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Rempelos L, Wang J, Sufar EK, Almuayrifi MSB, Knutt D, Leifert H, Leifert A, Wilkinson A, Shotton P, Hasanaliyeva G, Bilsborrow P, Wilcockson S, Volakakis N, Markellou E, Zhao B, Jones S, Iversen PO, Leifert C. Breeding Bread-Making Wheat Varieties for Organic Farming Systems: The Need to Target Productivity, Robustness, Resource Use Efficiency and Grain Quality Traits. Foods 2023; 12:1209. [PMID: 36981136 PMCID: PMC10048768 DOI: 10.3390/foods12061209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/29/2023] [Accepted: 02/27/2023] [Indexed: 03/16/2023] Open
Abstract
Agronomic protocols (rotation, tillage, fertilization and crop protection) commonly used in organic and conventional crop production differ significantly and there is evidence that modern varieties developed for conventional high-input farming systems do not have the combination of traits required for optimum performance in organic farming systems. Specifically, there is evidence that prohibition on the use of water-soluble, mineral N, P and K fertilizers and synthetic pesticide inputs in organic farming results in a need to revise both breeding and selection protocols. For organic production systems, the focus needs to be on the following: (i) traits prioritized by organic farmers such as high nutrient use efficiency from organic fertilizer inputs, competitiveness against weeds, and pest and disease resistance, (ii) processing quality parameters defined by millers and bakers and (iii) nutritional quality parameters demanded by organic consumers. In this article, we review evidence from variety trials and factorial field experiments that (i) studied to what extent there is a need for organic farming focused breeding programs, (ii) investigated which traits/trait combinations should be targeted in these breeding programs and/or (iii) compared the performance of modern varieties developed for the conventional sector with traditional/older varieties favored by organic farmers and/or new varieties developed in organic farming focused breeding programs. Our review focuses on wheat because there have been organic and/or low-input farming focused wheat breeding programs for more than 20 years in Europe, which has allowed the performance of varieties/genotypes from organic/low-input and conventional farming focused breeding programs to be compared.
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York LM. Functional phenomics: an emerging field integrating high-throughput phenotyping, physiology, and bioinformatics. J Exp Bot 2019; 70:379-386. [PMID: 30380107 DOI: 10.1093/jxb/ery379] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 10/22/2018] [Indexed: 05/03/2023]
Abstract
The emergence of functional phenomics signifies the rebirth of physiology as a 21st century science through the use of advanced sensing technologies and big data analytics. Functional phenomics seeks to fill the significant knowledge gaps that still exist in the relationship of plant phenotype to function. Here, a general approach for the theory and practice of functional phenomics is outlined. The functional phenomics pipeline is proposed as a general method for conceptualizing, measuring, and validating utility of plant phenes, or elemental units of phenotype. The functional phenomics pipeline begins with ideotype development. Second, a phenotyping platform is developed to maximize the throughput of phene measurements. Target phenes and indicators of plant function, or performance, are measured in a mapping population. Forward genetics allows genetic mapping, while functional phenomics links phenes to plant performance. Based on these data, genotypes with contrasting phenotypes can be selected for smaller yet more intensive experiments to understand phene-environment interactions in depth. Simulation modeling is used to further understand the phenotypes, and all stages of the pipeline feed back to ideotype and phenotyping platform development. In total, functional phenomics represents an evolution of pre-existing disciplines, but the goals and unique methodologies constitute a novel research program.
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Picat MQ, Pellegrin I, Bitard J, Wittkop L, Proust-Lima C, Liquet B, Moreau JF, Bonnet F, Blanco P, Thiébaut R. Integrative Analysis of Immunological Data to Explore Chronic Immune T-Cell Activation in Successfully Treated HIV Patients. PLoS One 2017; 12:e0169164. [PMID: 28046052 PMCID: PMC5207686 DOI: 10.1371/journal.pone.0169164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/13/2016] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVES To unravel the complex relationships between cytomegalovirus-induced-, autoimmune-induced responses, microbial translocation and chronic immune activation (CIA) in successfully treated HIV-infected patients and to explore the mediating role of alpha-interferon in these processes. DESIGN Cross-sectional study nested in the ANRS CO3 Aquitaine Cohort, a prospective hospital-based cohort of HIV-1-infected patients in South-Western France. METHODS Patients initiated antiretroviral therapy between 2005 and 2008 and were treated with sustained virological suppression for at least two years. CIA was defined by the percentage of HLA-DR+/CD38+ among CD8+T-cells. Integrative analyses were performed using structural equation modelling (SEM). RESULTS The main analysis was performed in 57 HLA-A*0201 positive patients, due to availability of percentages of actin-, vimentin-, lamin-specific CD8+T-cells (HLA-A2-restricted tests) to further characterize autoimmune response. Cytomegalovirus-induced response was assessed by Quantiferon and pp-65 ELISPOT. SEM revealed a direct effect of cytomegalovirus-induced response on CIA (standardized estimate βstd = 0.56, p-value = 0.0004). The effect of autoimmune-induced response on CIA was indirect through alpha-interferon pathway, assessed by expression levels of 5 alpha-interferon-stimulated genes ADAR, ISG15, IFIT1, Mx1 and OAS1 (effect of autoimmune response on alpha-interferon: βstd = 0.36, p-value = 0.0401; effect of alpha-interferon on CIA: βstd = 0.39, p-value = 0.0044). There was no direct effect of autoimmune-induced response on CIA (p-value = 0.3169). Microbial translocation as measured by 16SrDNA and sCD14 in plasma was not associated with CIA. Results were consistent in 142 patients in whom cytomegalovirus and auto-immunity responses were measured by Quantiferon and anti-nuclear antibodies, respectively. All analyses performed in HLA-A*0201 positive patients and in the overall population revealed a significant effect of IFN-α latent variable on CIA. CONCLUSION The role of cytomegalovirus-induced response on CIA was confirmed as well as the involvement of alpha-interferon on CIA. The indirect effect of auto-immunity response on CIA revealed through the alpha-interferon pathway requires further investigation to confirm the potential role of auto-immunity for CIA in HIV-infected patients.
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Affiliation(s)
- Marie-Quitterie Picat
- Centre INSERM U1219 Bordeaux Population Health, Bordeaux, France
- Univ. Bordeaux, ISPED, Bordeaux, France
- Service d’Information Médicale, USMR, CHU de Bordeaux - Pôle de Santé Publique, Bordeaux, France
- INRIA, Team SISTM, Bordeaux, France
- Vaccine Research Institute-VRI, Hôpital Henri Mondor, Créteil, France
| | - Isabelle Pellegrin
- Laboratoire d’Immunologie-Immunogénétique, Pôle de Biologie, CHU Bordeaux, Bordeaux, France
| | - Juliette Bitard
- Laboratoire d’Immunologie-Immunogénétique, Pôle de Biologie, CHU Bordeaux, Bordeaux, France
| | - Linda Wittkop
- Centre INSERM U1219 Bordeaux Population Health, Bordeaux, France
- Univ. Bordeaux, ISPED, Bordeaux, France
- Service d’Information Médicale, USMR, CHU de Bordeaux - Pôle de Santé Publique, Bordeaux, France
- INRIA, Team SISTM, Bordeaux, France
| | - Cécile Proust-Lima
- Centre INSERM U1219 Bordeaux Population Health, Bordeaux, France
- Univ. Bordeaux, ISPED, Bordeaux, France
| | - Benoît Liquet
- Laboratoire de Mathématiques et de leurs Applications, Université de Pau et des Pays de l’Adour, UMR CNRS 5142, Pau, France
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology (QUT), Brisbane, Australia
| | - Jean-François Moreau
- Laboratoire d’Immunologie-Immunogénétique, Pôle de Biologie, CHU Bordeaux, Bordeaux, France
- Univ. Bordeaux, Bordeaux, France
- CNRS, UMR 5164, Bordeaux, France
| | - Fabrice Bonnet
- Centre INSERM U1219 Bordeaux Population Health, Bordeaux, France
- Univ. Bordeaux, Bordeaux, France
- Service de Médecine Interne et maladies Infectieuses, CHU de Bordeaux, Bordeaux, France
| | - Patrick Blanco
- Laboratoire d’Immunologie-Immunogénétique, Pôle de Biologie, CHU Bordeaux, Bordeaux, France
- Univ. Bordeaux, Bordeaux, France
- CNRS, UMR 5164, Bordeaux, France
| | - Rodolphe Thiébaut
- Centre INSERM U1219 Bordeaux Population Health, Bordeaux, France
- Univ. Bordeaux, ISPED, Bordeaux, France
- Service d’Information Médicale, USMR, CHU de Bordeaux - Pôle de Santé Publique, Bordeaux, France
- INRIA, Team SISTM, Bordeaux, France
- Vaccine Research Institute-VRI, Hôpital Henri Mondor, Créteil, France
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Jenkins SN, Murphy DV, Waite IS, Rushton SP, O'Donnell AG. Ancient landscapes and the relationship with microbial nitrification. Sci Rep 2016; 6:30733. [PMID: 27480661 PMCID: PMC4969748 DOI: 10.1038/srep30733] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/06/2016] [Indexed: 11/09/2022] Open
Abstract
Ammonia oxidizing archaea (AOA) and bacteria (AOB) drive nitrification and their population dynamics impact directly on the global nitrogen cycle. AOA predominate in the majority of soils but an increasing number of studies have found that nitrification is largely attributed to AOB. The reasons for this remain poorly understood. Here, amoA gene abundance was used to study the distribution of AOA and AOB in agricultural soils on different parent materials and in contrasting geologic landscapes across Australia (n = 135 sites). AOA and AOB abundances separated according to the geologic age of the parent rock with AOB higher in the more weathered, semi-arid soils of Western Australia. AOA dominated the younger, higher pH soils of Eastern Australia, independent of any effect of land management and fertilization. This differentiation reflects the age of the underlying parent material and has implications for our understanding of global patterns of nitrification and soil microbial diversity. Western Australian soils are derived from weathered archaean laterite and are acidic and copper deficient. Copper is a co-factor in the oxidation of ammonia by AOA but not AOB. Thus, copper deficiency could explain the unexpectedly low populations of AOA in Western Australian soils.
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Affiliation(s)
- Sasha N Jenkins
- Soil Biology and Molecular Ecology Group, School of Earth and Environment and the Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Daniel V Murphy
- Soil Biology and Molecular Ecology Group, School of Earth and Environment and the Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Ian S Waite
- Soil Biology and Molecular Ecology Group, School of Earth and Environment and the Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Steven P Rushton
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, England, UK
| | - Anthony G O'Donnell
- Soil Biology and Molecular Ecology Group, School of Earth and Environment and the Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
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Reid WDK, Close AJ, Humphrey S, Chaloner G, Lacharme-Lora L, Rothwell L, Kaiser P, Williams NJ, Humphrey TJ, Wigley P, Rushton SP. Cytokine responses in birds challenged with the human food-borne pathogen Campylobacter jejuni implies a Th17 response. R Soc Open Sci 2016; 3:150541. [PMID: 27069644 PMCID: PMC4821255 DOI: 10.1098/rsos.150541] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/16/2016] [Indexed: 05/25/2023]
Abstract
Development of process orientated understanding of cytokine interactions within the gastrointestinal tract during an immune response to pathogens requires experimentation and statistical modelling. The immune response against pathogen challenge depends on the specific threat to the host. Here, we show that broiler chickens mount a breed-dependent immune response to Campylobacter jejuni infection in the caeca by analysing experimental data using frequentist and Bayesian structural equation models (SEM). SEM provides a framework by which cytokine interdependencies, based on prior knowledge, can be tested. In both breeds important cytokines including pro-inflammatory interleukin (IL)-1β, , IL-4, IL-17A, interferon (IFN)-γ and anti-inflammatory IL-10 and transforming growth factor (TGF)-β4 were expressed post-challenge. The SEM revealed a putative regulatory pathway illustrating a T helper (Th)17 response and regulation of IL-10, which is breed-dependent. The prominence of the Th17 pathway indicates the cytokine response aims to limit the invasion or colonization of an extracellular bacterial pathogen but the time-dependent nature of the response differs between breeds.
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Affiliation(s)
- William D. K. Reid
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne NE1 7RU, UK
| | - Andrew J. Close
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne NE1 7RU, UK
| | - Suzanne Humphrey
- Department of Infection Biology, Institute of Global Health, University of Liverpool, Leahurst Campus, Neston, Chester CH64 7TE, UK
| | - Gemma Chaloner
- Department of Infection Biology, Institute of Global Health, University of Liverpool, Leahurst Campus, Neston, Chester CH64 7TE, UK
| | - Lizeth Lacharme-Lora
- Department of Infection Biology, Institute of Global Health, University of Liverpool, Leahurst Campus, Neston, Chester CH64 7TE, UK
| | - Lisa Rothwell
- The Roslin Institute and Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Pete Kaiser
- The Roslin Institute and Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Nicola J. Williams
- Department of Epidemiology and Population Health, Institute of Global Health, University of Liverpool, Leahurst Campus, Neston, Chester CH64 7TE, UK
| | - Tom J. Humphrey
- College of Medicine, Swansea University, Singleton Park, Swansea SA2 8PP, UK
| | - Paul Wigley
- Department of Infection Biology, Institute of Global Health, University of Liverpool, Leahurst Campus, Neston, Chester CH64 7TE, UK
| | - Stephen P. Rushton
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne NE1 7RU, UK
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