Recent Submissions

  • Journal Article

    Biodiversity in Tomatoes: Is It Reflected in Nutrient Density and Nutritional Yields Under Organic Outdoor Production? 

    Erika, Cut; Griebel, Stefanie; Naumann, Marcel; Pawelzik, Elke
    Frontiers in Plant Science 2020; 11 p.1-14: Art. 589692
    In many regions of the world, human nutrition is still characterized by an insufficient intake of essential nutrients like minerals such as iron (Fe) and zinc (Zn). In view of decreasing resources and a growing world population, the efficiency and the sustainability of cultivation systems should be considered not only in terms of crop yield and profit margin but also in terms of the yield of essential nutrients. Tomatoes are the most consumed vegetable in the world. Organic outdoor tomato cultivation is generally characterized by a higher diversity of varieties and lower fertilization input compared to conventional production. A 2-year field experiment with a set of 20 cultivars was performed to evaluate their variation regarding fruit mineral concentrations [potassium (K), calcium (Ca), magnesium (Mg), phosphorous (P), Fe, and Zn], their contribution to the dietary reference intake (DRI), and the nutritional yields (adults ha$^{–1}$ year$^{–1}$). Results show that mineral concentrations differed significantly by cultivar and by year. However, even though significant genotype-by-year effects appear, several cultivars exhibit high genotype stability across years for the single traits studied. Taking this together with medium-to-high heritability, genetics strongly controls most studied traits. Among the cultivars, the contribution of 100 g fresh fruits varied from 4.5 to 7.7% for K, 0.8 to 1.8% for Ca, 2.3 to 4.4% for Mg, 3 to 6.6% for P, 3.1 to 6.9% for Fe, and 1.9 to 4.2% for Zn to meet daily requirements. Based on average fruit yields per hectare, the cultivars varied with regard to the nutritional yields for all the studied minerals, but most strongly for Fe (44–120 adults ha$^{–1}$ year$^{–1}$) and Zn (22–84 adults ha$^{–1}$ year$^{–1}$). In terms of contribution to the DRI and nutritional yield for Fe, the cocktail cultivar “Bartelly F1” produced the highest results, while for Zn the salad cultivar “Bocati F1” showed the highest values. Our results show that the targeted use of tomato biodiversity in organic outdoor production can be suitable to achieve high fruit yields as well as to produce high nutritional yields per unit area, thus contributing to more effective land use and improved food security. These findings also provide valuable insights for tomato breeders to improve the tomato fruit quality while maintaining yield.
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  • Journal Article

    Factors influencing German farmer’s decision to grow alley cropping systems as ecological focus areas: a regression analysis 

    Beer, Lara; Theuvsen, Ludwig
    International Food and Agribusiness Management Review 2020; 23(4) p.529-546
    The cultivation of alley cropping agricultural wood is an opportunity to comply with the greening requirements of the common agricultural policy (CAP; 2014-2020), but farmers are not permitted to display the whole alley cropping system (ACS) as ecological focus area (EFA) in Germany. They can display the agricultural wood stripes separately as EFA instead. The willingness of farmers is of key importance for a successful establishment, but, so far, the acceptance of this greening measure is extremely low. The aim of this paper is therefore to point out factors which have linkages to the acceptance of ACS as EFAs by conducting an online survey among German conventional farmers. The results of the regression analysis show that factors such as attitude towards agricultural wood, level of professional education, location and social environment affect the acceptance of ACS as EFA. To conclude, starting points that promote this type of greening measure are identified.
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  • Journal Article

    Using Local Convolutional Neural Networks for Genomic Prediction 

    Pook, Torsten; Freudenthal, Jan; Korte, Arthur; Simianer, Henner
    Frontiers in Genetics 2020; 11 p.1-14: Art. 561497
    The prediction of breeding values and phenotypes is of central importance for both livestock and crop breeding. In this study, we analyze the use of artificial neural networks (ANN) and, in particular, local convolutional neural networks (LCNN) for genomic prediction, as a region-specific filter corresponds much better with our prior genetic knowledge on the genetic architecture of traits than traditional convolutional neural networks. Model performances are evaluated on a simulated maize data panel (n = 10,000; p = 34,595) and real Arabidopsis data (n = 2,039; p = 180,000) for a variety of traits based on their predictive ability. The baseline LCNN, containing one local convolutional layer (kernel size: 10) and two fully connected layers with 64 nodes each, is outperforming commonly proposed ANNs (multi layer perceptrons and convolutional neural networks) for basically all considered traits. For traits with high heritability and large training population as present in the simulated data, LCNN are even outperforming state-of-the-art methods like genomic best linear unbiased prediction (GBLUP), Bayesian models and extended GBLUP, indicated by an increase in predictive ability of up to 24%. However, for small training populations, these state-of-the-art methods outperform all considered ANNs. Nevertheless, the LCNN still outperforms all other considered ANNs by around 10%. Minor improvements to the tested baseline network architecture of the LCNN were obtained by increasing the kernel size and of reducing the stride, whereas the number of subsequent fully connected layers and their node sizes had neglectable impact. Although gains in predictive ability were obtained for large scale data sets by using LCNNs, the practical use of ANNs comes with additional problems, such as the need of genotyping all considered individuals, the lack of estimation of heritability and reliability. Furthermore, breeding values are additive by design, whereas ANN-based estimates are not. However, ANNs also comes with new opportunities, as networks can easily be extended to account for additional inputs (omics, weather etc.) and outputs (multi-trait models), and computing time increases linearly with the number of individuals. With advances in high-throughput phenotyping and cheaper genotyping, ANNs can become a valid alternative for genomic prediction.
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  • Journal Article

    Bringing Policy Decisions to the People—Education for Sustainable Development through a Digital Simulation Game 

    Ivens, Sven; Wiese, Gerlinde; Dittert, Klaus; Mußhoff, Oliver; Oberle, Monika
    Sustainability 2020; 12(20) p.1-18: Art. 8743
    After repeated warnings by the European Commission regarding high nitrate concentrations in German waters, in 2017, Germany implemented a new fertilizer application ordinance (FO) with stricter nitrate value limits. The new regulations have severely affected agricultural regions in Germany and could lead to a high number of job losses if farmers must conform to the new regulations and do not implement new production methods. Therefore, a simulation game was developed to educate farmers and residents about the new FO and to facilitate adaptation to the new environmentally friendly legislation. The aims of the newly developed simulation game are to educate residents and farmers in affected regions about the new FO and to develop new ideas on how to comply with the new regulations. The aims of the present study are, first, to research participants’ evaluation of the simulation game and, second, to assess the effect of the simulation game on subjective knowledge, internal efficacy, and attitude towards the new FO. This pre- and post-comparison design study was based on pre-test and post-test with participants in two games (N = 90). The results were analyzed using descriptive statistics, multiple regression analyses, qualitative content analysis, and mean value comparisons. The simulation game had a positive effect on participants’ subjective knowledge (Cohen’s d 0.65) and internal efficacy (Cohen’s d 0.36), but it did not have an effect on their attitudes toward the new FO, and it was shown to slightly lower their interest in agriculture politics (Cohen’s d −0.33). The participants reported that the game made them more aware of both the difficulty and necessity of finding compromises in the field of agriculture politics. Overall, the simulation was rated very positively and was perceived as interesting and informative by the participants.
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  • Journal Article

    High microphone signal-to-noise ratio enhances acoustic sampling of wildlife 

    Darras, Kevin F.A.; Deppe, Franziska; Fabian, Yvonne; Kartono, Agus P.; Angulo, Andres; Kolbrek, Bjørn; Mulyani, Yeni A.; Prawiradilaga, Dewi M.
    PeerJ 2020; 8 p.1-21: Art. e9955
    Background. Automated sound recorders are a popular sampling tool in ecology. However, the microphones themselves received little attention so far, and specifications that determine the recordings' sound quality are seldom mentioned. Here, we demonstrate the importance of microphone signal-to-noise ratio for sampling sonant animals. Methods. We tested 12 different microphone models in the field and measured their signal-to-noise ratios and detection ranges. We also measured the vocalisation activity of birds and bats that they recorded, the bird species richness, the bat call types richness, as well as the performance of automated detection of bird and bat calls. We tested the relationship of each one of these measures with signal-to-noise ratio in statistical models. Results. Microphone signal-to-noise ratio positively affects the sound detection space areas, which increased by a factor of 1.7 for audible sound, and 10 for ultrasound, from the lowest to the highest signal-to-noise ratio microphone. Consequently, the sampled vocalisation activity increased by a factor of 1.6 for birds, and 9.7 for bats. Correspondingly, the species pool of birds and bats could not be completely detected by the microphones with lower signal-to-noise ratio. The performance of automated detection of bird and bat calls, as measured by its precision and recall, increased significantly with microphone signal-to-noise ratio. Discussion. Microphone signal-to-noise ratio is a crucial characteristic of a sound recording system, positively affecting the acoustic sampling performance of birds and bats. It should be maximised by choosing appropriate microphones, and be quantified independently, especially in the ultrasound range.
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  • Journal Article

    A Global Survey on Diseases and Pests in Oilseed Rape—Current Challenges and Innovative Strategies of Control 

    Zheng, Xiaorong; Koopmann, Birger; Ulber, Bernd; von Tiedemann, Andreas
    Frontiers in Agronomy 2020; 2 p.1-15: Art. 590908
    The introduction of high-yielding and hybrid cultivars and the opening of new markets in the food and feed sector have steadily increased rapeseed production since the 1980s in the main production regions, Canada, Europe, China, India, and Australia. Since the 1990s, however, the average growth rate of yields has declined in Europe and Australia, which has been associated with a less effective control of biotic stresses. A global survey including the knowledge of 22 experts from 10 countries revealed a total of 16 diseases, 37 insect pests, several species of nematodes, and slugs currently affecting rapeseed production globally. A ranking of the top 10 most important biotic stresses in the four global regions where Brassica napus is grown (Canada, China, Europe, Australia) indicated an increase in several important stresses and distinct regional differences in the priority of prevailing diseases and pests. A stronger overlap exists among diseases, with Sclerotinia stem rot, Phoma stem canker, and clubroot occurring in all the four global regions on the top 10 list, while the range of prevailing insect pests was more diverse among the regions, with no top 10 insect playing an equally important role worldwide. Management options are substantially broader in disease than in pest control, making the latter the larger challenge. Since common integrated pest management (IPM) tools such as crop rotation, soil management, resistant cultivars or biocontrol are ineffective or not available, insect control largely relies on insecticides. Increasing restrictions on insecticide use, particularly in Europe, and losses in insecticide efficacy threaten the profitability of oilseed rape production and its role as an important break crop in cereal dominated cropping systems. Since the survival time of insects in the absence of their main host is relatively short (<1 year), a regional synchronization of cropping schemes resulting in one or more years without the crop could lead to a substantial disruption of regional insect populations. If rotation schemes were implemented on the landscape instead the farm level, by coordination among growers in zones covering the range distances of insect pests, an efficient and chemical low management strategy could be established and enable a more sustainable rapeseed production in the future.
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  • Journal Article

    BioSounds: an open-source, online platform for ecoacoustics 

    Darras, Kevin; Pérez, Noemí; -, Mauladi; Hanf-Dressler, Tara
    F1000Research 2020; 9 p.1-12: Art. 1224
    Passive acoustic monitoring of soundscapes and biodiversity produces vast amounts of audio recordings. However, the management of these raw data presents technical challenges and their analysis suffers from bottlenecks. A multitude of software solutions exist, but none can perform all the data processing needed by ecologists for analysing large acoustic data sets. The field of ecoacoustics needs a software tool that is free, evolving, and accessible. We take a step in that direction and present BioSounds: an open-source, online platform for ecoacoustics designed by ecologists and built by software engineers. Biosounds can be used for archiving and sharing recordings, manually creating and reviewing annotations of sonant animals in soundscapes, analysing audio in time and frequency, and storing reference recordings for different taxa. We present its features and structure, and compare it with similar software. We describe its operation mode and the workflow for typical use cases such as the analysis of bird and bat communities sampled in soundscape recordings. BioSounds is available from: https://github.com/nperezg/biosounds
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  • Journal Article

    Correction to: Unexpected high frequency of neurofibroma in the celiac ganglion of German cattle 

    Dammann, Insa; Wemheuer, Wiebke M.; Wrede, Arne; Wemheuer, Wilhelm E.; Campe, Amely; Petschenka, Jutta; Schulze-Sturm, Ulf; Hahmann, Uwe; Czerny, Claus P.; Münster, Pia; et al.
    Brenig, BertramKreienbrock, LotharHerden, ChristianeSchulz-Schaeffer, Walter J.
    Veterinary Research. 2020 Oct 15;51(1):130
    An amendment to this paper has been published and can be accessed via the original article.
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  • Journal Article

    Protection of Citrus Fruits from Postharvest Infection with Penicillium digitatum and Degradation of Patulin by Biocontrol Yeast Clavispora lusitaniae 146 

    Díaz, Mariana Andrea; Pereyra, Martina María; Santander, Fabricio Fabián Soliz; Perez, María Florencia; Córdoba, Josefina María; Alhussein, Mohammad; Karlovsky, Petr; Dib, Julián Rafael
    Microorganisms 2020; 8(10) p.1-12: Art. 1477
    Fungal rots are one of the main causes of large economic losses and deterioration in the quality and nutrient composition of fruits during the postharvest stage. The yeast Clavispora lusitaniae 146 has previously been shown to efficiently protect lemons from green mold caused by Penicillium digitatum. In this work, the effect of yeast concentration and exposure time on biocontrol efficiency was assessed; the protection of various citrus fruits against P. digitatum by C. lusitaniae 146 was evaluated; the ability of strain 146 to degrade mycotoxin patulin was tested; and the effect of the treatment on the sensory properties of fruits was determined. An efficient protection of lemons was achieved after minimum exposure to a relatively low yeast cell concentration. Apart from lemons, the yeast prevented green mold in grapefruits, mandarins, oranges, and tangerines, implying that it can be used as a broad-range biocontrol agent in citrus. The ability to degrade patulin indicated that strain 146 may be suitable for the control of further Penicillium species. Yeast treatment did not alter the sensory perception of the aroma of fruits. These results corroborate the potential of C. lusitaniae 146 for the control of postharvest diseases of citrus fruits and indicate its suitability for industrial-scale fruit processing.
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  • Journal Article

    Flesh ID: Nanopore Sequencing Combined with Offline BLAST Search for the Identification of Meat Source 

    Kissenkötter, Jonas; Böhlken-Fascher, Susanne; Abd El Wahed, Ahmed
    Foods 2020; 9(10) p.1-13: Art. 1392
    Detection of animal species in meat product is crucial to prevent adulterated and unnecessary contamination during processing, in addition to avoid allergy and religious consequences. Gold standard is the real-time PCR assays, which has a limited target capability. In this study, we have established a rapid sequencing protocol to identify animal species within hours. Sequencing was achieved by nanopore sequencing and data analysis via offline BLAST search. The whole procedure was conducted in a mobile suitcase lab. As per national and international regulations, the developed assay detected adulteration of pork meat with 0.1% of horse, chicken, turkey, cattle, sheep, duck, rabbit, goat, and donkey. The developed test could be used on-site as a rapid and mobile detection system to determine contamination of meat products
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  • Journal Article

    Meta-analyses of genome wide association studies in lines of laying hens divergently selected for feather pecking using imputed sequence level genotypes 

    Falker-Gieske, Clemens; Iffland, Hanna; Preuß, Siegfried; Bessei, Werner; Drögemüller, Cord; Bennewitz, Jörn; Tetens, Jens
    BMC Genetics. 2020 Oct 01;21(1):114
    Abstract Background Feather pecking (FP) is damaging behavior in laying hens leading to global economic losses in the layer industry and massive impairments of animal welfare. The objective of the study was to discover genetic variants and affected genes that lead to FP behavior. To achieve that we imputed low-density genotypes from two different populations of layers divergently selected for FP to sequence level by performing whole genome sequencing on founder and half-sib individuals. In order to decipher the genetic structure of FP, genome wide association studies and meta-analyses of two resource populations were carried out by focusing on the traits ‘feather pecks delivered’ (FPD) and the ‘posterior probability of a hen to belong to the extreme feather pecking subgroup’ (pEFP). Results In this meta-analysis, we discovered numerous genes that are affected by polymorphisms significantly associated with the trait FPD. Among them SPATS2L, ZEB2, KCHN8, and MRPL13 which have been previously connected to psychiatric disorders with the latter two being responsive to nicotine treatment. Gene set enrichment analysis revealed that phosphatidylinositol signaling is affected by genes identified in the GWAS and that the Golgi apparatus as well as brain structure may be involved in the development of a FP phenotype. Further, we were able to validate a previously discovered QTL for the trait pEFP on GGA1, which contains variants affecting NIPA1, KIAA1211L, AFF3, and TSGA10. Conclusions We provide evidence for the involvement of numerous genes in the propensity to exhibit FP behavior that could aid in the selection against this unwanted trait. Furthermore, we identified variants that are involved in phosphatidylinositol signaling, Golgi metabolism and cell structure and therefore propose changes in brain structure to be an influential factor in FP, as already described in human neuropsychiatric disorders.
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  • Journal Article

    Understanding German Pig Farmers’ Intentions to Design and Construct Pig Housing for the Improvement of Animal Welfare 

    Winkel, Carolin; von Meyer-Höfer, Marie; Heise, Heinke
    Animals 2020; 10(10) p.1-22: Art. 1760
    Improving farm animal welfare requires modifications to the behavior of many stakeholders. Investments in more animal-friendly barns to improve animal welfare have already been made by some farmers. However, more farmers must be persuaded to modernize their barns. The marketing of animal-friendly products is the responsibility of retailers, and consumers have to purchase these products. Currently, little is known about what (and how) underlying psychological factors influence a farmer’s intention to construct pig housing to improve farm animal welfare. Pig farmers in Germany were questioned via an online questionnaire in May 2020 (n = 424). Based on the Theory of Planned Behavior (TPB), partial least squares path modeling was used. The constructs: attitude, subjective norm, direct and indirect experience associated with the construction of pig housing substantially influenced the farmers’ behaviors. As expected, the impact of perceived behavioral control on intention was negative but was also very low and only slightly significant. Contrary to expectations, the perceived behavioral control had no significant influence on farmers’ behaviors. Pig farmers who have already rebuilt their pigs’ housing should be motivated to share their experiences to influence their colleagues’ intentions to construct. Our results will encourage policy makers to consider the important role of the different psychological and intrinsic factors influencing pig farmers. Thus, the sustainability of pig farming can be improved by giving politicians a better understanding of farmers´ behaviors.
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  • Journal Article

    Point-Of-Care or Point-Of-Need Diagnostic Tests: Time to Change Outbreak Investigation and Pathogen Detection 

    Hansen, Sören; Abd El Wahed, Ahmed
    Tropical Medicine and Infectious Disease 2020; 5(4) p.1-15: Art. 151
    In the recent years, the progress of international trade and travel has led to an increased risk of emerging infections. Around 75 percent of the pathogens causing these infections are of animal origin. Point-of-care tests (POCT) and point-of-need tests (PONT) have been established in order to directly provide accurate and rapid diagnostics at field level, the patient bed-side or at the site of outbreaks. These assays can help physicians and decision makers to take the right action without delay. Typically, POCT and PONT rely on genomic identification of pathogens or track their immunological fingerprint. Recently, protocols for metagenomic diagnostics in the field have been developed. In this review, we give an overview of the latest developments in portable diagnostic methods. In addition, four mobile platforms for the implementation of these techniques at point-of-care and point-of-need are described. These approaches can provide reliable diagnostics and surveillance, especially in low resource settings as well as at the level of one health.
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  • Journal Article

    Pan-genomic open reading frames: A potential supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction 

    Li, Zhengcao; Simianer, Henner
    PLOS Genetics 2020; 16(8) p.1-19: Art. e1008995
    Pan-genomic open reading frames (ORFs) potentially carry protein-coding gene or coding variant information in a population. In this study, we suggest that pan-genomic ORFs are promising to be utilized in estimation of heritability and genomic prediction. A Saccharomyces cerevisiae dataset with whole-genome SNPs, pan-genomic ORFs, and the copy numbers of those ORFs is used to test the effectiveness of ORF data as a predictor in three prediction models for 35 traits. Our results show that the ORF-based heritability can capture more genetic effects than SNP-based heritability for all traits. Compared to SNP-based genomic prediction (GBLUP), pan-genomic ORF-based genomic prediction (OBLUP) is distinctly more accurate for all traits, and the predictive abilities on average are more than doubled across all traits. For four traits, the copy number of ORF-based prediction(CBLUP) is more accurate than OBLUP. When using different numbers of isolates in training sets in ORF-based prediction, the predictive abilities for all traits increased as more isolates are added in the training sets, suggesting that with very large training sets the prediction accuracy will be in the range of the square root of the heritability. We conclude that pan-genomic ORFs have the potential to be a supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction.
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  • Journal Article

    Molecular and Serological Footprints of Mycobacterium avium Subspecies Infections in Zoo Animals 

    Roller, Marco; Hansen, Sören; Böhlken-Fascher, Susanne; Knauf-Witzens, Tobias; Czerny, Claus-Peter; Goethe, Ralph; Abd El Wahed, Ahmed
    Veterinary Sciences 2020; 7(3) p.1-14: Art. 117
    Background: Mycobacteria of the Mycobacterium avium complex (MAC) pose a significant risk to zoological collections. Mycobacterium avium subspecies paratuberculosis (MAP) is a member of MAC and the causative agent of Johne’s disease. Despite many reports in animals kept in zoological gardens, systemic surveillance has rarely been reported. Methods: In this study, archived serum samples collected from animal species at the Wilhelma Zoological and Botanical Gardens in Stuttgart, Germany, were screened for the presence of antibodies against MAC and MAP. In addition, molecular investigations were performed on necropsy, fecal, and environmental samples. Results: In total, 30/381 serum samples of various mammalian species were positive for MAC antibodies in ELISA, while one sample of a reticulated giraffe (Giraffa camelopardalis reticulata) was positive in MAP-specific ELISA. Samples from many species were positive in pan-Mycobacterium real-time PCR (40/43 fecal samples, 27/43 environmental samples, and 31/90 necropsy samples). Surprisingly, no sample was positive in the MAP-specific molecular assays. However, two environmental samples from primate enclosures were positive in Mycobacterium avium subspecies hominissuis (MAH)-specific real-time PCR. Conclusions: The results reveal serological indications of MAC infections in the zoological collection. However, the presence of a MAP-contaminated environment by a high-shedding individual animal or MAP-infected population is unlikely.
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  • Journal Article

    Meat Quality Parameters and Sensory Properties of One High-Performing and Two Local Chicken Breeds Fed with Vicia faba 

    Escobedo del Bosque, Cynthia I.; Altmann, Brianne A.; Ciulu, Marco; Halle, Ingrid; Jansen, Simon; Nolte, Tanja; Weigend, Steffen; Mörlein, Daniel
    Foods 2020; 9(8) p.1-18: Art. 1052
    The current practices of the poultry industry have raised concerns among consumers. Among these is the culling of day-old male chicks of laying hybrids; a suitable alternative for this could be the use of dual-purpose breeds where both sexes are used. Another practice that causes concern is the import of large quantities of soybeans for feedstuff production. Substitutes for these soybean-based products are regional protein crops, such as faba beans (Vicia faba L.; FBs). The objective of this study was to test the suitability of FB as a locally produced soybean meal replacement for two local dual-purpose chicken breeds and one high-performing layer line. The breast and leg meat of male Bresse Gauloise (BG), Vorwerkhuhn (VH), and White Rock (WR) animals was evaluated for different meat quality parameters: pH, color, water holding capacity, and tenderness. Sensory properties of the samples were evaluated by a trained panel with a conventional descriptive analysis. Results show different effects of FB diets on meat quality parameters in the different breeds. The attributes mostly affected by the diet are related to aroma, flavor, and texture, particularly in VH and WR. Overall, faba beans appear to be an acceptable dietary protein source for rearing these breeds for meat production.
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  • Journal Article

    The Effect of Algae or Insect Supplementation as Alternative Protein Sources on the Volatile Profile of Chicken Meat 

    Gkarane, Vasiliki; Ciulu, Marco; Altmann, Brianne A.; Schmitt, Armin O.; Mörlein, Daniel
    Foods 2020; 9(9) p.1-15: Art. 1235
    The aim of this study was to investigate the differences in the volatile profile of meat from chickens fed with alternative protein diets (such as algae or insect) through two different trials. In Trial 1, broiler chicken at one day of age were randomly allocated to three experimental groups: a basal control diet (C) and two groups in which the soybean meal was replaced at 75% (in the starter phase) and 50% (in the grower phase) with partially defatted Hermetia illucens (HI) larvae or Arthrospira platensis (SP). In Trial 2, broiler chickens were housed and reared similar to Trial 1, with the exception that the experimental diets replaced soybean meal with either 100% partially defatted HI or 100% SP. In both trials, chickens were slaughtered at day 35. Per group, 10 chickens were submitted to volatile analysis by using solid-phase microextraction (HS-SPME) and gas chromatography–mass spectrometry (GC-MS) analysis. Results in both trials showed that levels of several lipid-derived compounds were found to be lower in chickens fed an HI diet, which could be linked to a possibly lower level of polyunsaturated fatty acid content in HI-fed chicken. In addition, the dietary treatments could be discriminated based on the volatile profile, i.e., the substitution of soy with HI or SP distinctively affected the levels of flavor compounds.
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  • Journal Article

    Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data 

    Peripolli, Elisa; Reimer, Christian; Ha, Ngoc-Thuy; Geibel, Johannes; Machado, Marco A; Panetto, João C; do Egito, Andréa A; Baldi, Fernando; Simianer, Henner; da Silva, Marcos V G B
    BMC Genomics. 2020 Sep 11;21(1):624
    Abstract Background The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing data from indicine and Brazilian locally adapted taurine cattle breeds were used to detect genomic regions under selective pressure. Within-population and cross-population statistics were combined separately in a single score using the de-correlated composite of multiple signals (DCMS) method. Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics. Results A total of 33,328,447 biallelic SNPs with an average read depth of 12.4X passed the hard filtering process and were used to access putative sweep regions. Admixture has occurred in some locally adapted taurine populations due to the introgression of exotic breeds. The genomic inbreeding coefficient based on runs of homozygosity (ROH) concurred with the populations’ historical background. Signatures of selection retrieved from the DCMS statistics provided a comprehensive set of putative candidate genes and revealed QTLs disclosing cattle production traits and adaptation to the challenging environments. Additionally, several candidate regions overlapped with previous regions under selection described in the literature for other cattle breeds. Conclusion The current study reported putative sweep regions that can provide important insights to better understand the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. Such regions likely harbor traces of natural selection pressures by which these populations have been exposed and may elucidate footprints for adaptation to the challenging climatic conditions.
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  • Journal Article

    Buffalopox Virus: An Emerging Virus in Livestock and Humans 

    Eltom, Kamal; Samy, Abdallah; Abd El Wahed, Ahmed; Czerny, Claus-Peter
    Pathogens 2020; 9(9) p.1-9: Art. 676
    Buffalopox virus (BPXV) is the cause of buffalopox, which was recognized by the FAO/WHO Joint Expert Committee on Zoonosis as an important zoonotic disease. Buffalopox was first described in India, later in other countries, and has become an emerging contagious viral zoonotic disease infecting milkers with high morbidity among affected domestic buffalo and cattle. BPXV is a member of the genus Orthopoxvirus and a close variant of the vaccinia virus (VACV). Recent genome data show that BPXV shares a most recent common ancestor of VACV Lister strain, which had been used for inoculating buffalo calves to produce a Smallpox vaccine. Over time, VACV evolved into BPXV by establishing itself in buffaloes to be increasingly pathogenic to this host and to make infections in cattle and humans. Together with the current pandemic of SARS-COV2/COVID 19, BPXV infections illustrate how vulnerable the human population is to the emergence and re-emergence of viral pathogens from unsuspected sources. In view that majority of the world population are not vaccinated against smallpox and are most vulnerable in the event of its re-emergence, reviewing and understanding the biology of vaccinia-like viruses are necessary for developing a new generation of safer smallpox vaccines in the smallpox-free world.
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  • Journal Article

    Egg Production and Bone Stability of Local Chicken Breeds and Their Crosses Fed with Faba Beans 

    Nolte, Tanja; Jansen, Simon; Halle, Ingrid; Scholz, Armin Manfred; Simianer, Henner; Sharifi, Ahmad Reza; Weigend, Steffen
    Animals 2020; 10(9) p.1-20: Art. 1480
    Poultry production is raising concerns within the public regarding the practice of culling day-old chicks and the importation of soy from overseas for feedstuff. Therefore, an alternative approach to poultry production was tested. In two consecutive experiments, two traditional chicken breeds, Vorwerkhuhn and Bresse Gauloise, and White Rock as a commercial layer genotype as well as crossbreds thereof were fed diets containing either 20% vicin-rich or vicin-poor faba beans, though addressing both subjects of debate. Hen performance traits and bone stability were recorded. All parameters were considerably influenced by the genotype with White Rock showing the significantly highest (p < 0.05) laying performance (99.4% peak production) and mean egg weights (56.6 g) of the purebreds, but the lowest bone breaking strength (tibiotarsus 197.2 N, humerus 230.2 N). Regarding crossbreds, the Bresse Gauloise × White Rock cross performed best (peak production 98.1%, mean egg weight 58.0 g). However, only limited dietary effects were found as only the feeding of 20% vicin-rich faba beans led to a significant reduction of egg weights of at most 1.1 g (p < 0.05) and to a significant reduction of the shell stability in the crossbred genotypes. In terms of dual-purpose usage, crossing of Bresse Gauloise with White Rock seems to be the most promising variant studied here.
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