wei, Y. M.. Chinese Academy of Agricultural Sciences; ChinaFil: Giovambattista, Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico La Plata. Instituto de Genética Veterinaria "Ingeniero Fernando Noel Dulout"; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias; Argentin

Evaluation of six single nucleotide polymorphisms for bovine traceability in the context of the argentine-chinese beef trade

Genetic traceability refers to methods associated with the identification of animals and their products through DNA characterization of individuals, breeds or species. To trace breeds, it is necessary to define the breed groups to analyze, and the most appropriate molecular marker set. The selection of genetic markers depends on the gene frequency distribution, the genetic distance among breeds and the presence of private alleles. In this study, we assessed six single nucleotide polymorphisms (SNPs) located in the DGAT1, TG, LEP, GH, FABP4 and GnRHR genes, as potential genetic markers to be included into a panel for genetic traceability for the identification of breed origin associated with the bovine beef trade. The results of the genetic characterization of four of the main Chinese cattle populations and of the principal breeds raised in Argentina and in the world (five Bos taurus and two B. indicus) suggest that these SNP markers can be successfully used as a part of an effective traceability system for the identification of cattle breed origin in the context of the Chinese meat imports, and in particular in the Argentine-Chinese beef trade.La trazabilidad genética, la cual se basa en la identificación de animales y sus productos, permite la identificación individual, racial o de especie. Esta metodología es útil para detectar fraudes y valorizar producciones locales. Para llevar a cabo la trazabilidad es necesario definir los grupos raciales a analizar y el panel de marcadores más apropiados a utilizar. La selección de marcadores depende de la distribución de las frecuencias génicas, de la distancia genética entre las razas y de la presencia de alelos privativos. El objetivo de este trabajo consistió en evaluar seis polimorfismos de nucleótido simple (SNPs) ubicados en los genes DGAT1, TG, LEP, GH, FABP4 y GnRHR como posibles marcadores genéticos apropiados para ser incluidos en un panel de trazabilidad para la identificación de la raza de origen en el contexto de la comercialización de carne bovina. Los resultados de la caracterización genética de cuatro de las principales poblaciones bovinas chinas y de las razas más importantes de nuestro país (cinco Bos taurus y dos B. indicus) sugieren que los marcadores estudiados pueden ser utilizados exitosamente como parte de un sistema de trazabilidad efectivo para identificar el origen de la carne bovina en el contexto de la importación de carne en el mercado chino y en particular en el comercio entre Argentina y China.Instituto de Genética Veterinari

Variability in gene expression underlies incomplete penetrance

The phenotypic differences between individual organisms can often be ascribed to underlying genetic and environmental variation. However, even genetically identical organisms in homogeneous environments vary, indicating that randomness in developmental processes such as gene expression may also generate diversity. To examine the consequences of gene expression variability in multicellular organisms, we studied intestinal specification in the nematode Caenorhabditis elegans in which wild-type cell fate is invariant and controlled by a small transcriptional network. Mutations in elements of this network can have indeterminate effects: some mutant embryos fail to develop intestinal cells, whereas others produce intestinal precursors. By counting transcripts of the genes in this network in individual embryos, we show that the expression of an otherwise redundant gene becomes highly variable in the mutants and that this variation is subjected to a threshold, producing an ON/OFF expression pattern of the master regulatory gene of intestinal differentiation. Our results demonstrate that mutations in developmental networks can expose otherwise buffered stochastic variability in gene expression, leading to pronounced phenotypic variation.National Institutes of Health (U.S.). Pioneer AwardMathematical Sciences Postdoctoral Research Fellowships (DMS-0603392)National Institutes of Health (U.S.). Ruth L. Kirschstein National Research Service Award (5F32GM080966

An Advanced Method to Assess the Diet of Free-Ranging Large Carnivores Based on Scats

<div><h3>Background</h3><p>The diet of free-ranging carnivores is an important part of their ecology. It is often determined from prey remains in scats. In many cases, scat analyses are the most efficient method but they require correction for potential biases. When the diet is expressed as proportions of consumed mass of each prey species, the consumed prey mass to excrete one scat needs to be determined and corrected for prey body mass because the proportion of digestible to indigestible matter increases with prey body mass. Prey body mass can be corrected for by conducting feeding experiments using prey of various body masses and fitting a regression between consumed prey mass to excrete one scat and prey body mass (correction factor 1). When the diet is expressed as proportions of consumed individuals of each prey species and includes prey animals not completely consumed, the actual mass of each prey consumed by the carnivore needs to be controlled for (correction factor 2). No previous study controlled for this second bias.</p> <h3>Methodology/Principal Findings</h3><p>Here we use an extended series of feeding experiments on a large carnivore, the cheetah (<em>Acinonyx jubatus</em>), to establish both correction factors. In contrast to previous studies which fitted a linear regression for correction factor 1, we fitted a biologically more meaningful exponential regression model where the consumed prey mass to excrete one scat reaches an asymptote at large prey sizes. Using our protocol, we also derive correction factor 1 and 2 for other carnivore species and apply them to published studies. We show that the new method increases the number and proportion of consumed individuals in the diet for large prey animals compared to the conventional method.</p> <h3>Conclusion/Significance</h3><p>Our results have important implications for the interpretation of scat-based studies in feeding ecology and the resolution of human-wildlife conflicts for the conservation of large carnivores.</p> </div

Assessing anti-rabies baiting – what happens on the ground?

BACKGROUND: Rabies is one of the most hazardous zoonoses in the world. Oral mass vaccination has developed into the most effective management method to control fox rabies. The future need to control the disease in large countries (i.e. Eastern Europe and the Americas) forces cost-benefit discussions. The 'Increase bait density' option refers to the usual management assumption that more baits per km(2 )could compensate for high fox abundance and override the imperfect supply of bait pieces to the individual fox. METHODS: We use a spatial simulation, which combines explicitly fox space use (tessellation polygons) and aeroplane flight lines (straight lines). The number of baits actually falling into each polygon is measured. The manager's strategic options are converted into changes of the resulting bait distribution on the ground. The comparison enables the rating of the options with respect to the management aim (i.e. accessibility of baits). RESULTS: Above 5% (approx. 10%) of all fox groups without any bait (at most 5 baits) relate to the baiting strategy applied in the field (1 km spaced parallel flight lines, 20 baits per km(2 )distributed) under habitat conditions comparable to middle and western Europe (fox group home-range 1 km(2), 2.5 adults; reference strategy). Increasing the bait density on the same flight-line pattern neither reduces the number of under-baited fox group home-ranges, nor improves the management outcome and hence wastes resources. However, reducing the flight line distance provides a more even bait distribution and thus compensates for missed fox groups or extra high fox density. The reference strategy's bait density can be reduced when accounting for the missed fox groups. The management result with the proper strategy is likely the same but with reduced costs. CONCLUSION: There is no overall optimal strategy for the bait distribution in large areas. For major parts of the landscape, the reference strategy will be more competitive. In situations where set backs are attributed to non-homogeneous bait accessibility the distribution scheme has to be refined zone-based (i.e. increase of the flight line length per unit area). However, increase in bait density above the reference strategy appears inappropriate at least for non-urban abundance conditions of the red fox

Emergency vaccination of rabies under limited resources – combating or containing?

BACKGROUND: Rabies is the most important viral zoonosis from a global perspective. Worldwide efforts to combat the disease by oral vaccination of reservoirs have managed to eradicate wildlife rabies in large areas of central Europe and North-America. Thus, repeated vaccination has been discontinued recently on a geographical scale. However, as rabies has not yet been eradicated globally, a serious risk of re-introduction remains. What is the best spatial design for an emergency vaccination program – particularly if resources are limited? Either, we treat a circular area around the detected case and run the risk of infected hosts leaving the limited control area, because a sufficient immunisation level has not yet been built up. Or, initially concentrate the SAME resources in order to establish a protective ring which is more distant from the infected local area, and which then holds out against the challenge of the approaching epidemic. METHODS: We developed a simulation model to contrast the two strategies for emergency vaccination. The spatial-explicit model is based on fox group home-ranges, which facilitates the simulation of rabies spread to larger areas relevant to management. We used individual-based fox groups to follow up the effects of vaccination in a detailed manner. Thus, regionally – bait distribution orientates itself to standard schemes of oral immunisation programs and locally – baits are assigned to individual foxes. RESULTS: Surprisingly, putting the controlled area ring-like around the outbreak does not outperform the circular area of the same size centred on the outbreak. Only during the very first baitings, does the ring area result in fewer breakouts. But then as rabies is eliminated within the circle area, the respective ring area fails, due to the non-controlled inner part. We attempt to take advantage of the initially fewer breakouts beyond the ring when applying a mixed strategy. Therefore, after a certain number of baitings, the area under control was increased for both strategies towards the same larger circular area. The circle-circle strategy still outperforms the ring-circle strategy and analysis of the spatial-temporal disease spread reveals why: improving control efficacy by means of a mixed strategy is impossible in the field, due to the build-up time of population immunity. CONCLUSION: For practical emergency management of a new outbreak of rabies, the ring-like application of oral vaccination is not a favourable strategy at all. Even if initial resources are substantially low and there is a serious risk of rabies cases outside the limited control area, our results suggest circular application instead of ring vaccination

Diet of sympatric pine marten (Martes martes) and stone marten (Martes foina) identified by genotyping of DNA from faeces

Martes martes and Martes foina occur sympatrically in most of Europe. Little is known about differences between trophic niches of these species, because martens are difficult to observe and it is impossible to distinguish between scats of both species based on their morphological features. To resolve this problem, we used DNA extracted from faeces for species identification. This method allowed us to compare the diet of the two species in the area of their sympatric occurrence in central Poland. We analysed the composition of 287 scats of stone martens and 155 of pine martens. Both species fed mainly on small rodents, birds and fruits. Although the trophic niches of both martens highly overlapped, we found significant quantitative differences in their food composition. Pine martens fed more frequently on rodents and birds, and stone martens on fruits and insects. These differences were also visible in the seasonal perspective. Although both martens exploited the same forest habitat, genetic identification of faeces allowed us to indicate significant differences in the diet of these closely related species. © Finnish Zoological and Botanical Publishing Board 2007