Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025

Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity’s Aichi Target 13, signatories should ensure that “… the genetic diversity of … farmed and domesticated animals and of wild relatives … is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity.” However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorised into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g. socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organised in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterise genomic resources and its application to many non commercial and local breeds, hampering the consistent utilisation of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratisation of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development

Ohmic Heating for the dairy industry: a potential technology to develop probiotic dairy foods in association with modifications of whey protein structure

The use of whey in dairy probiotics is a topic of great interest to the scientific community and the food industries. However, few studies address the effect of ohmic heating (OH) on cell metabolism and growth parameters of probiotic microorganisms. Despite of this, OH under sub-lethal conditions presents promising results regarding the enhancement of growth rate and bacteriocin activity, leading to considerable improvements in the fermentation process. Thus, this review highlights the main findings and advances on the effect of OH on probiotic metabolism, while addressing the modification of whey protein structure as potential carrier of probiotic entities, aiming at stimulating interest and encouraging the development of functional products using OH.This work was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684) and by BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020 — Programa Operacional Regional do Norte. Pedro Santos is recipient of a fellowship supported by a doctoral advanced training (call NORTE-69-2015-15), funded by the European Social Fund under the scope of Norte2020 — Programa Operacional Regional do Norte. Ricardo Pereira is recipient of a fellowship supported by FCT (SFRH/BPD/81887/2011).info:eu-repo/semantics/publishedVersio

N2 Gas Flushing Limits the Rise of Antibiotic-Resistant Bacteria in Bovine Raw Milk during Cold Storage

Antibiotic resistance has been noted to be a major and increasing human health issue. Cold storage of raw milk promotes the thriving of psychrotrophic/psychrotolerant bacteria, which are well known for their ability to produce enzymes that are frequently heat stable. However, these bacteria also carry antibiotic resistance (AR) features. In places, where no cold chain facilities are available and despite existing recommendations numerous adulterants, including antibiotics, are added to raw milk. Previously, N-2 gas flushing showed real potential for hindering bacterial growth in raw milk at a storage temperature ranging from 6 to 25 degrees C. Here, the ability of N-2 gas (N) to tackle antibiotic-resistant bacteria was tested and compared to that of the activated lactoperoxidase system (HT) for three raw milk samples that were stored at 6 degrees C for 7 days. To that end, the mesophiles and psychrotrophs that were resistant to gentamycin (G), ceftazidime (Ce), levofloxacin (L), and trimethoprim-sulfamethoxazole (TS) were enumerated. For the log(10) ratio (which is defined as the bacterial counts from a certain condition divided by the counts on the corresponding control), classical Analyses of Variance (ANOVA) was performed, followed by a mean comparison with the Ryan-Einot-Gabriel-Welsch multiple range test (REGWQ). If the storage "time" factor was the major determinant of the recorded effects, cold storage alone or in combination with HT or with N promoted a sample-dependent response in consideration of the AR levels. The efficiency of N in limiting the increase in AR was highest for fresh raw milk and was judged to be equivalent to that of HT for one sample and superior to that of HT for the two other samples; moreover, compared to HT, N seemed to favor a more diverse community at 6 degrees C that was less heavily loaded with antibiotic multi-resistance features. Our results imply that N-2 gas flushing could strengthen cold storage of raw milk by tackling the bacterial spoilage potential while simultaneously hindering the increase of bacteria carrying antibiotic resistance/multi-resistance features.Peer reviewe

Extensive profiling of three varieties of Opuntia spp. fruit for innovative food ingredients

[EN] Consumer interest in the use of natural ingredients is creating a growing trend in the food industry, leading to research into the development of natural products such as colorants, antimicrobials and antioxidant compounds. This work involves an extensive morphological (using physico-chemical assays), chemical (antioxidant activity assays) and microbiological (Gram-positive and negative strains) characterization of prickly peras (Opuntia ficusindica (OFI) var. sanguigna, gialla and Opuntia engelmannii) fruits. Through chromatographic assays, these species have shown interesting contents of hydrophilic (sugars, organic acids and betalains) and lipophilic (tocopherols and fatty acids) compounds. While Opuntia engelmannii exhibited higher content of betacyanins and mucilage, OFI varieties sanguigna and gialla displayed greater organic acid content. The sanguigna variety also showed the highest ¿-tocopherol content. All this compounds could be the responsible of enhancing the bioactivity of this variety, which can be observed in its antimicrobial potential, tested in the studied strains too. Results revealed that Opuntia spp. could be used as a nutraceutical and/or food additive, maintaining and promoting health and life quality.The authors are grateful to the Foundation for Science and Technology (FCT, Portugal) and FEDER under Programme PT2020 for financial support to CIMO (UID/AGR/00690/2013) and L. Barros contract. This work is funded by the European Structural and Investment Funds (FEEI) through the Regional Operational Program North 2020, within the scope of Project NORTE-01-0145-FEDER-023289 (DeCodE) and ValorNatural (R). B. Melgar (No. 329930) also thanks CONACyT for his grant. The authors are grateful for a grant from the Serbian Ministry of Education, Sciences and Technological Development (no. 173032). The authors would also like to thank Dr. Carlos Aguiar for the botanical identification of these species.Melgar-Castañeda, B.; Pereira, E.; Oliveira, MBP.; Garcia-Castello, EM.; Rodríguez López, AD.; Sokovic, M.; Barros, L.... (2017). Extensive profiling of three varieties of Opuntia spp. fruit for innovative food ingredients. Food Research International. 101:259-265. https://doi.org/10.1016/j.foodres.2017.09.024S25926510

Assessing the utility of geospatial technologies to investigate environmental change within lake systems

Over 50% of the world's population live within 3. km of rivers and lakes highlighting the on-going importance of freshwater resources to human health and societal well-being. Whilst covering c. 3.5% of the Earth's non-glaciated land mass, trends in the environmental quality of the world's standing waters (natural lakes and reservoirs) are poorly understood, at least in comparison with rivers, and so evaluation of their current condition and sensitivity to change are global priorities. Here it is argued that a geospatial approach harnessing existing global datasets, along with new generation remote sensing products, offers the basis to characterise trajectories of change in lake properties e.g., water quality, physical structure, hydrological regime and ecological behaviour. This approach furthermore provides the evidence base to understand the relative importance of climatic forcing and/or changing catchment processes, e.g. land cover and soil moisture data, which coupled with climate data provide the basis to model regional water balance and runoff estimates over time. Using examples derived primarily from the Danube Basin but also other parts of the World, we demonstrate the power of the approach and its utility to assess the sensitivity of lake systems to environmental change, and hence better manage these key resources in the future

Interrogation of modern and ancient genomes reveals the complex domestic history of cattle

The analysis of mitochondrial and nuclear DNA sequence polymorphisms from modern cattle populations has had a profound impact on our understanding of the events surrounding the domestication of cattle. From these studies, it has been possible to distinguish between pre- and post-domestic genetic differentiation, supporting previous assertions from archaeological studies and, in some cases, revealing novel aspects of the demographic history of cattle. Analyses of genetic material retrieved from the remains of extinct ancestral wild cattle have also added valuable layers of information pertaining to cattle domestic origins; however, information from these investigations have, in general, been limited to small, variable portions of the mitochondrial genome owing to technical challenges associated with the retrieval and amplification of ancient DNA. In recent years, however, new high-throughput, massively parallel genomics technology platforms, such as single-nucleotide polymorphism (SNP) genotyping arrays and next-generation sequencing (NGS), have provided a new impetus to the studies of genetic variation in extant and ancient cattle. Arrays of SNP have facilitated high-resolution genetic surveys of global cattle populations and detection of ancient and recent genomic selective sweeps. Next-generation sequencing analyses of modern and ancient cattle hold great promise for identifying and cataloging of pre- and post-domestication patterns of genomic variation and correlating this with natural and artificial selection processes

Supercritical fluid extraction of fish oil from fish by-products: A comparison with other extraction methods

Fish and fish by-products are the main natural source of omega-3 polyunsaturated fatty acids, especially EPA (eicosapentaenoic acid) and DHA (docosahexaenoic acid), both of them with a great importance in the food and pharmaceutical industries. Comparing to conventional fish oil extraction processes such as cold extraction, wet reduction or enzymatic extraction, supercritical fluid extraction with carbon dioxide under moderate conditions (25 MPa and 313 K) may be useful for reducing fish oil oxidation, especially when fish oil is rich in omega-3 such as salmon oil, and the amount of certain impurities, such as some species of arsenic. Furthermore, taking profit of the advantages of supercritical carbon dioxide as extractive solvent, a coupled extraction-fractionation process is proposed as a way to remove free fatty acids and improve fish oil quality, alternatively to physical and chemical refining procedures.Ministry of Education and Science (CTQ2005-07301), Junta de Castilla y León (GR 167) and Pescanova S.A. (Spain

Land use conversion from peat swamp forest to oil palm agriculture greatly modifies microclimate and soil conditions

Oil palm (Elaeis guineensis) agriculture is rapidly expanding and requires large areas of land in the tropics to meet the global demand for palm oil products. Land cover conversion of peat swamp forest to oil palm (large- and small-scale oil palm production) is likely to have negative impacts on microhabitat conditions. This study assessed the impact of peat swamp forest conversion to oil palm plantation on microclimate conditions and soil characteristics. The measurement of microclimate (air temperature, wind speed, light intensity and relative humidity) and soil characteristics (soil surface temperature, soil pH, soil moisture, and ground cover vegetation temperature) were compared at a peat swamp forest, smallholdings and a large-scale plantation. Results showed that the peat swamp forest was 1.5–2.3 °C cooler with significantly greater relative humidity, lower light intensities and wind speed compared to the smallholdings and large-scale plantations. Soil characteristics were also significantly different between the peat swamp forest and both types of oil palm plantations with lower soil pH, soil and ground cover vegetation surface temperatures and greater soil moisture in the peat swamp forest. These results suggest that peat swamp forests have greater ecosystem benefits compared to oil palm plantations with smallholdings agricultural approach as a promising management practice to improve microhabitat conditions. Our findings also justify the conservation of remaining peat swamp forest as it provides a refuge from harsh microclimatic conditions that characterize large plantations and smallholdings

Quality Protein Maize Germplasm Characterized for Amino Acid Profiles and Endosperm Opacity

Quality protein maize (QPM) is improved over normal (non-QPM) maize in grain concentrations of the essential amino acids lysine and tryptophan. Quality protein maize has a long history as tropical adapted germplasm, but little effort has been made to incorporate temperate or sub-tropical germplasm for temperate adaptation and interactions between different modifier loci in these backgrounds are poorly understood. A design-II mating scheme including new temperate and subtropical lines produced 69 hybrids. Large hybrid genetic variation components resulted in substantial broad-sense heritability H2 estimates, specifically tryptophan (0.46) and endosperm opacity (0.82). A microbial assay for amino acid estimation proved robust across diverse environments with minimal genotype × environment (G×E) effects. Endosperm opacity had no G×E effects across both Texas and Iowa locations demonstrating stability for this trait. Endosperm opacity primarily followed an additive, midparent trend, with a few hybrids deviating from the trend (36%) suggesting a complex nature of multiple modifier loci across diverse germplasm. The top QPM hybrid outperformed the top commercial hybrid by 35 and 30% for lysine and tryptophan as a proportion of grain, respectively. QPM line Tx832 was a parent of top hybrids for lysine and tryptophan, and the highest noncommercial hybrids for methionine. Minimal correlations with yield and other traits suggest that future breeding should result in QPM hybrids with increasingly competitive yields