39 research outputs found
Presentation of "A plant biodiversity effect resolved to a single chromosomal region" by Wuest et al. (2018)
WP leader : Timothée FLUTRE (GQE - Le Moulon)Doctora
Development of a low cost open-source ultrasonic device for plant height measurements
Plant height is commonly used to characterize crops in various domains such as plant breeding or precision farming. Despite significant advances in sensing technologies, plant height is still very often measured manually in many research applications where high-throughput alternatives are not always suitable. Here, we have developed a low cost, open-source ultrasonic device for semi-automated plant height measurements in small- to medium-scale applications. The main innovation compared to previous developments is the combination of a low-cost ultrasonic sensor and a plastic backscatter plate to improve plant tip detection. We compared the device to the manual method under controlled laboratory conditions and in a field experiment with 26 sorghum (Sorghum bicolor) inbred lines. The accuracy of the device was close to 1 cm in controlled conditions and 2 cm in the field, and the bias was close to 0 in both cases. In the field, measurements were 42% faster when compared with the classical ruler, and sensor-based values were strongly correlated with ruler-based values (RÂČ = 0.9965). Overall, the device allows significant time savings while maintaining very high accuracy compared to the manual method. Its low cost (âŒ75 âŹ) and compact design make it suitable for a wide range of applications, either for crop species, natural species, or model organisms. We encourage such implementations by providing all code and materials in free and open access
Diversité vs uniformité ˞ combiner les approches écologiques et évolutives pour concevoir des systÚmes de culture durables
Most of the worldwide food production is based on genetically homogeneous crop varieties, that is single-genotype varieties. However, the patterns observed in natural ecosystems suggest that higher levels of genetic diversity could increase agricultural sustainability. A straightforward method to increase diversity in agrosystems is to grow varietal mixtures. So far, the results accumulated on varietal mixtures are very contrasted and it remains difficult to predict mixture performance. The aim of the thesis is to better understand the relationship between genetic diversity and agronomic performance in light of ecological and evolutionary theories. We combine experimental and theoretical approaches, using rice (Oryza sativa) and durum wheat (Triticum turgidum ssp. durum) as model species. A first experiment in controlled conditions fails to demonstrate any productivity benefit associated with root depth differences in rice mixtures, contrasting with the pattern expected under the resource-use complementarity theory. In a second experiment conducted in field conditions with durum wheat mixtures, we show that a multivariate description of the niche allows us to capture a significant proportion of the mixing effects on several components of the agronomic performance. Using the same experiment, we show that allelic diversity at a single locus decreases grain yield and increases disease susceptibility in the mixtures. Such a negative effect of allelic diversity is consistent with a âgreenbeardâ effect, classically described in evolutionary biology to characterize genes which are able to favor their own transmission by making their bearer more cooperative towards individuals who bear the same gene copy. Lastly, we investigate the temporal effects associated with genetic diversity in the context of a dynamic management of diversity. Indeed, as formalized by the Tragedy of the Commons, phenotypes that are more competitive are expected to increase in frequency over generations, thus reducing the whole group performance. We thus develop a theoretical model to identify selection methods that allow us to prevent invasion by competitive phenotypes that lower yield. Overall, the interdisciplinary approach developed in this thesis has provided invaluable insights into the understanding, detection, and selection of the effects that arise from plan-plant interactions, which opens up promising opportunities for tackling both applied issues in agriculture and theoretical issues in ecology and evolutionary biology.Une grande partie de la production alimentaire mondiale repose sur des variĂ©tĂ©s gĂ©nĂ©tiquement homogĂšnes, câest-Ă -dire composĂ©es dâun seul gĂ©notype. Cependant, les patrons observĂ©s dans les Ă©cosystĂšmes naturels suggĂšrent quâune diversitĂ© gĂ©nĂ©tique plus importante pourrait rendre les agrosystĂšmes plus durables. Une façon simple dâaugmenter la diversitĂ© dans les agrosystĂšmes consiste Ă cultiver plusieurs variĂ©tĂ©s dâune mĂȘme espĂšce en mĂ©lange. A ce jour, cette pratique a fourni des rĂ©sultats contrastĂ©s, et la performance des mĂ©langes variĂ©taux reste difficile Ă prĂ©dire. Lâobjectif de cette thĂšse est de mieux comprendre la relation entre la diversitĂ© gĂ©nĂ©tique et la performance agronomique Ă la lumiĂšre des thĂ©ories Ă©cologiques et Ă©volutives. Nous combinons des approches expĂ©rimentales et thĂ©oriques, et nous utilisons le riz (Oryza sativa) et le blĂ© dur (Triticum turgidum ssp. durum) comme espĂšces modĂšles. Dans une premiĂšre expĂ©rience en conditions contrĂŽlĂ©es, nous montrons que les diffĂ©rences de profondeurs racinaires entre des variĂ©tĂ©s de riz cultivĂ©es en mĂ©lange ne gĂ©nĂšrent pas une productivitĂ© supĂ©rieure en mĂ©lange, comme cela pourrait ĂȘtre attendu sous lâhypothĂšse de complĂ©mentaritĂ© dâutilisation des ressources. Dans une deuxiĂšme expĂ©rience conduite au champ avec des mĂ©langes de blĂ© dur, nous montrons quâune description multivariĂ©e de la niche Ă©cologique des gĂ©notypes permet de mieux comprendre les effets de la diversitĂ© gĂ©nĂ©tique sur plusieurs composantes de la performance agronomique. Ensuite, nous testons les thĂ©ories Ă©cologiques et Ă©volutives au niveau gĂ©nomique. Sur la base des donnĂ©es acquises dans les mĂ©langes de blĂ© dur, nous identifions un locus auquel une plus grande diversitĂ© allĂ©lique est associĂ©e Ă des rendements plus faibles et Ă une incidence plus forte de la septoriose. Le patron gĂ©nĂ©tique identifiĂ© est compatible avec un effet « barbe verte », classiquement dĂ©crit en biologie Ă©volutive pour caractĂ©riser un gĂšne capable de favoriser sa propre transmission en rendant les individus qui le portent plus coopĂ©ratifs envers les individus partageant ce mĂȘme gĂšne. Enfin, nous nous intĂ©ressons aux effets temporels de la diversitĂ© gĂ©nĂ©tique dans le contexte dâune gestion dynamique de la diversitĂ© cultivĂ©e. Comme formalisĂ© par le concept de la TragĂ©die des Communs, les phĂ©notypes les plus compĂ©titifs dans un mĂ©lange sont en effet amenĂ©s Ă augmenter en frĂ©quence au fil des gĂ©nĂ©rations, entraĂźnant une diminution de la performance du groupe. Nous dĂ©veloppons donc un modĂšle thĂ©orique afin dâidentifier des mĂ©thodes de sĂ©lection permettant dâempĂȘcher les variĂ©tĂ©s les plus compĂ©titives dâaugmenter en frĂ©quence. Dans lâensemble, lâapproche interdisciplinaire dĂ©veloppĂ©e dans cette thĂšse permet de progresser dans la dĂ©tection, la comprĂ©hension, et la sĂ©lection des effets issus des interactions plante-plante, ouvrant ainsi des opportunitĂ©s stimulantes dans le domaine appliquĂ© et dans le domaine thĂ©orique
Diversity vs uniformityËž mixing ecological and evolutionary approaches to design sustainable cropping systems
Une grande partie de la production alimentaire mondiale repose sur des variĂ©tĂ©s gĂ©nĂ©tiquement homogĂšnes, câest-Ă -dire composĂ©es dâun seul gĂ©notype. Cependant, les patrons observĂ©s dans les Ă©cosystĂšmes naturels suggĂšrent quâune diversitĂ© gĂ©nĂ©tique plus importante pourrait rendre les agrosystĂšmes plus durables. Une façon simple dâaugmenter la diversitĂ© dans les agrosystĂšmes consiste Ă cultiver plusieurs variĂ©tĂ©s dâune mĂȘme espĂšce en mĂ©lange. A ce jour, cette pratique a fourni des rĂ©sultats contrastĂ©s, et la performance des mĂ©langes variĂ©taux reste difficile Ă prĂ©dire. Lâobjectif de cette thĂšse est de mieux comprendre la relation entre la diversitĂ© gĂ©nĂ©tique et la performance agronomique Ă la lumiĂšre des thĂ©ories Ă©cologiques et Ă©volutives. Nous combinons des approches expĂ©rimentales et thĂ©oriques, et nous utilisons le riz (Oryza sativa) et le blĂ© dur (Triticum turgidum ssp. durum) comme espĂšces modĂšles. Dans une premiĂšre expĂ©rience en conditions contrĂŽlĂ©es, nous montrons que les diffĂ©rences de profondeurs racinaires entre des variĂ©tĂ©s de riz cultivĂ©es en mĂ©lange ne gĂ©nĂšrent pas une productivitĂ© supĂ©rieure en mĂ©lange, comme cela pourrait ĂȘtre attendu sous lâhypothĂšse de complĂ©mentaritĂ© dâutilisation des ressources. Dans une deuxiĂšme expĂ©rience conduite au champ avec des mĂ©langes de blĂ© dur, nous montrons quâune description multivariĂ©e de la niche Ă©cologique des gĂ©notypes permet de mieux comprendre les effets de la diversitĂ© gĂ©nĂ©tique sur plusieurs composantes de la performance agronomique. Ensuite, nous testons les thĂ©ories Ă©cologiques et Ă©volutives au niveau gĂ©nomique. Sur la base des donnĂ©es acquises dans les mĂ©langes de blĂ© dur, nous identifions un locus auquel une plus grande diversitĂ© allĂ©lique est associĂ©e Ă des rendements plus faibles et Ă une incidence plus forte de la septoriose. Le patron gĂ©nĂ©tique identifiĂ© est compatible avec un effet « barbe verte », classiquement dĂ©crit en biologie Ă©volutive pour caractĂ©riser un gĂšne capable de favoriser sa propre transmission en rendant les individus qui le portent plus coopĂ©ratifs envers les individus partageant ce mĂȘme gĂšne. Enfin, nous nous intĂ©ressons aux effets temporels de la diversitĂ© gĂ©nĂ©tique dans le contexte dâune gestion dynamique de la diversitĂ© cultivĂ©e. Comme formalisĂ© par le concept de la TragĂ©die des Communs, les phĂ©notypes les plus compĂ©titifs dans un mĂ©lange sont en effet amenĂ©s Ă augmenter en frĂ©quence au fil des gĂ©nĂ©rations, entraĂźnant une diminution de la performance du groupe. Nous dĂ©veloppons donc un modĂšle thĂ©orique afin dâidentifier des mĂ©thodes de sĂ©lection permettant dâempĂȘcher les variĂ©tĂ©s les plus compĂ©titives dâaugmenter en frĂ©quence. Dans lâensemble, lâapproche interdisciplinaire dĂ©veloppĂ©e dans cette thĂšse permet de progresser dans la dĂ©tection, la comprĂ©hension, et la sĂ©lection des effets issus des interactions plante-plante, ouvrant ainsi des opportunitĂ©s stimulantes dans le domaine appliquĂ© et dans le domaine thĂ©orique.Most of the worldwide food production is based on genetically homogeneous crop varieties, that is single-genotype varieties. However, the patterns observed in natural ecosystems suggest that higher levels of genetic diversity could increase agricultural sustainability. A straightforward method to increase diversity in agrosystems is to grow varietal mixtures. So far, the results accumulated on varietal mixtures are very contrasted and it remains difficult to predict mixture performance. The aim of the thesis is to better understand the relationship between genetic diversity and agronomic performance in light of ecological and evolutionary theories. We combine experimental and theoretical approaches, using rice (Oryza sativa) and durum wheat (Triticum turgidum ssp. durum) as model species. A first experiment in controlled conditions fails to demonstrate any productivity benefit associated with root depth differences in rice mixtures, contrasting with the pattern expected under the resource-use complementarity theory. In a second experiment conducted in field conditions with durum wheat mixtures, we show that a multivariate description of the niche allows us to capture a significant proportion of the mixing effects on several components of the agronomic performance. Using the same experiment, we show that allelic diversity at a single locus decreases grain yield and increases disease susceptibility in the mixtures. Such a negative effect of allelic diversity is consistent with a âgreenbeardâ effect, classically described in evolutionary biology to characterize genes which are able to favor their own transmission by making their bearer more cooperative towards individuals who bear the same gene copy. Lastly, we investigate the temporal effects associated with genetic diversity in the context of a dynamic management of diversity. Indeed, as formalized by the Tragedy of the Commons, phenotypes that are more competitive are expected to increase in frequency over generations, thus reducing the whole group performance. We thus develop a theoretical model to identify selection methods that allow us to prevent invasion by competitive phenotypes that lower yield. Overall, the interdisciplinary approach developed in this thesis has provided invaluable insights into the understanding, detection, and selection of the effects that arise from plan-plant interactions, which opens up promising opportunities for tackling both applied issues in agriculture and theoretical issues in ecology and evolutionary biology
Diversité vs uniformité ˞ combiner les approches écologiques et évolutives pour concevoir des systÚmes de culture durables
Most of the worldwide food production is based on genetically homogeneous crop varieties, that is single-genotype varieties. However, the patterns observed in natural ecosystems suggest that higher levels of genetic diversity could increase agricultural sustainability. A straightforward method to increase diversity in agrosystems is to grow varietal mixtures. So far, the results accumulated on varietal mixtures are very contrasted and it remains difficult to predict mixture performance. The aim of the thesis is to better understand the relationship between genetic diversity and agronomic performance in light of ecological and evolutionary theories. We combine experimental and theoretical approaches, using rice (Oryza sativa) and durum wheat (Triticum turgidum ssp. durum) as model species. A first experiment in controlled conditions fails to demonstrate any productivity benefit associated with root depth differences in rice mixtures, contrasting with the pattern expected under the resource-use complementarity theory. In a second experiment conducted in field conditions with durum wheat mixtures, we show that a multivariate description of the niche allows us to capture a significant proportion of the mixing effects on several components of the agronomic performance. Using the same experiment, we show that allelic diversity at a single locus decreases grain yield and increases disease susceptibility in the mixtures. Such a negative effect of allelic diversity is consistent with a âgreenbeardâ effect, classically described in evolutionary biology to characterize genes which are able to favor their own transmission by making their bearer more cooperative towards individuals who bear the same gene copy. Lastly, we investigate the temporal effects associated with genetic diversity in the context of a dynamic management of diversity. Indeed, as formalized by the Tragedy of the Commons, phenotypes that are more competitive are expected to increase in frequency over generations, thus reducing the whole group performance. We thus develop a theoretical model to identify selection methods that allow us to prevent invasion by competitive phenotypes that lower yield. Overall, the interdisciplinary approach developed in this thesis has provided invaluable insights into the understanding, detection, and selection of the effects that arise from plan-plant interactions, which opens up promising opportunities for tackling both applied issues in agriculture and theoretical issues in ecology and evolutionary biology.Une grande partie de la production alimentaire mondiale repose sur des variĂ©tĂ©s gĂ©nĂ©tiquement homogĂšnes, câest-Ă -dire composĂ©es dâun seul gĂ©notype. Cependant, les patrons observĂ©s dans les Ă©cosystĂšmes naturels suggĂšrent quâune diversitĂ© gĂ©nĂ©tique plus importante pourrait rendre les agrosystĂšmes plus durables. Une façon simple dâaugmenter la diversitĂ© dans les agrosystĂšmes consiste Ă cultiver plusieurs variĂ©tĂ©s dâune mĂȘme espĂšce en mĂ©lange. A ce jour, cette pratique a fourni des rĂ©sultats contrastĂ©s, et la performance des mĂ©langes variĂ©taux reste difficile Ă prĂ©dire. Lâobjectif de cette thĂšse est de mieux comprendre la relation entre la diversitĂ© gĂ©nĂ©tique et la performance agronomique Ă la lumiĂšre des thĂ©ories Ă©cologiques et Ă©volutives. Nous combinons des approches expĂ©rimentales et thĂ©oriques, et nous utilisons le riz (Oryza sativa) et le blĂ© dur (Triticum turgidum ssp. durum) comme espĂšces modĂšles. Dans une premiĂšre expĂ©rience en conditions contrĂŽlĂ©es, nous montrons que les diffĂ©rences de profondeurs racinaires entre des variĂ©tĂ©s de riz cultivĂ©es en mĂ©lange ne gĂ©nĂšrent pas une productivitĂ© supĂ©rieure en mĂ©lange, comme cela pourrait ĂȘtre attendu sous lâhypothĂšse de complĂ©mentaritĂ© dâutilisation des ressources. Dans une deuxiĂšme expĂ©rience conduite au champ avec des mĂ©langes de blĂ© dur, nous montrons quâune description multivariĂ©e de la niche Ă©cologique des gĂ©notypes permet de mieux comprendre les effets de la diversitĂ© gĂ©nĂ©tique sur plusieurs composantes de la performance agronomique. Ensuite, nous testons les thĂ©ories Ă©cologiques et Ă©volutives au niveau gĂ©nomique. Sur la base des donnĂ©es acquises dans les mĂ©langes de blĂ© dur, nous identifions un locus auquel une plus grande diversitĂ© allĂ©lique est associĂ©e Ă des rendements plus faibles et Ă une incidence plus forte de la septoriose. Le patron gĂ©nĂ©tique identifiĂ© est compatible avec un effet « barbe verte », classiquement dĂ©crit en biologie Ă©volutive pour caractĂ©riser un gĂšne capable de favoriser sa propre transmission en rendant les individus qui le portent plus coopĂ©ratifs envers les individus partageant ce mĂȘme gĂšne. Enfin, nous nous intĂ©ressons aux effets temporels de la diversitĂ© gĂ©nĂ©tique dans le contexte dâune gestion dynamique de la diversitĂ© cultivĂ©e. Comme formalisĂ© par le concept de la TragĂ©die des Communs, les phĂ©notypes les plus compĂ©titifs dans un mĂ©lange sont en effet amenĂ©s Ă augmenter en frĂ©quence au fil des gĂ©nĂ©rations, entraĂźnant une diminution de la performance du groupe. Nous dĂ©veloppons donc un modĂšle thĂ©orique afin dâidentifier des mĂ©thodes de sĂ©lection permettant dâempĂȘcher les variĂ©tĂ©s les plus compĂ©titives dâaugmenter en frĂ©quence. Dans lâensemble, lâapproche interdisciplinaire dĂ©veloppĂ©e dans cette thĂšse permet de progresser dans la dĂ©tection, la comprĂ©hension, et la sĂ©lection des effets issus des interactions plante-plante, ouvrant ainsi des opportunitĂ©s stimulantes dans le domaine appliquĂ© et dans le domaine thĂ©orique
Shift in beneficial interactions during crop evolution
International audiencePlant domestication can be viewed as a form of co-evolved interspecific mutualism between humans and crops for the benefit of the two partners. Here, we ask how this plant-human mutualism has, in turn, impacted beneficial interactions within crop species, between crop species, and between crops and their associated microbial partners. We focus on beneficial interactions resulting from three main mechanisms that can be promoted by manipulating genetic diversity in agrosystems: niche partitioning, facilitation, and kin selection. We show that a combination of factors has impacted either directly or indirectly plant-plant interactions during domestication and breeding, with a trend toward reduced benefits arising from niche partitioning and facilitation. Such factors include marked decrease of molecular and functional diversity of crops and other organisms present in the agroecosystem, mass selection, and increased use of chemical inputs. For example, the latter has likely contributed to the relaxation of selection pressures on nutrient-mobilizing traits such as those associated to root exudation and plant nutrient exchanges via microbial partners. In contrast, we show that beneficial interactions arising from kin selection have likely been promoted since the advent of modern breeding. We highlight several issues that need further investigation such as whether crop phenotypic plasticity has evolved and could trigger beneficial interactions in crops, and whether human-mediated selection has impacted cooperation via kin recognition. Finally, we discuss how plant breeding and agricultural practices can help promoting beneficial interactions within and between species in the context of agroecology where the mobilization of diversity and complexity of crop interactions is viewed as a keystone of agroecosystem sustainability
Shift in beneficial interactions during crop evolution
none6noneFréville, HélÚne; Montazeaud, Germain; Forst, Emma; David, Jacques; Papa, Roberto; Tenaillon, Maud I.Fréville, HélÚne; Montazeaud, Germain; Forst, Emma; David, Jacques; Papa, Roberto; Tenaillon, Maud I
Farming plant cooperation in crops
AGAP : Ge2popSelection of the fittest can promote individual competitiveness but often results in the erosion of group performance. Recently, several authors revisited this idea in crop production and proposed new practices based on selection for cooperative phenotypes, i.e. phenotypes that increase crop yield through decreased competitiveness. These recommendations, however, remain difficult to evaluate without a formal description of crop evolutionary dynamics under different selection strategies. Here, we develop a theoretical framework to investigate the evolution of cooperation-related traits in crops, using plant height as a case study. Our model is tailored to realistic agricultural practices and shows that combining high plant density, high relatedness and selection among groups favours the evolution of shorter plants that maximize grain yield. Our model allows us to revisit past and current breeding practices in light of kin selection theory, and yields practical recommendations to increase cooperation among crops and promote sustainable agriculture
Predicting wheat maturity and stayâgreen parameters by modeling spectral reflectance measurements and their contribution to grain yield under rainfed conditions
AGAP : Ă©quipe GE2popInternational audienceThe normalized difference vegetation index (NDVI) continues to provide easy and fast methodologiesto characterize wheat genetic resources in response to abiotic stresses. This study identifies ways tomaximize green leaf area duration during grain filling and develops NDVI models to predict physio-logical maturity and different stay âgreen parameters to increase grain yield of rainfed winter wheatunder terminal drought. Three wheat populations were evaluated: one containing 240 landraces fromAfghanistan, the second with 250 modern lines and varieties, tested for two years under low rainfall con-ditions in Turkey, and the third with 291 landraces from Central and Western Asia (grown for one yearin the same location). The onset of senescence, maximum âgreennessâ, rate of senescence and residualâgreennessâ at physiological maturity were estimated using sequential measurements of NDVI and haveshown significant correlations with grain yield under low rainfall rainfed conditions. Trade-offs wereidentified among the different stay âgreen attributes, e.g. delayed onset of senescence and high maxi-mum âgreennessâ resulted in accelerated rates of senescence and highest yields and were most evidentin the landrace populations. It is concluded, that the use of rate of senescence to select for stay âgreenmust be coupled with other stay âgreen components, e.g. onset of senescence or maximum âgreennessâto avoid the effects of the trade-offs on final grain yield. The NDVI decay curves (using the last three NDVImeasurements up to maturity) were used to estimate days to maturity using the NDVI decay during thesenescence period and days to heading. A training and testing set (20 and 80% of each population, respec-tively) were used for calibrations allowing for correlations between predicted and observed maturity ofup to r = +0.85 (P < 0.0001). This procedure will facilitate large âscale wheat phenotyping in the future