Disinfection exhibits systematic impacts on the drinking water microbiome
Dai, Zihan ; Sevillano-Rivera, Maria C. ; Calus, Szymon T. ; Bautista-De Los Santos, Q.M. ; Eren, A.M. ; Wielen, Paul W.J.J. Van Der; Ijaz, Umer Z. ; Pinto, Ameet J. - \ 2020
Microbiome 8 (2020)1. - ISSN 2049-2618
Disinfection - Drinking water microbiome - Metagenomics - Selection
Limiting microbial growth during drinking water distribution is achieved either by maintaining a disinfectant residual or through nutrient limitation without using a disinfectant. The impact of these contrasting approaches on the drinking water microbiome is not systematically understood. We use genome-resolved metagenomics to compare the structure, metabolic traits, and population genomes of drinking water microbiome samples from bulk drinking water across multiple full-scale disinfected and non-disinfected drinking water systems. Microbial communities cluster at the structural- and functional potential-level based on the presence/absence of a disinfectant residual. Disinfectant residual alone explained 17 and 6.5% of the variance in structure and functional potential of the drinking water microbiome, respectively, despite including multiple drinking water systems with variable source waters and source water communities and treatment strategies. The drinking water microbiome is structurally and functionally less diverse and variable across disinfected compared to non-disinfected systems. While bacteria were the most abundant domain, archaea and eukaryota were more abundant in non-disinfected and disinfected systems, respectively. Community-level differences in functional potential were driven by enrichment of genes associated with carbon and nitrogen fixation in non-disinfected systems and γ-aminobutyrate metabolism in disinfected systems likely associated with the recycling of amino acids. Genome-level analyses for a subset of phylogenetically-related microorganisms suggests that disinfection selects for microorganisms capable of using fatty acids, presumably from microbial decay products, via the glyoxylate cycle. Overall, we find that disinfection exhibits systematic selective pressures on the drinking water microbiome and may select for microorganisms able to utilize microbial decay products originating from disinfection-inactivated microorganisms. [MediaObject not available: see fulltext.]
Effect of divergent selection for intramuscular fat content on muscle lipid metabolism in chickens
Liu, Lu ; Cui, Huanxian ; Xing, Siyuan ; Zhao, Guiping ; Wen, Jie - \ 2020
Animals 10 (2020)1. - ISSN 2076-2615
Chicken - Differential lipid metabolism - Intramuscular fat - Selection - Signaling pathway
Intramuscular fat (IMF)—an important factor affecting meat quality—can be appropriately increased by genetic selection. Chicken lines divergently selected for IMF content were used in this study to investigate the mechanisms behind differential IMF deposition. Sixty 15th generation chickens were genotyped using the IASCHICK 55K single nucleotide polymorphism (SNP) chip. After quality control, 59 chickens and 36,893 SNPs were available for subsequent analysis. Population structure assessment indicated that the lines were genetically differentiated. Based on the top 1% paired fixation index values, three pathways were significantly (p < 0.05) enriched, and nine genes were considered candidate genes for differential IMF deposition. Differences between the lines in the expressions of representative genes involved in the above pathways were detected in 16th generation chickens. This study suggests that genetic selection for increased IMF in the pectoralis major muscle may enhance fatty acid synthesis, transport, and esterification, and reduce triglyceride hydrolysis. The peroxisome proliferator-activated receptor (PPAR) signaling pathway, glycerolipid metabolism, and fatty acid degradation pathway may have contributed to the differences in IMF deposition between the lines. These results contribute to the understanding of the genetic mechanisms behind IMF deposition, and the improvement of chicken meat quality.
Optimizing selection of the reference population for genotype imputation from array to sequence variants
Butty, Adrien M. ; Sargolzaei, Mehdi ; Miglior, Filippo ; Stothard, Paul ; Schenkel, Flavio S. ; Gredler-Grandl, Birgit ; Baes, Christine F. - \ 2019
Frontiers in Genetics Livestock Genomics 10 (2019). - ISSN 1664-8021
Accuracy - Dairy cattle - Haplotypes - Imputation - Selection - Sequencing
Imputation of high-density genotypes to whole-genome sequences (WGS) is a cost-effective method to increase the density of available markers within a population. Imputed genotypes have been successfully used for genomic selection and discovery of variants associated with traits of interest for the population. To allow for the use of imputed genotypes for genomic analyses, accuracy of imputation must be high. Accuracy of imputation is influenced by multiple factors, such as size and composition of the reference group, and the allele frequency of variants included. Understanding the use of imputed WGSs prior to the generation of the reference population is important, as accurate imputation might be more focused, for instance, on common or on rare variants. The aim of this study was to present and evaluate new methods to select animals for sequencing relying on a previously genotyped population. The Genetic Diversity Index method optimizes the number of unique haplotypes in the future reference population, while the Highly Segregating Haplotype selection method targets haplotype alleles found throughout the majority of the population of interest. First the WGSs of a dairy cattle population were simulated. The simulated sequences mimicked the linkage disequilibrium level and the variants' frequency distribution observed in currently available Holstein sequences. Then, reference populations of different sizes, in which animals were selected using both novel methods proposed here as well as two other methods presented in previous studies, were created. Finally, accuracies of imputation obtained with different reference populations were compared against each other. The novel methods were found to have overall accuracies of imputation of more than 0.85. Accuracies of imputation of rare variants reached values above 0.50. In conclusion, if imputed sequences are to be used for discovery of novel associations between variants and traits of interest in the population, animals carrying novel information should be selected and, consequently, the Genetic Diversity Index method proposed here may be used. If sequences are to be used to impute the overall genotyped population, a reference population consisting of common haplotypes carriers selected using the proposed Highly Segregating Haplotype method is recommended.
Sephadex filtration as successful alternative to density-gradient centrifugation procedures for ram sperm selection with improved kinetics
Galarza, D.A. ; López-Sebastián, A. ; Woelders, H. ; Blesbois, E. ; Santiago-Moreno, J. - \ 2018
Animal Reproduction Science 192 (2018). - ISSN 0378-4320 - p. 261 - 270.
Centrifugation - Filtration - Gradients - Selection - Sperm
Density-gradients centrifugation (DGC) and filtration columns (FC) are used to separate deformed or dead sperm, debris, and other cells that may negatively affect the fertilizing capacity of sperm in fresh, chilled and frozen/thawed semen. The present study was conducted to evaluate the suitability of DGC (BoviPure®, Percoll® and Accudenz®) and FC (Sephadex G-15®) sperm selection procedures for fresh-extended and cold-stored ram semen by assessment of post-treatment sperm quality variables. Twenty normospermic ejaculates from ten adult Merino rams were used. Sperm concentration of recovered cells was greater (P < 0.001) after BoviPure treatment than other procedures in both fresh and cold semen. With the Sephadex method, there were more desirable values than with use of DGC procedures in several sperm motility variables measured by using the CASA system. In non-refrigerated semen samples, the percentage of progressive sperm motility (%PSM) after Sephadex filtration was greater (P < 0.05) than after BoviPure treatment; the straightline velocity (VSL) value after Sephadex filtration was greater (P < 0.01) than after Accudenz treatment; the amplitude of lateral head displacement (ALH) after Sephadex and Accudenz treatment was less than non-filtered semen (P < 0.001) and after Percoll (P < 0.01) and BoviPure (P < 0.05) treatments. In cold-stored semen samples, the %PSM after Sephadex filtration was greater than non-filtered (P < 0.05) semen and after BoviPure (P < 0.05), Percoll (P < 0.05) and Accudenz (P < 0.001) treatments. It is concluded that Sephadex column filtration can be used to select ram sperm in non-refrigerated and cooled semen, because percentage progressively motile sperm and some other sperm motility characteristics are greater with use of this techniques as compared with use of DGC methods.
Improving feed efficiency in fish using selective breeding : A review
Verdal, Hugues de; Komen, Hans ; Quillet, Edwige ; Chatain, Béatrice ; Allal, François ; Benzie, John A.H. ; Vandeputte, Marc - \ 2018
Reviews in Aquaculture 10 (2018)4. - ISSN 1753-5123 - p. 833 - 851.
Feed conversion ratio - Feed efficiency - Feed intake - Fish - Genetics - Selection
Improving feed efficiency (FE) is key to reducing production costs in aquaculture and to achieving sustainability for the aquaculture industry. Feed costs account for 30-70% of total production costs in aquaculture; much work has been done on nutritional and husbandry approaches to improve FE but only a limited amount of research has been devoted to using genetics, despite its potential. This paper reviews past work to improve FE in fish using selective breeding and assess future directions. Direct selection on FE traits requires methods to measure individual feed consumption and estimate FE efficiently and accurately. This is particularly difficult to do in fish because of the environment in which they live. Many of the published studies on FE were found to be inaccurate because of methodological problems. The relatively low heritability estimates of FE traits in fish published to date are probably partly as a result of inaccurate measurements of feed intake. Improving ways to measure the individual feed intake with high accuracy will be critical to the successful application of genetics to improving FE. Indirect selection criteria that could be used to improve FE (including growth after starvation/refeeding, body composition, neuropeptides or hormone levels) are discussed. Promising approaches to measuring feed intake accurately that may enable these studies to be undertaken are identified. More work using these will be needed prior to assessing the practicality of the introduction of direct or indirect traits for FE in fish genetic improvement programmes.
Genetic parameters for semen quality and quantity traits in five pig lines
Marques, D.B.D. ; Lopes, Marcos S. ; Broekhuijse, M.L.W.J. ; Guimarães, S.E.F. ; Kno, E.F. ; Bastiaansen, J.W.M. ; Silva, F. ; Lopes, Paulo S. - \ 2017
Journal of Animal Science 95 (2017)10. - ISSN 0021-8812 - p. 4251 - 4259.
Multiple-trait analysis - Pig - Selection - Semen - Variation analysis
We aimed to estimate genetic parameters for semen quality and quantity traits as well as for within-boar variation of these traits to evaluate their inclusion in breeding goals. Genetic parameters were estimated within line using a multiple-trait (4 × 4) repeatability animal model fitted for 5 pig lines, considering 4 semen traits: sperm motility (MOT), sperm progressive motility (PROMOT), log-transformed number of sperm cells per ejaculate (lnNcells), and total morphological abnormalities (ABN). The within-boar variation of these traits was analyzed based on a multiple-trait (2 × 2) approach for SD and average (AVG) and a single-trait analysis for CV. The average heritabilities across the 5 lines estimated by multiple-trait analysis were 0.18 ± 0.07 (MOT), 0.22 ± 0.08 (PROMOT), 0.16 ± 0.04 (lnNcells), and 0.20 ± 0.04 (ABN). The average genetic correlations were favorable between MOT and PROMOT (0.86 ± 0.10), between MOT and ABN (−0.66 ± 0.25), and between PROMOT and ABN (−0.65 ± 0.25). As determined by within-boar variation analysis, AVG exhibited the greatest heritabilities followed by SD and CV, respectively, for the traits MOT and ABN. For PROMOT, average SD heritability was lower than CV heritability, whereas for lnNcells, they were the same. The average genetic correlations between AVG and SD were favorable for MOT (−0.60 ± 0.13), PROMOT (−0.79 ± 0.14), and ABN (0.78 ± 0.17). The moderate heritabilities indicate the possibility of effective selection of boars based on semen traits. Average and SD are proposed as appropriate traits for selection regarding uniformity.
Response to selection in finite locus models with nonadditive effects
Esfandyari, Hadi ; Henryon, Mark ; Berg, Peer ; Thomasen, Jørn Rind ; Bijma, Piter ; Sørensen, Anders Christian - \ 2017
Journal of Heredity 108 (2017)3. - ISSN 0022-1503 - p. 318 - 327.
Finite locus model - Nonadditive effects - Selection
Under the finite-locus model in the absence of mutation, the additive genetic variation is expected to decrease when directional selection is acting on a population, according to quantitative-genetic theory. However, some theoretical studies of selection suggest that the level of additive variance can be sustained or even increased when nonadditive genetic effects are present. We tested the hypothesis that finite-locus models with both additive and nonadditive genetic effects maintain more additive genetic variance (VA) and realize larger medium-to long-term genetic gains than models with only additive effects when the trait under selection is subject to truncation selection. Four genetic models that included additive, dominance, and additive-by-additive epistatic effects were simulated. The simulated genome for individuals consisted of 25 chromosomes, each with a length of 1 M. One hundred bi-allelic QTL, 4 on each chromosome, were considered. In each generation, 100 sires and 100 dams were mated, producing 5 progeny per mating. The population was selected for a single trait (h2 = 0.1) for 100 discrete generations with selection on phenotype or BLUP-EBV. VA decreased with directional truncation selection even in presence of nonadditive genetic effects. Nonadditive effects influenced long-term response to selection and among genetic models additive gene action had highest response to selection. In addition, in all genetic models, BLUP-EBV resulted in a greater fixation of favorable and unfavorable alleles and higher response than phenotypic selection. In conclusion, for the schemes we simulated, the presence of nonadditive genetic effects had little effect in changes of additive variance and VA decreased by directional selection.
Darwinian evolution : Process or pattern?
Jagers op Akkerhuis, Gerard A.J.M. ; Spijkerboer, Hendrik Pieter ; Koelewijn, Hans Peter - \ 2016
In: Evolution and Transitions in Complexity: The Science of Hierarchical Organization in Nature / Jagers op Akkerhuis, Gerard A.J.M., Springer International Publishing Switzerland - ISBN 9783319438016 - p. 65 - 95.
Avolution - Darwin - Derivation - Evolution theory - Extended synthesis - Ontology - Selection
Darwinian evolution is a central tenet in biology. Conventionally, the defi nition of Darwinian evolution is linked to a population-based process that can be measured by focusing on changes in DNA/allele frequencies. However, in some publications it has been suggested that selection represents a state, not a process. If this is true any defi nition of Darwinian evolution that includes selection no longer can represent a process, because the ontological kind of selection is that of a state. There are other publications that also suggest that the concept of evolution needs a rethink, for example to deal with epigenetics, niche construction and horizontal DNA transfer. As a basis for contributing to both demands for re-conceptualisation, we will explore in this chapter whether or not the defi nition of the concept of Darwinian evolution can be defi ned in a stringent individual/object-based way, in terms of individual parents and their individual offspring, instead of in terms of populations of parents and offspring. The reason why we focus on an individual/ object-based approach is that this offers a basis for explicit descriptions of the objects involved and of the kinds of relationships between the objects, while a combination of these aspects offers a basis for decisions about which kind of over-all graph-pattern can be used for defi ning the concept of Darwinian evolution. Taking advantage of such possibilities, we suggest a graph-pattern for Darwinian evolution at the smallest scale. This smallest graph-pattern also offers a foundation for future scaling and extension. In the context of evolution, where everything seems prone to change, the pattern of Darwinian evolution at the smallest scale would also offer an unchanging core conceptualisation. We emphasise that the population viewpoint and the use of DNA/allele frequencies offer a solid and practical basis for calculations. In addition to this, we see theoretical reasons for the application of objectbased graph-patterns as a means to solve ambiguities about how Darwinian evolution can be defi ned conceptually.
To sing or not to sing : seasonal changes in singing vary with personality in wild great tits
Naguib, Marc ; Rooij, Erica P. van; Snijders, Lysanne ; Oers, Kees Van - \ 2016
Behavioral Ecology 27 (2016)3. - ISSN 1045-2249 - p. 932 - 938.
Aposematism - Color patterns - Evolution - Imperfect Batesian mimicry - Predator - Selection - Visual signals
Many putative Batesian mimics only approximately resemble their supposed models, and such "imperfect" mimics are readily distinguished from defended species by humans and other vertebrates. One explanation for the existence of imperfect mimics is that the most important predators of many mimics have very different sensory and cognitive abilities from those of a typical vertebrate. In such circumstances, selection for more accurate mimicry, as perceived by humans, may be reduced. Little is known, however, about how invertebrate predators perceive and respond to mimicry in insect prey. Here, we investigate the foraging behavior of the crab spider Synema globosum, an important predator of flower-visiting insects at our field site, which frequently encounters both Batesian mimics (hoverflies-Diptera: Syrphidae) and their models (bees and wasps-Hymenoptera). In the field, we found that spiders can distinguish among dipteran and hymenopteran prey taxa, frequently attacking some models and mimics, but avoiding others. Laboratory experiments suggest that some apparently accurate mimic taxa are more likely to be avoided when spiders have prior experience of an aversive wasp model. Avoidance by spiders of black and yellow striped artificial prey suggests visual cues play a role in prey selection, but there was no evidence that olfactory cues are used to identify dangerous or noxious species. Overall, our results provide some support for the hypothesis that invertebrate predator behavior can generate selection on visual signals in putative Batesian mimics.
Environmental impacts of genetic improvement of growth rate and feed conversion ratio in fish farming under rearing density and nitrogen output limitations
Besson, M. ; Aubin, J. ; Komen, H. ; Poelman, M. ; Quillet, E. ; Vandeputte, M. ; Arendonk, J.A.M. Van; Boer, I.J.M. De - \ 2016
Journal of Cleaner Production 116 (2016). - ISSN 0959-6526 - p. 100 - 109.
African catfish - Feed efficiency - Life cycle assessment - Recirculating aquaculture system - Selection - Thermal growth coefficient
Today, fish farming faces an increasing demand in fish products, but also various environmental challenges. Genetic improvement in growth rate and feed conversion ratio is known to be an efficient way to increase production and increase efficiency in fish farming. The environmental consequences of genetic improvement in growth rate and feed conversion ratio, however, are unknown. In this study, we investigated the environmental consequences of genetic improvement in growth rate and feed conversion ratio in an African catfish farm, using Recirculating Aquaculture System (RAS). In RAS, total fish production of the farm is limited by rearing density or by the capacity to treat dissolved nitrogen. To evaluate the environmental consequences of genetic improvement in growth rate and feed conversion ratio, we combined life cycle assessment and bioeconomic modelling of genetic response to selection. We explored different impact categories, such as climate change, eutrophication, acidification and energy use, and we expressed impacts per ton of fish produced. Results show that the environmental impact of genetic improvement in growth rate and feed conversion ratio varies among impact categories and depends on the factor limiting production at farm level (i.e. rearing density or nitrogen treatment capacity). Genetic improvement of feed conversion ratio reduces environmental impacts in each scenario tested, while improving growth rate reduces environmental impacts only when rearing density limits farm production. Environmental responses to genetic selection were generally positive and show similar trends as previously determined economic responses to genetic improvement in growth rate and feed conversion ratio in RAS. These results suggest that genetic improvement of growth rate and feed conversion ratio for species kept in RAS will benefit both the environmental impacts and the economics of the production system.
Artificial selection on introduced Asian haplotypes shaped the genetic architecture in european commercial pigs
Bosse, Mirte ; Soares Lopes, Marcos ; Madsen, Ole ; Megens, Hendrik Jan ; Crooijmans, Richard P.M.A. ; Frantz, Laurent A.F. ; Harlizius, Barbara ; Bastiaansen, John W.M. ; Groenen, Martien A.M. - \ 2015
Proceedings of the Royal Society. B: Biological Sciences 282 (2015)1821. - ISSN 0962-8452 - 9 p.
Adaptive introgression - Commercial breeding - Domestication - Hybridization - Selection - Sus scrofa
Early pig farmers in Europe importedAsian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds.We propose that the Asian variants are still present because they affect phenotypes thatwere important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes thatwere historically under selection.We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs.
Genetic improvement of percids
Blonk, R.J.W. ; Komen, J. - \ 2015
In: Biology and Culture of Percid Fishes / Kestemont, P., Dabrowski, K., Summerfelt, R.C., Springer Netherlands - ISBN 9789401772266 - p. 699 - 722.
Breeding programme - Genetics - Inbreeding - Percids - Selection
During the past years, breeding programs for aquaculture have shown fast development. Globally, economically highly relevant species have experienced implementation of large scale breeding programs and it is impossible to imagine life today without them as they significantly improve production and profitability of enterprises. However, there are still many aquatic species cultured that rely on wild broodstock and for which there is no breeding program. The reasons for not having breeding programs are diverse: The knowledge to execute a breeding program is often not available, and more importantly, breeding programs are considered expensive. Costs for separate family rearing systems, testing environments, extensive tagging etc. are often limiting. Farming of percids is a new sector where pioneering farmers have to develop rearing systems, reproduction methodology, fish feeds, etc., all at the same time. Especially in such cases, low-cost methods are required to get their business up and running. For this reason, many farms consider the foundation of a basic breeding program as their least concern, only to reduce costs. However, we argue that there are good reasons to start with selective breeding at the very start of an aquaculture enterprise. In the next chapters, the principles of selective breeding programs will be described. This includes a basic description of the concept of estimating the heritable components of the phenotypic appearance of fish. Next the most commonly used selection methods and their implication for percids will be discussed. The potential traits for selection that should be relevant in percid culture are reviewed. Some insights into the optimisation of breeding programs and an overview of basic breeding program management will be presented. We present an outline of how to maintain genetic diversity within cultured stocks, with a special focus on limiting rates of inbreeding while selecting. Finally, some insights on how to manage costs and benefits of breeding programs are discussed.
Detection of molecular signatures of selection at microsatellite loci in the South African abalone (Haliotis midae) using a population genomic approach
Rhode, Clint ; Vervalle, Jessica ; Bester-van der Merwe, Aletta E. ; Roodt-Wilding, Rouvay - \ 2013
Marine Genomics 10 (2013). - ISSN 1874-7787 - p. 27 - 36.
Adaptation - F-outlier - Linkage disequilibrium - Neutrality - Population genomics - Selection
Identifying genomic regions that may be under selection is important for elucidating the genetic architecture of complex phenotypes underlying adaptation to heterogeneous environments. A population genomic approach, using a classical neutrality test and various Fst-outlier detection methods was employed to evaluate genome-wide polymorphism data in order to identify loci that may be candidates for selection amongst six populations (three cultured and three wild) of the South African abalone, Haliotis midae. Approximately 9% of the genome-wide microsatellite markers were putatively subject to directional selection, whilst 6-18% of the genome is thought to be influenced by balancing selection. Genetic diversity estimates for candidate loci under directional selection was significantly reduced in comparison to candidate neutral loci, whilst candidate balancing selection loci demonstrated significantly higher levels of genetic diversity (Kruskal-Wallis test, P<0.05). Pairwise Fst estimates based on candidate directional selection loci also demonstrated increased levels of differentiation between study populations. Various candidate loci under selection showed significant inter-chromosomal linkage disequilibrium, suggesting possible gene-networks underling adaptive phenotypes. Furthermore, several loci had significant hits to known genes when performing BLAST searches to NCBI's non-redundant databases, whilst others are known to be derived from expressed sequences even though homology to a known gene could not be established. A number of loci also demonstrated relatively high similarity to transposable elements. The association of these loci to functional and genomically active sequences could in part explain the observed signatures of selection.