Evaluation Of Population-Varieties Developed Within A Wheat Participatory Breeding Program In France: Performances, Diversity, Stability And Adaptation

Modern agricultural systems rely on little crop genetic diversity, especially with the use of homogeneous varieties grown on large areas. However crop genetic diversity within fields is a lever for a more sustainable production, allowing for a greater stability through combined resistances to biotic and abiotic stress, and buffering environmental heterogeneity which characterizes organic systems. In France, a Participatory Plant Breeding (PPB) project has been applied on bread wheat since 2006 involving farmers and facilitators of the farmers' seed network Réseau Semences Paysannes and INRA researchers for the development of populations based on a decentralized selection in farmers' fields. This project leads to the development of heterogeneous populations whose intra-variety genetic diversity should allow them to adapt to farmers' practices and environments. We evaluated the agronomic behavior, genetic diversity, stability and local adaptation of ten populations developed within the PPB program compared to two commercial pure line varieties. Some populations had very interesting responses when considering grain yield, biomass production and protein content, and six of them were not significantly less productive than the two commercial varieties when comparing overall grain yield per population. While no clear evidence of local adaptation was detected, we found that populations' quality and in a lesser extent grain yield were more stable over years than that of commercial varieties. Protein content stability over time was positively correlated to genetic diversity with no significant drawback on protein production

Rare and low-frequency coding variants alter human adult height

Height is a highly heritable, classic polygenic trait with ~700 common associated variants identified so far through genome - wide association studies . Here , we report 83 height - associated coding variants with lower minor allele frequenc ies ( range of 0.1 - 4.8% ) and effects of up to 2 16 cm /allele ( e.g. in IHH , STC2 , AR and CRISPLD2 ) , >10 times the average effect of common variants . In functional follow - up studies, rare height - increasing alleles of STC2 (+1 - 2 cm/allele) compromise d proteolytic inhibition of PAPP - A and increased cleavage of IGFBP - 4 in vitro , resulting in higher bioavailability of insulin - like growth factors . The se 83 height - associated variants overlap genes mutated in monogenic growth disorders and highlight new biological candidates ( e.g. ADAMTS3, IL11RA, NOX4 ) and pathways ( e.g . proteoglycan/ glycosaminoglycan synthesis ) involved in growth . Our results demonstrate that sufficiently large sample sizes can uncover rare and low - frequency variants of moderate to large effect associated with polygenic human phenotypes , and that these variants implicate relevant genes and pathways

Cohort profile : demographic and clinical characteristics of the MILESTONE longitudinal cohort of young people approaching the upper age limit of their child mental health care service in Europe

Purpose: The presence of distinct child and adolescent mental health services (CAMHS) and adult mental health services (AMHS) impacts continuity of mental health treatment for young people. However, we do not know the extent of discontinuity of care in Europe nor the effects of discontinuity on the mental health of young people. Current research is limited, as the majority of existing studies are retrospective, based on small samples or used non-standardised information from medical records. The MILESTONE prospective cohort study aims to examine associations between service use, mental health and other outcomes over 24 months, using information from self, parent and clinician reports. Participants: Seven hundred sixty-three young people from 39 CAMHS in 8 European countries, their parents and CAMHS clinicians who completed interviews and online questionnaires and were followed up for 2 years after reaching the upper age limit of the CAMHS they receive treatment at. Findings to date: This cohort profile describes the baseline characteristics of the MILESTONE cohort. The mental health of young people reaching the upper age limit of their CAMHS varied greatly in type and severity: 32.8% of young people reported clinical levels of self-reported problems and 18.6% were rated to be ‘markedly ill’, ‘severely ill’ or ‘among the most extremely ill’ by their clinician. Fifty-seven per cent of young people reported psychotropic medication use in the previous half year. Future plans: Analysis of longitudinal data from the MILESTONE cohort will be used to assess relationships between the demographic and clinical characteristics of young people reaching the upper age limit of their CAMHS and the type of care the young person uses over the next 2 years, such as whether the young person transitions to AMHS. At 2 years follow-up, the mental health outcomes of young people following different care pathways will be compared. Trial registration number: NCT03013595

Whole-genome sequence-based analysis of thyroid function

Tiina Paunio on työryhmän UK10K Consortium jäsen.Normal thyroid function is essential for health, but its genetic architecture remains poorly understood. Here, for the heritable thyroid traits thyrotropin (TSH) and free thyroxine (FT4), we analyse whole-genome sequence data from the UK10K project (N = 2,287). Using additional whole-genome sequence and deeply imputed data sets, we report meta-analysis results for common variants (MAF >= 1%) associated with TSH and FT4 (N = 16,335). For TSH, we identify a novel variant in SYN2 (MAF = 23.5%, P = 6.15 x 10(-9)) and a new independent variant in PDE8B (MAF = 10.4%, P = 5.94 x 10(-14)). For FT4, we report a low-frequency variant near B4GALT6/ SLC25A52 (MAF = 3.2%, P = 1.27 x 10(-9)) tagging a rare TTR variant (MAF = 0.4%, P = 2.14 x 10(-11)). All common variants explain >= 20% of the variance in TSH and FT4. Analysis of rare variants (MAFPeer reviewe

Influence of experimental design on decentralized, on-farm evaluation of populations: a simulation study

International audienceParticipatory plant breeding (PPB) has received much attention in recent decades for its ability to develop varieties adapted to the diversity of farm conditions and to farmers' needs and practices. Specific methodological issues arise when working with on-farm experiments, one being the implementation of an experimental design that matches farmers' constraints and objectives, while allowing for accurate statistical analyses of the data. We took the example of a French PPB case on bread wheat, in which farmers, facilitators and researchers have co-constructed an experimental design that meets their needs, but is very unbalanced and required the development of Bayesian statistical models to compare populations on-farm, over environments and analyze their sensitivity to environments. Through a simulation study, we investigated the effects of different characteristics of the experimental design on the behavior of two of these Bayesian models to identify the range of values that are most appropriate and give recommendations for decentralized experiments. We analyzed the estimates obtained by the models using different simulated datasets that differed by the values of the experimental design's parameters. While within-environment population effects were well estimated even with few replicated controls, replicating populations of interest rather than controls within environments and including enough environments provided more power to detect significant differences. Population effects and sensitivities over environments were mainly impacted by the number of replications of populations across environments, therefore effort should be made to repeat populations in more environments if the aim is to characterize their behavior under various environmental conditions

The ESTMAP Project (Energy storage Mapping and Planning): focus on the subsurface data collection

International audienceThere is a strong link between energy security and the "2030 climate and energy framework" of European Commission. Reaching the goals of the "2030 framework" both efficiently and at the lowest possible costs for all is seen as a key step to address the energy security challenge in the long run. This requires elaboration of the framework for investments in renewables and energy efficiency. This planning has to be based on a robust and integrated set of data.As most data relevant to energy storage exists in a fragmented form, the major work in the ESTMAP project consists of compiling existing data in a unified database and exploiting it to optimise energy systems planning. Geologists, engineers and system modellers joined forces to define the format and the content of a database of both subsurface and above surface storage sites (existing, planned and potential). The idea is to ensure that the newly compiled dataset will fit the needs for robust modelling, planning and designing on a coherent basis and comparable among Member States and other European neighbouring countries. One of the project output consists of a geographical database providing information on distribution and expected capacity of existing and future energy storage sites in Europe, including costs and accessibility. Both subsurface storage options (hydrogen, compressed air, natural gas, underground pumped hydro, etc.) and above ground storages (pumped hydro, LNG, liquid air, etc.) are taken into account.In this project, BRGM, assisted by TNO, CGS and VITO, is in charge of data collection of subsurface energy storage. The objective of this task is to gather readily available and public data on existing and future potential storage sites. These data incorporate (1) the geographic location, description, characterization, subsurface properties and feasibility and capacity assessments of the subsurface reservoirs, as well as (2) the identification of known subsurface storage facilities attached to these reservoirs.A co-operation with European national geological institutions has been established. Co-operation agreements were concluded with members of EuroGeoSurveys and ENeRG groups. In countries not represented in these networks, national partners were contacted individually.The ESTMAP subsurface database populates data from EU member countries, the countries of the European Free Trade Association-EFTA (4 countries) and the Member of the Energy Community (8 countries). More than 920 sites spread around Europe have been identified during the subsurface data collection. Some of these have assessment information in term of proven, possible, probable, or assumed energy storages. All these data are forwarded for integration in the database to propose further modelling during the year 2016.ESTMAP project provides the opportunity to review the available public subsurface data in the European countries. The first encouraging results let open the possibility for further European cooperation in the next future

Sensory Analyses and Nutritional Qualities of Wheat Population Varieties Developed by Participatory Breeding

International audienceWheat is a staple food in many diets and is currently cultivated worldwide. It provides a large proportion of the daily energy intake and contributes to food balance. Changes in agro-industrial practices in the bread sector, from the field to bread-making, have led to an increase in chronic diseases and nutritional deficits, emphasizing the link between food and health. Several levers could be used to improve the nutritional quality of bread wheat. Organic farming, by avoiding the use of pesticides, might allow for greater consumption of wholegrain products. Breeding wheat cultivars with an enhanced mineral content may serve as another lever. In this context, the on-farm participatory plant-breeding of highly diversified varieties could provide promising resources. This study investigated the sensory and nutritional quality of nine population varieties resulting from a ten-year participatory plant-breeding process compared to two commercial pure-line varieties. Analysis of variance showed genotype effects for Mg and Zn concentration, so breeding for a high Mg and Zn concentration can reasonably be envisaged. Moreover, a positive correlation was found between plant height, peduncle height (distance between the Last Leaf and Spike (LLSD)) and nutrient content. Finally, as population varieties express more differences in their profile when grown in less fertile soils, these results emphasize the benefits of genetic diversity for diverse nutritional intake and sensory properties

SHiNeMaS: a web tool dedicated to seed lots history, phenotyping and cultural practices

Motivation: In 2005, researchers from the French National Research Institute for Agriculture, Food and Environment (Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, INRAE) started a collaboration with the French farmers' seed network Réseau Semences Paysannes (RSP) on bread wheat participatory breeding (PPB). The aims were: (1) to study on-farm management of crop diversity, (2) to develop population-varieties adapted to organic and low-inputs agriculture, (3) to co-develop tools and methods adapted to on-farm experiments. In this project, researchers and farmers' organizations needed to map the history and life cycle of the population-varieties using network formalism to represent relationships between seed lots. All this information had to be centralized and stored in a database. Results: We describe here SHiNeMaS (Seeds History and Network Management System) a web tool database. SHiNeMaS aims to provide useful interfaces to track seed lot history and related data (phenotyping, environment, cultural practices). Although SHiNeMaS has been developed in the context of a bread wheat participatory breeding program, the database has been designed to manage any kind and even multiple cultivated plant species. SHiNeMaS is available under Affero GPL licence and uses free technologies such as the Python language, Django framework or PostgreSQL database management system (DBMS). Conclusion: We developed SHiNeMaS, a web tool database, dedicated to the management of the history of seed lots and related data like phenotyping, environmental information and cultural practices. SHiNeMaS has been used in production in our laboratory for 5 years and farmers' organizations facilitators manage their own information in the system

Designing Innovative Management for Cultivated Biodiversity: Lessons from a Pioneering Collaboration between French Farmers, Facilitators and Researchers around Participatory Bread Wheat Breeding

International audienceThe industrialization of farming has significantly threatened cultivated biodiversity. Participatory breeding endeavours to overcome this issue by enabling farmers to select a wide range of crop varieties in different conditions, and to foster genetic mixing through seed exchanges, crosses or mixtures. This necessitates the design of new forms of coordination and organization for the farmers and partners involved. This article reports on an ongoing initiative, aiming to facilitate the participatory design of such forms of coordination and organization. It first outlines the method used (Knowledge-Concept-Proposals or KCP ®), and how it has been tailored to this highly decentralized context involving politically engaged actors on a quest for autonomy. It then presents the exploratory results of the first two workshops: these include group consolidation, the sharing of heterogeneous knowledge, the generation of innovative ideas, and the elaboration of preliminary projects. Finally, this empirical case is compared with other initiatives supporting the participatory design of natural resource management strategies and tools. Its key original dimensions and benefits are that the workshop protocol is replicable, the data produced can be easily exploited, and it allows for testing hypotheses in the field of design science

Genetic Diversity and Stability of Performance of Wheat Population Varieties Developed by Participatory Breeding

Modern agricultural systems rely on reduced crop genetic diversity, due in particular to the use of homogeneous elite varieties grown in large areas. However, genetic diversity within fields is a lever for a more sustainable production, allowing greater stability and resistance to biotic and abiotic stresses. In France, a Participatory Plant Breeding (PPB) project on bread wheat, involving farmers, facilitators and researchers, has led to the development of heterogeneous populations whose within-variety genetic diversity is expected to confer the ability to adapt to farmers’ practices and environments. We studied the stability and local adaptation of ten of these farmers’ populations as well as two commercial varieties in relation to their within-variety genetic diversity. Although no clear evidence of local adaptation was detected, we found that populations’ grain yield and protein content were more stable over space and time respectively than those of commercial varieties. Moreover, the varieties’ stability over time in terms of protein content was positively correlated with within-variety genetic diversity with no significant drawback on protein yield. These results demonstrate the wide adaptive potential of PPB populations, highlighting the importance of seed exchange networks for agrobiodiversity management and use. They emphasize the benefits of genetic diversity for stability over time, which is of great interest to farmers