Recent Submissions

  • Journal Article

    Genetics of adaptation in modern chicken 

    Qanbari, Saber; Rubin, Carl-Johan; Maqbool, Khurram; Weigend, Steffen; Weigend, Annett; Geibel, Johannes; Kerje, Susanne; Wurmser, Christine; Peterson, Andrew Townsend; Brisbin, I. Lehr; et al.
    Preisinger, RuediFries, RuediSimianer, HennerAndersson, Leif
    PLOS Genetics 2019; 15(4): Art. e1007989
    We carried out whole genome resequencing of 127 chicken including red jungle fowl and multiple populations of commercial broilers and layers to perform a systematic screening of adaptive changes in modern chicken (Gallus gallus domesticus). We uncovered >21 million high quality SNPs of which 34% are newly detected variants. This panel comprises >115,000 predicted amino-acid altering substitutions as well as 1,100 SNPs predicted to be stop-gain or -loss, several of which reach high frequencies. Signatures of selection were investigated both through analyses of fixation and differentiation to reveal selective sweeps that may have had prominent roles during domestication and breed development. Contrasting wild and domestic chicken we confirmed selection at the BCO2 and TSHR loci and identified 34 putative sweeps co-localized with ALX1, KITLG, EPGR, IGF1, DLK1, JPT2, CRAMP1, and GLI3, among others. Analysis of enrichment between groups of wild vs. commercials and broilers vs. layers revealed a further panel of candidate genes including CORIN, SKIV2L2 implicated in pigmentation and LEPR, MEGF10 and SPEF2, suggestive of production-oriented selection. SNPs with marked allele frequency differences between wild and domestic chicken showed a highly significant deficiency in the proportion of amino-acid altering mutations (P<2.5×10-6). The results contribute to the understanding of major genetic changes that took place during the evolution of modern chickens and in poultry breeding.
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  • Journal Article

    Integrating Aquatic and Terrestrial Perspectives to Improve Insights Into Organic Matter Cycling at the Landscape Scale 

    Kayler, Zachary E.; Premke, Katrin; Gessler, Arthur; Gessner, Mark O.; Griebler, Christian; Hilt, Sabine; Klemedtsson, Leif; Kuzyakov, Yakov; Reichstein, Markus; Siemens, Jan; et al.
    Totsche, Kai-UweTranvik, LarsWagner, AnnekatrinWeitere, MarkusGrossart, Hans-Peter
    Frontiers in Earth Science 2019; 7: Art. 127
    Across a landscape, aquatic-terrestrial interfaces within and between ecosystems are hotspots of organic matter (OM) mineralization. These interfaces are characterized by sharp spatio-temporal changes in environmental conditions, which affect OM properties and thus control OM mineralization and other transformation processes. Consequently, the extent of OM movement at and across aquatic-terrestrial interfaces is crucial in determining OM turnover and carbon (C) cycling at the landscape scale. Here, we propose expanding current concepts in aquatic and terrestrial ecosystem sciences to comprehensively evaluate OM turnover at the landscape scale. We focus on three main concepts toward explaining OM turnover at the landscape scale: the landscape spatiotemporal context, OM turnover described by priming and ecological stoichiometry, and anthropogenic effects as a disruptor of natural OM transfer magnitudes and pathways. A conceptual framework is introduced that allows for discussing the disparities in spatial and temporal scales of OM transfer, changes in environmental conditions, ecosystem connectivity, and microbial–substrate interactions. The potential relevance of priming effects in both terrestrial and aquatic systems is addressed. For terrestrial systems, we hypothesize that the interplay between the influx of OM, its corresponding elemental composition, and the elemental demand of the microbial communities may alleviate spatial and metabolic thresholds. In comparison, substrate level OM dynamics may be substantially different in aquatic systems due to matrix effects that accentuate the role of abiotic conditions, substrate quality, and microbial community dynamics. We highlight the disproportionate impact anthropogenic activities can have on OM cycling across the landscape. This includes reversing natural OM flows through the landscape, disrupting ecosystem connectivity, and nutrient additions that cascade across the landscape. This knowledge is crucial for a better understanding of OM cycling in a landscape context, in particular since terrestrial and aquatic compartments may respond differently to the ongoing changes in climate, land use, and other anthropogenic interferences.
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  • Journal Article

    Conversion of monoculture cropland and open grassland to agroforestry alters the abundance of soil bacteria, fungi and soil-N-cycling genes 

    Beule, Lukas; Corre, Marife D.; Schmidt, Marcus; Göbel, Leonie; Veldkamp, Edzo; Karlovsky, Petr
    PLOS ONE 2019; 14(6): Art. e0218779
    Integration of trees in agroforestry systems can increase the system sustainability compared to monocultures. The resulting increase in system complexity is likely to affect soil-N cycling by altering soil microbial community structure and functions. Our study aimed to assess the abundance of genes encoding enzymes involved in soil-N cycling in paired monoculture and agroforestry cropland in a Phaeozem soil, and paired open grassland and agroforestry grassland in Histosol and Anthrosol soils. The soil fungi-to-bacteria ratio was greater in the tree row than in the crop or grass rows of the monoculture cropland and open grassland in all soil types, possibly due to increased input of tree residues and the absence of tillage in the Phaeozem (cropland) soil. In the Phaeozem (cropland) soil, gene abundances of amoA indicated a niche differentiation between archaeal and bacterial ammonia oxidizers that distinctly separated the influence of the tree row from the crop row and monoculture system. Abundances of nitrate (napA and narG), nitrite (nirK and nirS) and nitrous oxide reductase genes (nosZ clade I) were largely influenced by soil type rather than management system. The soil types' effects were associated with their differences in soil organic C, total N and pH. Our findings show that in temperate regions, conversion of monoculture cropland and open grassland to agroforestry systems can alter the abundance of soil bacteria and fungi and soil-N-cycling genes, particularly genes involved in ammonium oxidation.
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  • Journal Article

    Species-Specific Conservation of Linear Antigenic Sites on Vaccinia Virus A27 Protein Homologs of Orthopoxviruses 

    Ahsendorf, Henrike; Gan, Li; Eltom, Kamal; Abd El Wahed, Ahmed; Hotop, Sven-Kevin; Roper, Rachel; Beutling, Ulrike; Broenstrup, Mark; Stahl-Hennig, Christiane; Hoelzle, Ludwig; et al.
    Czerny, Claus-Peter
    Viruses 2019; 11(6): Art. 493
    The vaccinia virus (VACV) A27 protein and its homologs, which are found in a large number of members of the genus Orthopoxvirus (OPXV), are targets of viral neutralization by host antibodies. We have mapped six binding sites (epitopes #1A: aa 32-39, #1B: aa 28-33, #1C: aa 26-31, #1D: 28-34, #4: aa 9-14, and #5: aa 68-71) of A27 specific monoclonal antibodies (mAbs) using peptide arrays. MAbs recognizing epitopes #1A-D and #4 neutralized VACV Elstree in a complement dependent way (50% plaque-reduction: 12.5-200 µg/mL). Fusion of VACV at low pH was blocked through inhibition of epitope #1A. To determine the sequence variability of the six antigenic sites, 391 sequences of A27 protein homologs available were compared. Epitopes #4 and #5 were conserved among most of the OPXVs, while the sequential epitope complex #1A-D was more variable and, therefore, responsible for species-specific epitope characteristics. The accurate and reliable mapping of defined epitopes on immuno-protective proteins such as the A27 of VACV enables phylogenetic studies and insights into OPXV evolution as well as to pave the way to the development of safer vaccines and chemical or biological antivirals.
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  • Journal Article

    Conventionalization of Organic Farms in Germany: An Empirical Investigation Based on a Composite Indicator Approach 

    Seidel, Claudia; Heckelei, Thomas; Lakner, Sebastian
    Sustainability 2019; 11(10): Art. 2934
    The term “conventionalization” of organic agriculture was created to depict the controversially discussed phenomenon that organic agriculture departs from the core organic principles on which it is based. We present an empirical, index-based approach to investigate developments of organic farming practices towards conventionalization. An index of conventionalization can be used as a monitoring tool to support policymakers to further develop agricultural regulations. We calculate composite indicators for three farm types: farms specialized on crop production, farms specialized on animal husbandry, and mixed farms. Principal component analysis serves to derive objective weights based on the correlations between indicators which then allow a linear aggregation to the composite indicator. Results show that developments towards conventionalization of the whole organic farming sector cannot be detected for German farms between 2000 and 2009. Therefore, we do not see the necessity for changes in regulation of the organic sector with regard to conventionalization.
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  • Journal Article

    Crop Diseases and Mycotoxin Accumulation in Temperate Agroforestry Systems 

    Beule, Lukas; Lehtsaar, Ena; Rathgeb, Anna; Karlovsky, Petr
    Sustainability 2019; 11(10): Art. 2925
    Background: Temperate agroforestry is regarded as a sustainable alternative to monoculture agriculture due to enhanced provisioning of ecosystem services. Plant health and food safety are crucial requirements for sustainable agriculture; however, studies of fungal diseases and mycotoxin contamination of crops grown under temperate agroforestry are lacking. This study therefore aimed to compare fungal colonization and mycotoxin contamination of crops grown in temperate agroforestry against conventional monoculture. Methods: The biomass of plant pathogenic fungi in oilseed rape plants and barley and wheat grain harvested in 2016 to 2018 at four paired agroforestry and monoculture sites was quantified using species-specific real-time PCR. Mycotoxin content of barley and wheat grain was determined by HPLC-MS/MS. Results: The colonization of oilseed rape plants with the vascular pathogen Verticillium longisporum and wheat grain with the head blight pathogen Fusarium tricinctum was lower in agroforestry than in conventional monoculture. Mycotoxin content of barley and wheat grain did not di er between agroforestry and monoculture systems and did not exceed the legal limits of the EU. Remarkably, fumonisin B1 was detected in wheat grains at two sites in two years, yet the low levels found do not raise food safety concerns. No di erences were found between the two production systems with regard to infection of wheat and barley grain with five Fusarium species (F. avenaceum, F. culmorum, F. graminearum, F. poae, and F. proliferatum) and oilseed rape with fungal pathogens Leptosphaeria biglobosa, Leptosphaeria maculans, and Sclerotinia sclerotiorum. Conclusions: Temperate agroforestry does not negatively a ect the infection of wheat, barley and oilseed rape with major fungal pathogens though it may suppress the infection of oilseed rape with V. longisporum and wheat grain with F. tricinctum. Furthermore, temperate agroforestry does not increase mycotoxin contamination of barley and wheat. Therefore, temperate agroforestry does not negatively a ect food safety.
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  • Journal Article

    The horse Y chromosome as an informative marker for tracing sire lines 

    Felkel, Sabine; Vogl, Claus; Rigler, Doris; Dobretsberger, Viktoria; Chowdhary, Bhanu P.; Distl, Ottmar; Fries, Ruedi; Jagannathan, Vidhya; Janečka, Jan E.; Leeb, Tosso; et al.
    Lindgren, GabriellaMcCue, MollyMetzger, JuliaNeuditschko, MarkusRattei, ThomasRaudsepp, TerjeRieder, StefanRubin, Carl-JohanSchaefer, RobertSchlötterer, ChristianThaller, GeorgTetens, JensVelie, BrandonBrem, GottfriedWallner, Barbara
    Scientific Reports 2019; 9(1): Art. 6095
    Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural breeds and nine Przewalski's horses. Among domestic horses we confirmed the predominance of a young'crown haplogroup' in Central European and North American breeds. Within the crown, we distinguished 58 haplotypes based on 211 variants, forming three major haplogroups. In addition to two previously characterised haplogroups, one observed in Arabian/Coldblooded and the other in Turkoman/Thoroughbred horses, we uncovered a third haplogroup containing Iberian lines and a North African Barb Horse. In a genealogical showcase, we distinguished the patrilines of the three English Thoroughbred founder stallions and resolved a historic controversy over the parentage of the horse 'Galopin', born in 1872. We observed two nearly instantaneous radiations in the history of Central and Northern European Y-chromosomal lineages that both occurred after domestication 5,500 years ago.
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  • Journal Article

    Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues 

    Steuernagel, Lukas; Meckbach, Cornelia; Heinrich, Felix; Zeidler, Sebastian; Schmitt, Armin O.; Gültas, Mehmet
    PLOS ONE 2019; 14(5): Art. e0216475
    Transcription factors (TFs) are a special class of DNA-binding proteins that orchestrate gene transcription by recruiting other TFs, co-activators or co-repressors. Their combinatorial interplay in higher organisms maintains homeostasis and governs cell identity by finely controlling and regulating tissue-specific gene expression. Despite the rich literature on the importance of cooperative TFs for deciphering the mechanisms of individual regulatory programs that control tissue specificity in several organisms such as human, mouse, or Drosophila melanogaster, to date, there is still need for a comprehensive study to detect specific TF cooperations in regulatory processes of cattle tissues. To address the needs of knowledge about specific combinatorial gene regulation in cattle tissues, we made use of three publicly available RNA-seq datasets and obtained tissue-specific gene (TSG) sets for ten tissues (heart, lung, liver, kidney, duodenum, muscle tissue, adipose tissue, colon, spleen and testis). By analyzing these TSG-sets, tissue-specific TF cooperations of each tissue have been identified. The results reveal that similar to the combinatorial regulatory events of model organisms, TFs change their partners depending on their biological functions in different tissues. Particularly with regard to preferential partner choice of the transcription factors STAT3 and NR2C2, this phenomenon has been highlighted with their five different specific cooperation partners in multiple tissues. The information about cooperative TFs could be promising: i) to understand the molecular mechanisms of regulating processes; and ii) to extend the existing knowledge on the importance of single TFs in cattle tissues.
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  • Journal Article

    The use of bat houses as day roosts in macadamia orchards, South Africa 

    Weier, Sina M.; Linden, Valerie M. G.; Grass, Ingo; Tscharntke, Teja; Taylor, Peter J.
    PeerJ 2019; 7: Art. e6954
    The loss of roost sites is one of the major drivers of the worldwide decline in bat populations and roost site preferences, either natural or artificially provided, are not well known for African bat species specifically. In this study we focus on the preference for different artificial roost sites by insectivorous bats in macadamia orchards in northern South Africa. From June 2016 to July 2017 we monitored 31 bat houses, mounted on poles in six macadamia orchards, for presence of bats or other occupants. Twentyone multi-chambered bat houses of three different designs were erected in sets of three. Additionally, five Rocket boxes, four bat houses in sets of two (painted black and white) and one colony bat house were erected. Bats were counted and visually identified to family or species level. From December 2016 to the end of March 2017 iButtons were installed to record and analyze temperature variation within one set of three bat houses. We related the occupancy of bat houses to the different types of houses and the environmental variables: distance to water, altitude and height of the bat houses above the ground. Overall bat house occupancy was significantly higher in the central bat house, in the set of three, and the black bat house, in the set of two. Mean temperatures differed between houses in the set of three with the central bat house having a significantly higher mean temperature than the houses flanking it. Our study might confirm previous assumptions that the microclimate of bat houses appears to be an important factor influencing occupancy. In conclusion, from the different bat houses tested in this study the designs we assume the warmest and best insulated attracted the most bats. Further research is needed on the preferred microclimate of different bat species, co-habitation within bat houses and the potential importance of altitude and distance to water. Our study provided little variation in both altitude and the distance to water.
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  • Journal Article

    Opportunities and Challenges in the Ethiopian Bamboo Sector: A Market Analysis of the Bamboo-Based Value Web 

    Lin, Jessie; Gupta, Saurabh; Loos, Tim; Birner, Regina
    Sustainability 2019; 11(6): Art. 1644
    Bamboo is one of the more important natural resources in Ethiopia and contributes to the bioeconomy as a potential source for high-value products. While the country is the largest producer of bamboo in Africa, the existing utilization of the bamboo sector in Ethiopia remains under-developed, with little value addition. This study identifies the current market challenges and opportunities for future developments of the northern Ethiopian bamboo sector, with a focus on the Injibara township. This research adopts the “value web” approach to assess the potentials of different product lines that create the bamboo biomass value web. We utilize qualitative data collection methods, in particular, semi-structured interviews and informal focus group discussions with key stakeholders. Our findings suggest that bamboo farmers in Injibara are constrained by a lack of local demand and market for bamboo products with high-value addition, leading to an absence of product diversification and innovation. Furthermore, there is an overreliance on foreign technology and methods that are poorly matched for local needs. We recommend that policymakers invest in targeted and effective training strategies on bamboo cultivation and processing. Furthermore, farmers can benefit from decreasing their reliance on middle men with cooperatives or contract arrangements.
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  • Journal Article

    A Comparison of Mainstream Genotyping Platforms for the Evaluation and Use of Barley Genetic Resources 

    Darrier, Benoit; Russell, Joanne; Milner, Sara G.; Hedley, Pete E.; Shaw, Paul D.; Macaulay, Malcolm; Ramsay, Luke D.; Halpin, Claire; Mascher, Martin; Fleury, Delphine L.; et al.
    Langridge, PeterStein, NilsWaugh, Robbie
    Frontiers in Plant Science 2019; 10: Art. 544
    We compared the performance of two commonly used genotyping platforms, genotyping-by-sequencing (GBS) and single nucleotide polymorphism-arrays (SNP), to investigate the extent and pattern of genetic variation within a collection of 1,000 diverse barley genotypes selected from the German Federal ex situ GenBank hosted at IPK Gatersleben. Each platform revealed equivalent numbers of robust bi-allelic SNPs (39,733 and 37,930 SNPs for the 50K SNP-array and GBS datasets respectively). A small overlap of 464 SNPs was common to both platforms, indicating that the methodologies we used selectively access informative polymorphism in different portions of the barley genome. Approximately half of the GBS dataset was comprised of SNPs with minor allele frequencies (MAFs) below 1%, illustrating the power of GBS to detect rare alleles in diverse germplasm collections. While desired for certain applications, the highly robust calling of alleles at the same SNPs across multiple populations is an advantage of the SNP-array, allowing direct comparisons of data from related or unrelated studies. Overall MAFs and diversity statistics (π) were higher for the SNP-array data, potentially reflecting the conscious removal of markers with a low MAF in the ascertainment population. A comparison of similarity matrices revealed a positive correlation between both approaches, supporting the validity of using either for entire GenBank characterization. To explore the potential of each dataset for focused genetic analyses we explored the outcomes of their use in genome-wide association scans for row type, growth habit and non-adhering hull, and discriminant analysis of principal components for the drivers of sub-population differentiation. Interpretation of the results from both types of analysis yielded broadly similar conclusions indicating that choice of platform used for such analyses should be determined by the research question being asked, group preferences and their capabilities to extract and interpret the different types of output data easily and quickly. Access to the requisite infrastructure for running, processing, analyzing, querying, storing, and displaying either datatype is an additional consideration. Our investigations reveal that for barley the cost per genotyping assay is less for SNP-arrays than GBS, which translates to a cost per informative datapoint being significantly lower for the SNP-array.
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  • Journal Article

    Reconciling Canopy Interception Parameterization and Rainfall Forcing Frequency in the Community Land Model for Simulating Evapotranspiration of Rainforests and Oil Palm Plantations in Indonesia 

    Fan, Yuanchao; Meijide, Ana; Lawrence, David M.; Roupsard, Olivier; Carlson, Kimberly M.; Chen, Hsin‐Yi; Röll, Alexander; Niu, Furong; Knohl, Alexander
    Journal of Advances in Modeling Earth Systems 2019; 11(3) p.732-751
    By mediating evapotranspiration processes, plant canopies play an important role in the terrestrial water cycle and regional climate. Substantial uncertainties exist in modeling canopy water interception and related hydrological processes due to rainfall forcing frequency selection and varying canopy traits. Here we design a new time interpolation method “zero” to better represent convective‐type precipitation in tropical regions. We also implement and recalibrate plant functional type‐specific interception parameters for rainforests and oil palm plantations, where oil palms express higher water interception capacity than forests, using the Community Land Model (CLM) versions 4.5 and 5.0 with CLM‐Palm embedded. Reconciling the interception scheme with realistic precipitation forcing produces more accurate canopy evaporation and transpiration for both plant functional types, which in turn improves simulated evapotranspiration and energy partitioning when benchmarked against observations from our study sites in Indonesia and an extensive literature review. Regional simulations for Sumatra and Kalimantan show that industrial oil palm plantations have 18–27% higher transpiration and 15–20% higher evapotranspiration than forests on an annual regional average basis across different ages or successional stages, even though the forests experience higher average precipitation according to reanalysis data. Our land‐only modeling results indicate that current oil palm plantations in Sumatra and Kalimantan use 15–20% more water (mean 220 mm or 20 Gt) per year compared to lowland rainforests of the same extent. The extra water use by oil palm reduces soil moisture and runoff that could affect ecosystem services such as productivity of staple crops and availability of drinking water in rural areas.
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  • Journal Article

    Insect and plant traits drive local and landscape effects on herbivory in grassland fragments 

    Rossetti, Maria Rosa; Rösch, Verena; Videla, Martín; Tscharntke, Teja; Batáry, Péter
    Ecosphere 2019; 10(5): Art. e02717
    Herbivory is one of the most important antagonistic insect–plant interactions and can be influenced by factors at local and landscape scales. Landscape fragmentation may reduce herbivory directly (i.e., decreasing abundance and species richness of herbivores), but also indirectly increase herbivory (i.e., releasing herbivores from top-down control). At a local scale, reduced plant diversity may enhance herbivory through lessened associated resistance, while resource availability (i.e., higher vegetation height and cover) may promote herbivory. Few studies have simultaneously considered the influence of local and landscape variables on insect herbivory. We evaluate effects of landscape (fragment size, connectivity, and arable land percentage) and local factors (plant cover and height and plant species richness) on insect herbivory in fragmented calcareous grasslands. Further, we ask whether these effects depend on feeding traits of herbivores (chewers vs. suckers) and habitat specialization of plants (specialists vs. generalists). Results show that herbivory was best explained by models including variables at both local and landscape scales. However, local factors were more important than landscape variables. Herbivory was in all cases positively related to height of herbs (i.e., taller and more heterogeneous food resources), whereas the effect of plant species richness varied with feeding traits of herbivores. Herbivory by chewers, which are commonly more generalist feeders, was negatively affected by plant species richness, supporting the idea of associated plant resistance. In contrast, herbivory by suckers, which tend to be more specialized, increased with plant richness. Although there was little influence of landscape scale, herbivory on specialist plants was significantly higher in smaller grasslands probably as a consequence of herbivore release from natural enemies. Functional redundancy among herbivore species would allow to maintain overall herbivory in fragmented calcareous grasslands. This study highlights the need to consider different herbivore and plant traits for a better understanding of herbivory responses to local and landscape factors.
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  • Journal Article

    The SYNBREED chicken diversity panel: a global resource to assess chicken diversity at high genomic resolution 

    Malomane, Dorcus K.; Simianer, Henner; Weigend, Annett; Reimer, Christian; Schmitt, Armin O.; Weigend, Steffen
    BMC Genomics. 2019 May 07;20(1):345
    Background Since domestication, chickens did not only disperse into the different parts of the world but they have also undergone significant genomic changes in this process. Many breeds, strains or lines have been formed and those represent the diversity of the species. However, other than the natural evolutionary forces, management practices (including those that threaten the persistence of genetic diversity) following domestication have shaped the genetic make-up of and diversity between today’s chicken breeds. As part of the SYNBREED project, samples from a wide variety of chicken populations have been collected across the globe and were genotyped with a high density SNP array. The panel consists of the wild type, commercial layers and broilers, indigenous village/local type and fancy chicken breeds. The SYNBREED chicken diversity panel (SCDP) is made available to serve as a public basis to study the genetic structure of chicken diversity. In the current study we analyzed the genetic diversity between and within the populations in the SCDP, which is important for making informed decisions for effective management of farm animal genetic resources. Results Many of the fancy breeds cover a wide spectrum and clustered with other breeds of similar supposed origin as shown by the phylogenetic tree and principal component analysis. However, the fancy breeds as well as the highly selected commercial layer lines have reduced genetic diversity within the population, with the average observed heterozygosity estimates lower than 0.205 across their breeds’ categories and the average proportion of polymorphic loci lower than 0.680. We show that there is still a lot of genetic diversity preserved within the wild and less selected African, South American and some local Asian and European breeds with the average observed heterozygosity greater than 0.225 and the average proportion of polymorphic loci larger than 0.720 within their breeds’ categories. Conclusions It is important that such highly diverse breeds are maintained for the sustainability and flexibility of future chicken breeding. This diversity panel provides opportunities for exploitation for further chicken molecular genetic studies. With the possibility to further expand, it constitutes a very useful community resource for chicken genetic diversity research.
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  • Journal Article

    Supplementing Tropical Cattle for Improved Nutrient Utilization and Reduced Enteric Methane Emissions 

    Ali; Wassie; Korir; Merbold; Goopy; Butterbach-Bahl; Dickhoefer; Schlecht
    Animals 2019; 9(5): Art. 210
    Given their high nitrogen (N) concentration and low costs, sweet potato vine silage (SPVS) and urea-molasses blocks (UMB) are recommended supplements for tropical regions; therefore, they were investigated in this study. Six heifers were allocated to three diets: the roughage diet (R) consisted of wheat straw (0.61) and Rhodes grass hay (0.39; on dry matter (DM) basis); R + SPVS combined R (0.81) and SPVS (0.19); and with R + UMB animals had access to UMB. During two experimental periods, feed intake, feces and urine excretion, digesta passage, and rumen microbial protein synthesis were determined during seven days and methane emissions during three days. There was no treatment effect (p > 0.05) on DM and N intake. Apparent DM digestibility of R + SPVS (510 g/kg) was higher (p < 0.05) than of R (474 g/kg). Digesta passage and duodenal microbial N flow were similar for all diets (p > 0.05), while N retention was highest with R + SPVS (p > 0.05). Methane emissions per unit of digested feed (g CH4/kg dDM) were lower (p < 0.05) for R + SPVS (55.2) than for R (64.7). Hence, SPVS supplementation to poor-quality roughage has the potential to increase diet digestibility and N retention while reducing CH4 emissions.
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  • Journal Article

    Selection Decisions and Trait Preferences for Local and Imported Cattle and Sheep Breeds in Peri-/Urban Livestock Production Systems in Ouagadougou, Burkina Faso 

    Roessler, Regina
    Animals 2019; 9(5): Art. 207
    BACKGROUND: Participatory approaches of designing livestock breeding programs for tropical production systems have been extensively applied for rural livestock, whereas the peri-/urban livestock production sector tends to be widely neglected. In order to ensure the viability of the commercial cattle and sheep production sector in Ouagadougou, Burkina Faso, structured breed improvement programs are needed. The study aims to better understand selection decisions of cattle and sheep breeders and their trait preferences for local and imported breeds. METHODS: 49 cattle and 31 sheep breeders in peri-/urban areas of the city were approached in personal interviews. Data were analyzed in R version 3.5.1. RESULTS: The main motivation for keeping cattle and sheep was to generate regular cash income through the selling of milk (cattle only) and surplus animals. Some (modern) breeders used imported breeds because of higher production performances. For imported cattle breeds, improved breeding technologies and management were applied to further enhance production outputs. Nevertheless, local livestock breeds were predominantly used due to their good adaptation. CONCLUSIONS: Selection decisions and trait preferences for local and imported cattle and sheep breeds were strongly based on performance traits. Especially sheep breeders, but also traditional cattle breeders, did not record performance traits and did not take conscious breeding decisions.
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  • Journal Article

    Energy expenditure and body temperature variations in llamas living in the High Andes of Peru 

    Riek, Alexander; Stölzl, Anna; Marquina Bernedo, Rodolfo; Ruf, Thomas; Arnold, Walter; Hambly, Catherine; Speakman, John R.; Gerken, Martina
    Scientific Reports 2019; 9(1): Art. 4037
    Some large herbivores exhibit seasonal adjustments in their energy metabolism. Therefore, our aim was to determine if the llama (one of the most extensively kept livestock breeds) exhibits seasonal adjustment of their energy expenditure, body temperature and locomotion, under its natural high altitude Andean habitat. For this purpose, energy expenditure, body temperature and locomotion were measured in seven non-pregnant llama dams for ten months on the Andean High Plateau (4400 m above sea level). Daily energy expenditure was measured as field metabolic rate using the doubly labelled water method at four different measurement times. Additionally, a telemetry system was used to continuously record activity, body temperature (3 min intervals) as well as the position (hourly) of each animal. The results show that llamas adjusted their body temperature and daily energy expenditure according to environmental conditions. Furthermore, llamas under high altitude Andean climatic conditions exhibited a pronounced daily rhythm in body temperature and activity, with low values at sunrise and increasing values towards sunset. Llamas also had remarkably low energy expenditure compared to other herbivores. Thus, despite the domestication process, llamas have not lost the ability to adjust their body temperature and daily energy expenditure under adverse environmental conditions, similar to some wild herbivores
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  • Journal Article

    Towards valuation of biodiversity in agricultural soils: A case for earthworms 

    Plaas, Elke; Meyer-Wolfarth, Friederike; Banse, Martin; Bengtsson, Jan; Bergmann, Holger; Faber, Jack; Potthoff, Martin; Runge, Tania; Schrader, Stefan; Taylor, Astrid
    Ecological Economics 2019; 159 p.291-300
    Soil biodiversity is deteriorating in Europe due to an on-going intensification of agriculture, climate change and food production supporting measures of the European Common Agricultural Policy (CAP). Nevertheless, the CAP tries to take biodiversity into account via proposing a range of agri-environmental measures. These ES contribute to food security, climate change mitigation, water retention and plant biomass growth. Healthy soils also help to prevent erosion, desertification, and landslides and to stabilise crop yields. The provision of ES by soil biota is a result of their impact on soil processes in interaction with soil conditions as well as soil management practices of the farmers such as tillage or crop rotations. Some taxa amongst soil biota play key roles in regulating soil processes. With respect to biocontrol of soil-borne pests, the earthworm species Lumbricus terrestris is known to play an important role in suppressing toxigenic plant pathogens, such as Fusarium culmorum and its mycotoxin deoxynivalenol (DON). We highlight the importance of earthworms for pest control to conceptualise and show how farmers' management practices influence soil ecosystem services and outline how this can be examined in a socio-ecological context by providing a concrete example of an economical evaluation of ES provided by earthworms.
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  • Journal Article

    Non-Synergistic Effect of Trichoderma harzianum and Glomus spp. in Reducing Infection of Fusarium Wilt in Banana 

    Castillo, Arfe; Puig, Cecirly; Cumagun, Christian
    Pathogens 2019; 8(2): Art. 43
    Philippine banana is currently threatened by Fusarium oxysporum f. sp. cubense Tropical Race 4 (FocR4). This study investigated the use of Trichoderma harzianum pre-treated with Glomus spp, as a means of managing Fusarium wilt on young 'Lakatan' banana seedlings. Results showed that Glomus applied basally significantly improved banana seedling growth with increased increment in plant height and pseudostem diameter and heavier root weight. The application of Glomus spp. alone offered 100% protection to the 'Lakatan' seedlings against FocR4 as indicated by the absence of the wilting symptom. A combination of T. harzianum and Glomus spp. also gave significant effect against Fusarium wilt through delayed disease progression in the seedlings but was not synergistic. Competitive effects were suspected when application of the two biological control agents on banana roots was done simultaneously.
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  • Journal Article

    Transcriptional Reprogramming of Arabidopsis thaliana Defence Pathways by the Entomopathogen Beauveria bassiana Correlates With Resistance Against a Fungal Pathogen but Not Against Insects 

    Raad, Maya; Glare, Travis R.; Brochero, Helena L.; Müller, Caroline; Rostás, Michael
    Frontiers in Microbiology 2019; 10: Art. 615
    The entomopathogenic fungus Beauveria bassiana can adopt an endophytic lifestyle by colonising a wide array of plant species. Beauveria-colonised plants can show enhanced resistance against insects and plant pathogens alike. However, little is known about the molecular and physiological mechanisms that govern such interactions. Here, we assessed the effects of two B. bassiana strains (BG11, FRh2) on the growth of Arabidopsis thaliana and its resistance against two herbivore species and a phytopathogen. Plant responses were studied on the transcriptomic and metabolic level using microarrays and by measuring changes in defence-related phytohormones and glucosinolates (GLSs). Root inoculation with B. bassiana BG11 significantly increased plant growth, while FRh2 had no such effect. Both Beauveria strains decreased leaf lesion area caused by the phytopathogen Sclerotinia sclerotiorum but did not affect population growth of the aphid Myzus persicae or the growth of Plutella xylostella caterpillars. Microarray analyses of leaves from endophyte-inoculated A. thaliana provided evidence for transcriptional reprogramming of plant defence pathways, with strain-specific changes in the expression of genes related to pathogenesis, phytoalexin, jasmonic (JA), and salicylic acid (SA) signalling pathways. However, B. bassiana colonisation did not result in higher concentrations of JA and SA or major changes in leaf GLS profiles. We conclude that the endophyte B. bassiana induces plant defence responses and hypothesise that these contribute to enhanced resistance against S. sclerotiorum.
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