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SCIENTIFIC PAPERS

To find the references of the scientific papers of the SPECIFICS project , it's here !

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HAL : Dernières publications

  • [hal-05470145] Les lég-lumineuses - Des graines riches en protéines qui font pousser l'avenir (présentation des projets SPECIFICS et LETSPROSEED)

    Présentation des projets de recherche (ANR) SPECIFICS et LETSPROSEED qui unissent leurs forces pour développer la production et la consommation des légumineuses à graines comme le pois, la féverole et le soja., afin de devenir des piliers d’une agriculture et d’une alimentation durables. SPECIFICS vise à concevoir des systèmes de culture sans pesticide, en mobilisant la diversité biologique, de nouvelles sources de résistance et des leviers agroécologiques pour renforcer la résilience des cultures et leur valorisation économique. LETSPROSEED tend à améliorer le rendement, la qualité et la transformation des graines de légumineuses pour développer des ingrédients et aliments riches en protéines végétales. Du sol à l’assiette, les légumineuses sèment l’avenir !

    ano.nymous@ccsd.cnrs.fr.invalid (Sandie Barbot) 21 Jan 2026

    https://hal.science/hal-05470145v1
  • [hal-05421240] Comparative genomic analysis of QTL for resistance to Aphanomyces euteiches between pea, lentil, faba bean, and the model species Medicago truncatula

    Key message: QTL mapping and GWAS detected resistance QTL to Aphanomyces euteiches in faba bean, lentil, and Medicago truncatula. Weak genomic conservation between resistance QTL was identified between these legumes and pea. Abstract: QTL mapping and GWAS detected resistance QTL to Aphanomyces euteiches in faba bean, lentil, and Medicago truncatula. Weak genomic conservation between resistance QTL was identified between these legumes and pea. Aphanomyces root rot, caused by Aphanomyces euteiches, is a damaging disease affecting various legume species. Quantitative trait loci (QTL) for partial resistance have been mainly identified in pea, and to a lesser extent in lentil and Medicago truncatula. This study aimed to identify novel resistance loci from available lentil and faba bean populations, and examine genomic conservation of resistance QTL across legume host species. QTL mapping in the Pop2 faba bean recombinant inbred line (RIL) population and genome-wide association study (GWAS) in the AGILE lentil diversity panel were performed for resistance to A. euteiches under controlled conditions, using genotyping data previously reported. A previous QTL mapping in the LR3 M. truncatula RIL population was updated using 1,536 new SNPs (single-nucleotide polymorphisms). Synteny between resistance QTL to A. euteiches was analyzed based on gene orthology in QTL regions projected onto genomes, using the OrthoLegKB graph database. Four loci, including a major-effect QTL on chromosome 3, Ae-Vf3.1, were associated with resistance in faba bean. In lentil, six minor-effect GWAS-SNPs and two favorable haplotypes at Ae-Lc1.1 and Ae-Lc2.1 loci were identified. Updated analyses in M. truncatula narrowed to 8 Kb the interval of the major-effect locus AER1 and revealed three candidate genes. No synteny between major-effect QTL, detected in this study or previously reported in the literature, was identified across grain legume genomes. These results pave the way for translational genomics approaches facilitating resistance gene discovery and for resistance QTL deployment strategies in legume rotations to preserve their durability.

    ano.nymous@ccsd.cnrs.fr.invalid (Théo Leprévost) 17 Dec 2025

    https://hal.science/hal-05421240v1
  • [hal-05372385] Processus biologiques par lesquels les couverts régulent les adventices ?

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    ano.nymous@ccsd.cnrs.fr.invalid (Cordeau, S.) 19 Nov 2025

    https://hal.inrae.fr/hal-05372385v1
  • [hal-05373048] Faut-il maximiser la diversité des espèces de couverts pour améliorer la régulation des adventices ?

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    ano.nymous@ccsd.cnrs.fr.invalid (Cordeau, S.) 19 Nov 2025

    https://hal.inrae.fr/hal-05373048v1
  • [hal-05372415] Adapter la densité de semis à la date de semis des couverts pour maximiser la biomasse à destruction : Vesce velue

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    ano.nymous@ccsd.cnrs.fr.invalid (Cordeau, S.) 19 Nov 2025

    https://hal.inrae.fr/hal-05372415v1
  • [hal-05372438] Effets intentionnels et non-intentionnels des techniques de destruction des couverts ?

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    ano.nymous@ccsd.cnrs.fr.invalid (Cordeau, S.) 19 Nov 2025

    https://hal.inrae.fr/hal-05372438v1
  • [hal-05232413] How contracting in the value chain can reduce farmer's exposure to risks and enhance crop diversification ? A case study approach in the crop sector in France

    Marketing contracts are widely used to organise the exchanges in minor crop value chains facing uncertainty. In this study, we investigate how this vertical coordination tool can incentivize farmers to adopt grain-legumes in their crop rotations by transferring part the production and market risks to downstream firms. The risk transfer mechanism is analysed using a methodology based on surveys of chain of agents involved in a given value chain. We examine 5 case studies based on the type of legume and the organisation of the value chain. The results show that the payment system, the design of the contracts and the material and immaterial resources reinforced by the relationship between farmers and downstream firms, especially technical knowledge resources, contribute to reduce farmer’s exposure to risks and favour the development of the legume value chain, which is key for the agro-ecological transition.

    ano.nymous@ccsd.cnrs.fr.invalid (Auguste Bréavoine) 01 Sep 2025

    https://hal.inrae.fr/hal-05232413v1
  • [hal-05265454] GWASpipe: a Nexflow pipeline for GWAS analyses incorporating quality control

    Genome-wide association studies (GWAS) are powerful tools to link genetic variants with phenotypic traits. However, running GWAS involves several complex steps, including VCF preprocessing, quality control, population structure and relatedness correction, and selecting the right statistical models. We developed GWASpipe, an easy-to-use and automated pipeline to make GWAS more accessible, especially for non-expert users. GWASpipe is built with Nextflow[1] and follows nf-core standards. All tools are packaged in Singularity containers, ensuring reproducibility and easy deployment on any computing system. The pipeline includes :Data quality control, Filtering of low-quality variants and individuals, Population structure analysis, Kinship calculation, Association testing using two R packages (MM4LMM[2] et GAPIT[3] )

    ano.nymous@ccsd.cnrs.fr.invalid (Sophia Marguerit) 17 Sep 2025

    https://hal.inrae.fr/hal-05265454v1
  • [hal-05148951] Reducing risks of crop diversification for the agroecological transition, is contracting in the value chain a part of the solution?

    The sustainability transition in the agri-food sector remains understudied (e.g. Vermunt et al., 2020). A key challenge is crop diversification, which implies a shift from a system dependent on a few major species (like cereals) to one based on many species (including legumes such as chickpeas, lentils, etc.), together with a reorganisation of the value chain, which implies the creation of niche markets, often regulated by contracts between farmers and their first buyer (Adjemian et al., 2016). In addition, low investment in this sector in the past led to a lock-in situation with lack of knowledge, higher yield variability and few outlets (Magrini et al., 2016). Such transformation creates uncertainty and new risks, especially for farmers, including production risks, which require technical knowledge and innovation, and market risks, such as fluctuations in quantity, quality and prices. New organisational arrangements in value chains with farmers, such as production contracts --- pre-planting commitments that fix a quantity, price formulas and technical requirements --- could address uncertainty and develop niche innovation in legumes crops (Cholez and Magrini, 2023). However, whether the governance of exchanges through such contracts could also increase farmers’ innovative capacity to adopt more sustainable practices remains an open question. Additionally, looking at the way the agricultural trade with farmers is structured is also important because market arrangements are major structural dimension of tensions and conflicts within value chains. Our study builds on Cholez and Magrini (2023) initial findings, which highlight the role of production contracts in fostering dialogue, trust, knowledge sharing and learning, which are key to mitigating tensions and conflicts (Andersen et al., 2023). We explore how this vertical coordination tool can support a collective risk management strategy in the French legume sector, and reduce tensions and conflicts within value chains. Our hypothesis is that, while production contracts are primarily designed to secure supply for buyers, they also strengthen trust and collective commitment to sustainable practices, because the contractual design could allow for a risk-sharing mechanism that benefits all parties involved in the long run by reducing opportunism. This encourages investment in both material and human resources needed to sustainably change of the production practices on farms and in processing plants. We developed an original analytical framework based on the economic literature on agricultural risks and contracts (e.g. Hardaker et al., 2004; Roussy et al., 2018, Vavra 2008), combined with the literature on transition studies, in particular on the role of niche innovations (e.g. Smith and Raven, 2012). We apply this framework through 5 in-depth case studies of contract chains, based on 21 interviews with commercial directors of processing and collecting companies and with farmers. Our results highlight the potential role of contracts in supporting the agroecological transition. This research is of particular interest to policy makers at various levels, from the European Commission to local agricultural institutions, and could also inspire other sectors facing value chain organisation challenges for sustainability transition.

    ano.nymous@ccsd.cnrs.fr.invalid (Auguste Bréavoine) 07 Jul 2025

    https://hal.inrae.fr/hal-05148951v1
  • [hal-05510318] Assessing the technical, economic and environmental performances of low-input and legume-based cropping systems

    Agriculture faces a number of environmental, economic and social challenges. Reducing the use of pesticides is one of them, as they are being questioned due to their harmful e!ects on the environment and human health. Diversification of cropping systems appears to be one of the main levers for reducing dependence on chemical inputs. One crop diversification practice consists of introducing minor crops into systems, such as legumes. Indeed, legumes play a major role in improving the protein autonomy of production systems but their adoption rate remains low due to a number of socio-technical lock-in. In this context, the aim of the thesis is to provide scientific knowledge on strategies for integrating legumes into low-input cropping systems, to characterize these systems in terms of management strategy, and to assess the consequences of their adoption in terms of productivity, profitability, reduced environmental impact, and social criteria such as feasibility in terms of work organization. The thesis will address these issues for the field crop sector (including mixed crop-livestock farming), using data produced by the DEPHY farm network and the CA-SYS (INRAE Dijon) and ABY (INRAE Bourges) experimental platforms.

    ano.nymous@ccsd.cnrs.fr.invalid (Simon Buresi) 13 Feb 2026

    https://hal.inrae.fr/hal-05510318v1

All SPECIFICS publications (ANR20-PCPA-0008) by following this link.

Contact

specifics-com@inrae.fr 

Modification date: 27 January 2026 | Publication date: 15 September 2022 | By: Sandie Barbot