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David I, Ricard A. An improved transmissibility model to detect transgenerational transmitted environmental effects. Genet Sel Evol 2023; 55:66. [PMID: 37735633 PMCID: PMC10512618 DOI: 10.1186/s12711-023-00833-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/24/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Evolutionary studies have reported that non-genetic information can be inherited across generations (epigenetic marks, microbiota, cultural inheritance). Non-genetic information is considered to be a key element to explain the adaptation of wild species to environmental constraints because it lies at the root of the transgenerational transmission of environmental effects. The "transmissibility model" was proposed several years ago to better predict the transmissible potential of each animal by taking these diverse sources of inheritance into account in a global transmissible potential. We propose to improve this model to account for the influence of the environment on the global transmissible potential as well. This extension of the transmissibility model is the "transmissibility model with environment" that considers a covariance between transmissibility samplings of animals sharing the same environment. The null hypothesis of "no transmitted environmental effect" can be tested by comparing the two models using a likelihood ratio test (LRT). RESULTS We performed simulations that mimicked an experimental design consisting of two lines of animals with one exposed to a particular environment at a given generation. This enabled us to evaluate the performances of the transmissibility model with environment so as to detect and quantify transgenerational transmitted environmental effects. The power and the realized type I error of the LRT were compared to those of a T-test comparing the phenotype of the two lines, three generations after the environmental exposure for different sets of parameters. The power of the LRT ranged from 45 to 94%, whereas that of the T-test was always lower than 26%. In addition, the realized type I error of the T-test was 15% and that of the LRT was 5%, as expected. Variances, the covariance between transmissibility samplings, and path coefficients of transmission estimated with the transmissibility model with environment were close to their true values for all sets of parameters. CONCLUSIONS The transmissibility model with environment is effective in modeling vertical transmission of environmental effects.
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Affiliation(s)
- Ingrid David
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet Tolosan, France.
| | - Anne Ricard
- INRAE, AgroParisTech, GABI, Université Paris Saclay, 78350, Jouy-en-Josas, France
- Département Recherche et Innovation, Institut Français du Cheval et de l'équitation, 61310, Exmes, France
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Sharifian A, Gantuya B, Wario HT, Kotowski MA, Barani H, Manzano P, Krätli S, Babai D, Biró M, Sáfián L, Erdenetsogt J, Qabel QM, Molnár Z. Global principles in local traditional knowledge: A review of forage plant-livestock-herder interactions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 328:116966. [PMID: 36521222 DOI: 10.1016/j.jenvman.2022.116966] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 10/24/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
An understanding of traditional ecological knowledge systems is increasingly acknowledged as a means of helping to develop global, regional and national, but locally relevant policies. Pastoralists often use lands that are unsuitable for crops due to biophysical and climatic extremities and variabilities. Forage plants of pastures are utilized by herding communities by applying locally relevant multigenerational knowledge. We analyzed the forage-related knowledge of pastoralists and herders by reviewing scientific papers and video documentaries on forage plants and indicators, their use in land management, and plant-livestock interactions. Semi-structured interviews were also conducted with key knowledge holders in Iran, Mongolia, Kenya, Poland and Hungary. We found 35 indicators used by herders to describe forage species. The indicators described botanical features, livestock behavior during grazing, and the impact of plants on livestock condition and health. The indicators were used in context-specific management decisions, with a variety of objectives to optimize grazing. We identified ten global principles, including, among others, a livestock-centered perspective, close monitoring and targeted pasturing of various (preferred or avoided) forages, and the use of different livestock types and well-planned spatial movements at multiple scales to optimize the utilization of available plant resources. Although pastoralists vary greatly across the globe, the character and use of their traditional forage-related knowledge do seem to follow strikingly similar principles. Understanding these may help the local-to-global-level understanding of these locally specific systems, support bottom-up pastoral initiatives and discussions on sustainable land management, and help to develop locally relevant global and national policies.
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Affiliation(s)
- Abolfazl Sharifian
- Department of Rangeland and Watershed Management, Gorgan University of Agricultural Sciences and Natural Resources, 49138-15749, Gorgan, Iran; Centre for Ecological Research, Institute of Ecology and Botany, Vácrátót, Hungary; Global Change and Conservation Lab, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, PL 65, FI-00014, Helsinki, Finland.
| | - Batdelger Gantuya
- Centre for Ecological Research, Institute of Ecology and Botany, Vácrátót, Hungary; Botanic Garden and Research Institute, Mongolian Academy of Science, Ulaanbaatar, Mongolia
| | - Hussein T Wario
- Center for Research and Development in Drylands, Marsabit, Kenya
| | - Marcin Andrzej Kotowski
- Botanical Garden Center for Biological Diversity Conservation in Powsin, Polish Academy of Sciences, Warsaw, Poland
| | - Hossein Barani
- Department of Rangeland and Watershed Management, Gorgan University of Agricultural Sciences and Natural Resources, 49138-15749, Gorgan, Iran
| | - Pablo Manzano
- Global Change and Conservation Lab, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, PL 65, FI-00014, Helsinki, Finland; Helsinki Institute of Sustainability Science (HELSUS), Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; Basque Centre for Climate Change (BC3), 48940, Leioa, Spain; Ikerbasque - Basque Foundation of Science, Euskadi Plaza, 5, E-48009, Bilbao, Spain
| | - Saverio Krätli
- German Institute for Tropical and Subtropical Agriculture, Transdisciplinary and Social-Ecological Landuse Research (DITSL), Witzenhausen, Germany
| | - Dániel Babai
- Institute of Ethnology, Research Centre for the Humanities, Budapest, Hungary
| | - Marianna Biró
- Centre for Ecological Research, Institute of Ecology and Botany, Vácrátót, Hungary
| | - László Sáfián
- Traditional Hungarian Shepherd, Hajdúsámson, Hungary
| | | | | | - Zsolt Molnár
- Centre for Ecological Research, Institute of Ecology and Botany, Vácrátót, Hungary
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Azzaz F, Fantini J. The epigenetic dimension of protein structure. Biomol Concepts 2022; 13:55-60. [PMID: 35189052 DOI: 10.1515/bmc-2022-0006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/08/2022] [Indexed: 11/15/2022] Open
Abstract
Accurate prediction of protein structure is one of the most challenging goals of biology. The most recent achievement is AlphaFold, a machine learning method that has claimed to have solved the structure of almost all human proteins. This technological breakthrough has been compared to the sequencing of the human genome. However, this triumphal statement should be treated with caution, as we identified serious flaws in some AlphaFold models. Disordered regions are often represented by large loops that clash with the overall protein geometry, leading to unrealistic structures, especially for membrane proteins. In fact, AlphaFold comes up against the notion that protein folding is not solely determined by genomic information. We suggest that all parameters controlling the structure of a protein without being strictly encoded in its amino acid sequence should be coined "epigenetic dimension of protein structure." Such parameters include for instance protein solvation by membrane lipids, or the structuration of disordered proteins upon ligand binding, but exclude sequence-encoded sites of post-translational modifications such as glycosylation. In our view, this paradigm is necessary to reconcile two opposite properties of living systems: beyond rigorous biological coding, evolution has given way to a certain level of uncertainty and anarchy.
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Affiliation(s)
- Fodil Azzaz
- Department of Biology, Aix-Marseille Université and INSERM UMR_S 1072, Marseille, France
| | - Jacques Fantini
- Department of Biology, Aix-Marseille Université and INSERM UMR_S 1072, Marseille, France
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Bai X, Plastow GS. Breeding for disease resilience: opportunities to manage polymicrobial challenge and improve commercial performance in the pig industry. CABI AGRICULTURE AND BIOSCIENCE 2022; 3:6. [PMID: 35072100 PMCID: PMC8761052 DOI: 10.1186/s43170-022-00073-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/06/2022] [Indexed: 05/31/2023]
Abstract
Disease resilience, defined as an animal's ability to maintain productive performance in the face of infection, provides opportunities to manage the polymicrobial challenge common in pig production. Disease resilience can deliver a number of benefits, including more sustainable production as well as improved animal health and the potential for reduced antimicrobial use. However, little progress has been made to date in the application of disease resilience in breeding programs due to a number of factors, including (1) confusion around definitions of disease resilience and its component traits disease resistance and tolerance, and (2) the difficulty in characterizing such a complex trait consisting of multiple biological functions and dynamic elements of rates of response and recovery from infection. Accordingly, this review refines the definitions of disease resistance, tolerance, and resilience based on previous studies to help improve the understanding and application of these breeding goals and traits under different scenarios. We also describe and summarize results from a "natural disease challenge model" designed to provide inputs for selection of disease resilience. The next steps for managing polymicrobial challenges faced by the pig industry will include the development of large-scale multi-omics data, new phenotyping technologies, and mathematical and statistical methods adapted to these data. Genome editing to produce pigs resistant to major diseases may complement selection for disease resilience along with continued efforts in the more traditional areas of biosecurity, vaccination and treatment. Altogether genomic approaches provide exciting opportunities for the pig industry to overcome the challenges provided by hard-to-manage diseases as well as new environmental challenges associated with climate change.
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Affiliation(s)
- Xuechun Bai
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Graham S. Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
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Rosenberg E, Zilber-Rosenberg I. Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations. Microorganisms 2021; 10:microorganisms10010070. [PMID: 35056519 PMCID: PMC8780831 DOI: 10.3390/microorganisms10010070] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Microbiomes are transmitted between generations by a variety of different vertical and/or horizontal modes, including vegetative reproduction (vertical), via female germ cells (vertical), coprophagy and regurgitation (vertical and horizontal), physical contact starting at birth (vertical and horizontal), breast-feeding (vertical), and via the environment (horizontal). Analyses of vertical transmission can result in false negatives (failure to detect rare microbes) and false positives (strain variants). In humans, offspring receive most of their initial gut microbiota vertically from mothers during birth, via breast-feeding and close contact. Horizontal transmission is common in marine organisms and involves selectivity in determining which environmental microbes can colonize the organism's microbiome. The following arguments are put forth concerning accurate microbial transmission: First, the transmission may be of functions, not necessarily of species; second, horizontal transmission may be as accurate as vertical transmission; third, detection techniques may fail to detect rare microbes; lastly, microbiomes develop and reach maturity with their hosts. In spite of the great variation in means of transmission discussed in this paper, microbiomes and their functions are transferred from one generation of holobionts to the next with fidelity. This provides a strong basis for each holobiont to be considered a unique biological entity and a level of selection in evolution, largely maintaining the uniqueness of the entity and conserving the species from one generation to the next.
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Ramos C, Calus M, Schokker D. Persistence of functional microbiota composition across generations. Sci Rep 2021; 11:19007. [PMID: 34561474 PMCID: PMC8463531 DOI: 10.1038/s41598-021-98097-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/30/2021] [Indexed: 12/11/2022] Open
Abstract
Holobionts are defined as a host and its microbiota, however, only a fraction of the bacteria are inherited vertically and thus coevolve with the host. The "it's the song, not the singer" theory proposes that functional traits, instead of taxonomical microbiota composition, could be preserved across generations if interspecies interaction patterns perpetuate themselves. We tested conservation of functional composition across generations using zooplankton, mosquito, and plant datasets. Then, we tested if there is a change of functional microbiota composition over time within a generation in human datasets. Finally, we simulated microbiota communities to investigate if (pairwise) interactions can lead to multiple stable community compositions. Our results suggest that the vertically transmitted microbiota starts a predictable change of functions performed by the microbiota over time, whose robustness depends on the arrival of diverse migrants. This succession culminates in a stable functional composition state. The results suggest that the host-microbiota interaction and higher order interactions in general have an important contribution to the robustness of the final community. If the proposed mechanism proves to be valid for a diverse array of host species, this would support the concept of holobionts being used as units of selection, including animal breeding, suggesting this has a wider applicability.
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Affiliation(s)
- Christian Ramos
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
- Carrera de Biología, Facultad de Ciencias Puras Y Naturales, Universidad Mayor de San Andrés, Casilla 10077-Correo Central, La Paz, Bolivia
| | - Mario Calus
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Dirkjan Schokker
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.
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Caven AJ, Leung KG, Vinton C, Krohn B, Wiese JD, Salter J, Ranglack DH. A Behavioral Index for Assessing Bison Stress Level during Handling and Demographic Predictors of Stress Response. J APPL ANIM WELF SCI 2021; 25:41-53. [PMID: 34409908 DOI: 10.1080/10888705.2021.1963250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
There are an estimated half-a-million Plains Bison (Bison bison) present in North America in commercial and conservation herds. Most bison are rounded up and "worked" annually for parasite control, veterinarian attention, and processing, making it important to understand the impacts of these operations. Research indicates bison generally experience higher levels of stress than cattle during similar handling processes. However, most methods for assessing stress-level during working are invasive, increase handling time, and paradoxically increase stress levels. We designed a behavioral index to assess bison stress level during handling and used it to evaluate various predictors of stress response in a semi-wild bison herd. We examined how sex, age, herd of origin, previous experience, calf rearing, and body condition influenced bison stress response during working operations from 2015 to 2017. Our results indicate that stress level decreased with age and previous experience being worked through a particular facility. Additionally, herd of origin influenced stress level, indicating that stress response may have a genetic or epigenetic component. Our study provides an easily applicable tool for monitoring bison stress levels.
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Affiliation(s)
- Andrew J Caven
- Science Department, Platte River Whooping Crane Maintenance Trust Crane Trust, Wood River, NE, USA
| | - Katie G Leung
- Science Department, Platte River Whooping Crane Maintenance Trust Crane Trust, Wood River, NE, USA
| | - Clara Vinton
- Department Of Biology, University Of Nebraska At Kearney, Kearney, NE, USA
| | - Brice Krohn
- Science Department, Platte River Whooping Crane Maintenance Trust Crane Trust, Wood River, NE, USA
| | - Joshua D Wiese
- Science Department, Platte River Whooping Crane Maintenance Trust Crane Trust, Wood River, NE, USA
| | - Jacob Salter
- Science Department, Platte River Whooping Crane Maintenance Trust Crane Trust, Wood River, NE, USA
| | - Dustin H Ranglack
- Department Of Biology, University Of Nebraska At Kearney, Kearney, NE, USA
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David I, Aliakbari A, Déru V, Garreau H, Gilbert H, Ricard A. Inclusive inheritance for residual feed intake in pigs and rabbits. J Anim Breed Genet 2020; 137:535-544. [PMID: 32697021 PMCID: PMC7589229 DOI: 10.1111/jbg.12494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 05/14/2020] [Accepted: 06/13/2020] [Indexed: 01/15/2023]
Abstract
Non‐genetic information (epigenetic, microbiota, behaviour) that results in different phenotypes in animals can be transmitted from one generation to the next and thus is potentially involved in the inheritance of traits. However, in livestock species, animals are selected based on genetic inheritance only. The objective of the present study was to determine whether non‐genetic inherited effects play a role in the inheritance of residual feed intake (RFI) in two species: pigs and rabbits. If so, the path coefficients of the information transmitted from sire and dam to offspring would differ from the expected transmission factor of 0.5 that occurs if inherited information is of genetic origin only. Two pigs (pig1, pig2) and two rabbits (rabbit1, rabbit2) datasets were used in this study (1,603, 3,901, 5,213 and 4,584 records, respectively). The test of the path coefficients to 0.5 was performed for each dataset using likelihood ratio tests (null model: transmissibility model with both path coefficients equal to 0.5, full model: unconstrained transmissibility model). The path coefficients differed significantly from 0.5 for one of the pig datasets (pig2). Although not significant, we observed, as a general trend, that sire path coefficients of transmission were lower than dam path coefficients in three of the datasets (0.46 vs 0.53 for pig1, 0.39 vs 0.44 for pig2 and 0.38 vs 0.50 for rabbit1). These results suggest that phenomena other than genetic sources of inheritance explain the phenotypic resemblance between relatives for RFI, with a higher transmission from the dam's side than from the sire's side.
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Affiliation(s)
- Ingrid David
- GenPhySE, INRAE, INPT, ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Amir Aliakbari
- GenPhySE, INRAE, INPT, ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Vanille Déru
- GenPhySE, INRAE, INPT, ENVT, Université de Toulouse, Castanet Tolosan, France.,France Génétique Porc, Le Rheu Cedex, France
| | - Hervé Garreau
- GenPhySE, INRAE, INPT, ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Hélène Gilbert
- GenPhySE, INRAE, INPT, ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Anne Ricard
- Département Sciences du Vivant, GABI, INRAE, UMR 1313, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France.,Département Recherche et Innovation, Institut Français du Cheval et de l'Equitation, Exmes, France
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Genetic control of non-genetic inheritance in mammals: state-of-the-art and perspectives. Mamm Genome 2020; 31:146-156. [PMID: 32529318 PMCID: PMC7369129 DOI: 10.1007/s00335-020-09841-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022]
Abstract
Thought to be directly and uniquely dependent from genotypes, the ontogeny of individual phenotypes is much more complicated. Individual genetics, environmental exposures, and their interaction are the three main determinants of individual's phenotype. This picture has been further complicated a decade ago when the Lamarckian theory of acquired inheritance has been rekindled with the discovery of epigenetic inheritance, according to which acquired phenotypes can be transmitted through fertilization and affect phenotypes across generations. The results of Genome-Wide Association Studies have also highlighted a big degree of missing heritability in genetics and have provided hints that not only acquired phenotypes, but also individual's genotypes affect phenotypes intergenerationally through indirect genetic effects. Here, we review available examples of indirect genetic effects in mammals, what is known of the underlying molecular mechanisms and their potential impact for our understanding of missing heritability, phenotypic variation. and individual disease risk.
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