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Au sein d'INRAE, il existe le réseau national INRAE NIRS qui est en fait un groupe de compagnonnage entre 80 utilisateurs de la spectrométrie proche infra-rouge. Suite à une enquête réalisée en 2021 auprès de ses membres, il a été décidé de créer un circuit inter-laboratoires entre les 18 implantations INRAE volontaires totalisant initialement une trentaine de spectromètres proche-infrarouges. En effet, les données spectrales proche infra-rouges sont de plus en plus exploitées pour des caractérisations à haut-débit des échantillons car c'est une technique d'analyse physico-chimique, rapide et non destructive. Mais, pour chaque paramètre étudié, il est nécessaire de développer en amont un étalonnage entre la base spectrale et les valeurs de référence associées (via une calibration). Par conséquent, la qualité et la fiabilité des spectres sont indispensables. Début 2024, le projet multi-départements INSPIR, qui porte l'ambition de ce circuit inter-laboratoires, a été accepté. Il est prévu de faire circuler les mêmes échantillons de farines de blé tendre pour réaliser l'acquisition des spectres proche infrarouge au sein des différents sites et ainsi comparer : - les différentes méthodologies de prise de spectres (bonnes pratiques) - la qualité des spectres pris par les différents instruments (gamme de longueur d'onde, résolution et performances prédictives) - les instruments entre eux (appareils de labo et portatifs de terrain) Une base de données avec les spectres obtenus sur les différents appareils, les métadonnées associées et leur teneur respective en protéines (Kjeldahl) sera établie par notre stagiaire Master 2 Paul CRESPIN, puis publiée sous forme de Data paper et rendue disponible sur le Dataverse INRAE. Cette base de données pourra également être très utile pour standardiser les spectromètres entre eux et entre sites INRAE. Cette possibilité de standardisation permettra d'assurer l'interopérabilité mais aussi le suivi en cas de panne ou de renouvellement d'un

Malgré le consensus croissant sur la nécessité d'une transition vers des pratiques agricoles plus durables, les céréales et, en particulier, le froment, ont pris du retard dans la conversion à l'agriculture biologique. Parmi les facteurs contribuant à ce retard figure le manque de variétés adaptées à ces pratiques agricoles et à leurs spécificités. Dans cette thèse, nous nous concentrons sur l’une des principales alternatives variétales pour répondre à ce problème :les populations hétérogènes. Par populations hétérogènes, nous désignons ici tout type de diversité intraspécifique, allant des mélanges variétaux jusqu’aux variétés-populations. Un avantage essentiel de cette hétérogénéité est que la présence de contrastes entre plantes peut donner lieu à des mécanismes de facilitation susceptibles d'améliorer les performances des cultures et leur stabilité face à des conditions défavorables. Malgré ces propriétés prometteuses, nous manquons cependant encore de clés pour guider ce type de sélection. Il s’agit là du principal objet de cette thèse.Ces dernières années, la recherche académique semble avoir mis l’accent sur la recherche d'associations de traits pouvant conduire aux mécanismes de facilitation que nous mentionnions ci-dessus. Dans ce travail, nous avons choisi de nous intéresser également à un autre type d'interaction qui a lieu au sein des populations hétérogènes :la compétition. En particulier, nous avons émis l'hypothèse qu'un certain type de compétition, que nous appelons « compétition individualiste », pourrait avoir des effets négatifs sur la culture. En effet, il arrive parfois que la sélection naturelle nous joue des tours en favorisant des individus qui ont pourtant un moindre potentiel de rendement, ou qui contribuent moins à la facilitation. Par conséquent, plus que la seule facilitation, le principal déterminant de la performance des populations hétérogènes pourrait plus précisément être l'équilibre entre compétition et facilitation. Dans les chapi, Despite the growing consensus on the need for a transition to more sustainable farming practices, cereals and, in particular, common wheat, have been lagging behind in the conversion to organic farming. We argue that one of the reasons for this is the lack of varieties that are adapted to these farming practices and their specificities. In this thesis, we focus on a main varietal alternative to respond to this issue: intra-crop diversity. By intra-crop diversity, we mean anything from variety mixtures to evolutionary populations, which we hereafter refer to with the umbrella term “heterogeneous stands”. One main advantage of intra-crop diversity is that trait contrasts between crop plants can give rise to facilitative mechanisms which can enhance crop performance and its stability in the face of unpredictable adverse conditions. However, we still know little about how to breed these heterogeneous stands. This is the main question that we try to address in this thesis.In recent years, a primary focus in the literature has been to identify favorable trait associations that can lead to facilitation. Here, we chose to also lend an eye to another type of plant interaction that unfolds in heterogeneous stands: competition. Indeed, we hypothesized that a specific type of competition, which we call “selfish competition”, could lead to negative effects on the crop. Sometimes, natural selection can indeed play tricks on us and favor genotypes that have lower grain yield potential or contribute less to facilitation. Hence, more than simply facilitation, it is the balance between competition and facilitation that may actually be the main determinant of heterogeneous stand performance. In chapters II and III, we thus sought to assess if selfish competition could indeed hinder heterogeneous stand performance, and to identify some of its underlying causes (with a focus on trait contrasts and sowing density). In agronomic trials with 12 variety mixtures and 2 Composite-Cross Popula, Doctorat en Sciences agronomiques et ingénierie biologique, info:eu-repo/semantics/nonPublished

Mixed cropping (MC) is a key strategy to harness agriculture for climate-change. Breeding adapted genotypes can unleash the full potential of MC, both in terms of yield potential and yield stability. To achieve this goal, concepts from both breeding and ecology have to be fused in order to develop a suitable methodology for breeding for MC. In order to advance the field of breeding for MC, we evaluated yield and trait data of pure stands (PS) and mixed stands (MS) of pea (P. sativum L.) and barley (H. vulgare L.) as a legume-cereal model system. Twenty-eight pea and seven barley lines, representing European breeding material, were grown in an incomplete factorial design at two organically managed sites across two years. The general mixing ability (GMA) of pea for total mixture yield was predominant as specific mixing ability (SMA) was absent, facilitating future breeding and seed marketing efforts. The most promising pea cultivar ‘Volt’ resulted in an average total mixture yield increase of 11% (+0.43 t/ha) in MC compared to the average, while the cultivar ’Florida’ led to a yield decrease of − 31% (−1.23 t/ha), highlighting the importance of the choice of the genotype in MS. The analysis of separated MS yields allowed to investigate the underlying mechanistic principles in genotypes’ contribution to MS yields and we revealed the major role of producer (Pr) effects in this context. The correlation between Pr effects and GMA revealed that GMA can be maximized by selecting for high Pr effects. Early vigor, onset of flowering, shoot biomass and stipule length were identified as key traits for indirect selection for high GMA in pea accounting for up to 17% of the identified variation in total mixture yield. PS yields were moderately correlated with mixture yields (r = 0.52, P = 0.013) and can serve as an additional selection criterion. Discrepancies between correlations with PS and MS yields can be exploited to identify unique MS traits that confer niche complementarity

Intercropping, also known as mixed cropping, consists on simultaneously growing more than one species on a field. It has a great potential for enhancing water- and nutrient-use efficiency and improving plant productivity, yield stability and resilience to biotic and abiotic stress, including those triggered by climate change. Despite their manifold benefits, the practice of intercropping has not risen above its niche status in many regions of the world. The selection of varieties specifically adapted to intercropping remains a major practical challenge to its widespread deployment. This Research Topic hosted at Frontiers in Plant Sciences entitled “Breeding for intercropping” gathers a series of articles covering new insights in the areas of quantitative genetics, ecology, ecophysiology and agronomy integrating theoretical, experimental as well as participatory approaches.

Cropping system diversification through annual intercropping provides a pathway for agricultural production with reduced inputs of fertilizer and pesticides. While several studies have shown that intercrop performance depends on the genotypes used, the available evidence has not been synthesized in an overarching analysis. Here, we review the effects of genotypes in cereal/legume intercropping systems, showing how genotype choice affects mixture performance. Furthermore, we discuss the mechanisms underlying the interactions between genotype and cropping system (i.e., sole cropping vs. intercropping). Data from 69 articles fulfilling inclusion criteria were analyzed, out of which 35 articles reported land equivalent ratio (LER), yielding 262 LER data points to be extracted. The mean and median LER were 1.26 and 1.24, respectively. The extracted genotype × cropping system interaction effects on yield were reported in 71% out of 69 publications. Out of this, genotype × cropping system interaction effects were significant in 75%, of the studies, whereas 25% reported non-significant interactions. The remaining studies did not report the effects of genotype × cropping system. Phenological and morphological traits, such as differences in days to maturity, plant height, or growth habit, explained variations in the performance of mixtures with different genotypes. However, the relevant genotype traits were not described sufficiently in most of the studies to allow for a detailed analysis. A tendency toward higher intercropping performance with short cereal genotypes was observed. The results show the importance of genotype selection for better in cereal/legume intercropping. This study highlights the hitherto unrevealed aspects of genotype evaluation for intercropping systems that need to be tackled. Future research on genotype effects in intercropping should consider phenology, root growth, and soil nutrient and water acquisition timing, as well as the effects of weeds and

Increasing the cultivated diversity has been identified as a major leverage for the agroecological transition as it can help improve the resilience of low input cropping systems. For wheat, which is the most cultivated crop worldwide in terms of harvested area, the use of cultivar mixtures is spreading in several countries, but studies have seldom focused on establishing mixing rules based on plant architecture. Yet, the aerial architecture of plants and the overall canopy structure are critical for field performance as they greatly influence light interception, plant interactions and yield. The very high number of trait combinations in wheat mixtures makes it difficult to conduct experimentations on this issue, which is why a modeling approach appears to be an appropriate solution. In this study, we used WALTer, a functional structural plant model (FSPM), to simulate wheat cultivar mixtures and try to better understand how differences between cultivars in key traits of the aerial architecture influence mixture performance. We simulated balanced binary mixtures of cultivars differing for different critical plant traits: final height, leaf dimensions, leaf insertion angle and tillering capability. Our study highlights the impact of the leaf dimensions and the tillering capability on the performance of the simulated mixtures, which suggests that traits impacting the plants' leaf area index (LAI) have more influence on the performance of the stand than traits impacting the arrangement of the leaves. Our results show that the performance of mixtures is very variable depending on the values of the explored architectural traits. In particular, the best performances were achieved by mixing cultivars with different leaf dimensions and different tillering capability, which is in agreement with numerous studies linking the diversity of functional traits in plant communities to their productivity. However, some of the worst performances were also achieved by mixing varieties d

Although widely used in ecology, trait-based approaches are seldom used to study agroecosystems. In particular, there is a need to evaluate how functional trait variability among varieties of a crop species compares to the variability among wild plant species and how variety selection can modify trait syndromes. Here, we quantified 18 above- and below-ground functional traits for 57 varieties of common wheat representative of different modern selection histories. We compared trait variability among varieties and among Pooideae species, and analyzed the effect of selection histories on trait values and trait syndromes. For traits under strong selection, trait variability among varieties was less than 10% of the variability observed among Pooideae species. However, for traits not directly selected, such as root N uptake capacity, the variability was up to 75% of the variability among Pooideae species. Ammonium absorption capacity by roots was counter-selected for conventional varieties compared with organic varieties and landraces. Artificial selection also altered some trait syndromes classically reported for Pooideae. Identifying traits that have high or low variability among varieties and characterizing the hidden effects of selection on trait values and syndromes will benefit the selection of varieties to be used especially for lower N input agroecosystems.

Mixed cropping has been suggested as a resource-efficient approach to meet high produce demands while maintaining biodiversity and minimizing environmental impact. Current breeding programs do not select for enhanced general mixing ability (GMA) and neglect biological interactions within species mixtures. Clear concepts and efficient experimental designs, adapted to breeding for mixed cropping and encoded into appropriate statistical models, are lacking. Thus, a model framework for GMA and SMA (specific mixing ability) was established. Results of a simulation study showed that an incomplete factorial design combines advantages of two commonly used full factorials, and enables to estimate GMA, SMA, and their variances in a resource-efficient way. This model was extended to the Producer (Pr) and Associate (As) concept to exploit additional information based on fraction yields. It was shown that the Pr/As concept allows to characterize genotypes for their contribution to total mixture yield, and, when relating to plant traits, allows to describe biological interaction functions (BIF) in a mixed crop. Incomplete factorial designs show the potential to drastically improve genetic gain by testing an increased number of genotypes using the same amount of resources. The Pr/As concept can further be employed to maximize GMA in an informed and efficient way. The BIF of a trait can be used to optimize species ratios at harvest as well as to extend our understanding of competitive and facilitative interactions in a mixed plant community. This study provides an integrative methodological framework to promote breeding for mixed cropping.

Conference paper on breeding for mixed cropping, putting a some focus on correlations between pure stand yields and mixture yields, as well as GxE interaction. Talk was given on the online conference "Intercropping for sustainability" organized by the Association of Applied Biologists, on January 20th 2021.

Im EU-Projekt ReMIX geht es darum, den Leguminosen-Mischanbau europaweit zu fördern. Dies auch vor dem Hintergrund des Klimawandels, denn Mischkulturen liefern stabilere Erträge, zum Teil bessere Qualität. Die Frage lautet: Braucht es eine eigene Züchtung für Mischkulturen? Oder reicht es, wenn man die besten vorhandenen Sorten miteinander kombiniert. Das will der Benedikt Haug in seiner Dissertation herausfinden. In seinen Feldversuchen kombiniert er dafür ein großes Set an europäischen Erbsensorten mit verschiedenen europäischen Gerstensorten. Im Video berichtet er über die ersten Ergebnisse.

Crop mixtures consisting of cereals and legumes have proven as a well-adapted arrangement due to their complementarity towards important resources, especially nitrogen. Crop mixtures combine high yield performance and yield stability. They can contribute to a diversified cropping landscape and adaptation to climate change. The search for alternatives to protein imports from overseas and investments in post-harvest separation technologies are currently fostering their adoption by farmers in Western-Europe, especially under organic and lowinput farming conditions. However, screening and breeding for mixed cropping has hardly been explored for arable crops. Thus, the objective was to develop novel breeding strategies and tools specifically for mixed cropping systems. We tested mixtures and pure stands of a morphologically diverse panel of 32 spring pea (Pisum sativum L.) and eight spring barley (Hordeum vulgare L.) cultivars in replicated field trials at two locations in Switzerland over two years with pea as the focal species. In an incomplete factorial design (Fig. 1) we determined general and specific mixing ability (GMA and SMA, respectively) of pea and barley in analogy to GCA and SCA (general and specific combining ability) in hybrid breeding. Key traits, such as early vigour, canopy height and leaf morphology parameters were measured, due to their potential use as covariates or indirect selection criteria for mixing ability. Our results show that total yield of mixtures can only partly be explained by pea pure stand yields (R² = 0.35), making the latter a weak predictor for mixture yield. Pea GMA variance was predominant over SMA variance which underlines the potential for breeding for mixing ability using a tester. Key traits, such as pea stipule area were correlated (R² = 0.56) with total mixture yield and merit further investigation as indirect selection criteria. The separated yield fractions of pea and barley in mixtures allow to decompose GMA of pea into t

Introduction Mixed cropping, i.e. mixing different crops in the same field, provides agronomic advantages as increased productivity under low inputs conditions (e.g. for organic farming: Bedoussac et al. 2015) and higher yield stability (Raseduzzaman and Jensen 2017). In mixed cropping, choosing the right cultivars is critical for the performance of the mixture, as shown for pea-barley mixtures (Hauggaard-Nielsen and Jensen 2001) and maize-bean mixtures (Hoppe 2016). As performance in pure stand can strongly diverge from performance in mixture, estimating the ability of a cultivar to be mixed with another crop is therefore of utmost importance. For this purpose, concepts of General and Specific Combining Ability in hybrid breeding (Griffing 1956) have been adapted to cultivar and crop mixtures. Thus, these effects are called General Mixing Ability (GMA) and Specific Mixing Ability (SMA) (Federer 1993). In contrast to intraspecific mixtures, interspecific mixed cropping experiments often provide additional information, since harvested lots can be separated into their different grain fractions. Until now, statistical developments mobilizing the additional information provided by separated harvest lots to estimate mixing abilities in intercropping experiments have been neglected. The concept of Producer- and Associate-effects (abbreviated Pr and As, respectively) describes interactions between varieties sown in alternate row trials (Forst 2018). The producer effect Pr is the average performance of a cultivar grown in mixture with other crop-species, whereas the associate effect As is the average effect of a cultivar on the performance of the mixing partner. We used the fraction yields of a spring-pea (Pisum sativum L.) and spring-barley (Hordeum vulgare L.) mixed cropping experiment to determine Pr and As effects of different pea genotypes. The additional information provided by this approach is biologically more informative than GMA/SMA estimates, since it better refl

There has been recently a renewed interest for variety mixtures due to their potential capacity to stabilize production through buffering abiotic and biotic stresses. Part of this results from complementarity and/or compensation between varieties which can be assessed under mixed stands only. Mixing ability of varieties can be partitioned into General and Specific Mixing Abilities (GMA and SMA) that have been estimated so far through the evaluation of binary mixtures in complete diallel designs. However, the number of mixtures increases exponentially with the number of studied varieties, and the only feasible devices are incomplete designs. Despite the long history of statistical analysis of variety mixtures, such incomplete design analysis has rarely been addressed so far. To fill the gap, we proposed a generalized statistical framework to assess mixing abilities based on mixed models and BLUP method, with an original modeling of plant-plant interactions. The approach has been applied to a panel of 25 winter wheat genotypes observed in two contrasted experimental designs: (i) an incomplete diallel of 75 binary mixtures, and (ii) a trial including higher order mixtures (four and eight components). The use of mixing ability models improved prediction accuracy (of modeled values for observed traits) in comparison to predictions from the mean of the pure stand components, especially in the first experiment. Genetic variability was detected for the GMA of yield and its components, whereas variability for SMA was lower. GMA predictions based on the diallel trial were highly correlated with the GMA of the second trial providing accurate inter-trial predictions. A new model has been proposed to jointly account for inter and intra-genotypic interactions for specific mixing ability, thus contributing to a better understanding of mixture functioning. This framework constitutes a step forward to the screening for mixing ability, and could be further integrated into breeding pr

Pour réduire les impacts négatifs des systèmes agricoles, la transition agroécologique appelle en premier lieu à l'utilisation d'une plus grande biodiversité cultivée. Une telle diversification peut être conduite à l'échelle de la parcelle, en associant différentes espèces, ou différentes variétés d'une même espèce. Nous abordons les avantages de cette diversification intra-parcellaire, en développant 5 exemples : (1) les mélanges variétaux de blé en France, (2) les populations de riz au YuanYang, (3) le colza associé à des plantes de services, (4) les mélanges d'espèces fourragères et (5) les associations céréales-légumineuses à graines. Nous discutons des avantages conférés par cette diversification sur : (i) l'optimisation et la stabilisation des productions, (ii) les interactions avec les pratiques culturales, (iii) la sélection variétale, et (iv) l'impact de ces peuplements et pratiques sur la biodiversité sauvage associée.

Investigating the origin and dispersal pathways is instrumental to mitigate threats and economic and environmental consequences of invasive crop pathogens. In the case of Puccinia striiformis causing yellow rust on wheat, a number of economically important invasions have been reported, e.g., the spreading of two aggressive and high temperature adapted strains to three continents since 2000. The combination of sequence-characterized amplified region (SCAR) markers, which were developed from two specific AFLP fragments, differentiated the two invasive strains, PstS1 and PstS2 from all other P. striiformis strains investigated at a worldwide level. The application of the SCAR markers on 566 isolates showed that PstS1 was present in East Africa in the early 1980s and then detected in the Americas in 2000 and in Australia in 2002. PstS2 which evolved from PstS1 became widespread in the Middle East and Central Asia. In 2000, PstS2 was detected in Europe, where it never became prevalent. Additional SSR genotyping and virulence phenotyping revealed 10 and six variants, respectively, within PstS1 and PstS2, demonstrating the evolutionary potential of the pathogen. Overall, the results suggested East Africa as the most plausible origin of the two invasive strains. The SCAR markers developed in the present study provide a rapid, inexpensive, and efficient tool to track the distribution of P. striiformis invasive strains, PstS1 and PstS2.