Microsatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collection for studying naturally occurring variation in Medicago truncatula

BACKGROUND: Exploiting genetic diversity requires previous knowledge of the extent and structure of the variation occurring in a species. Such knowledge can in turn be used to build a core-collection, i.e. a subset of accessions that aim at representing the genetic diversity of this species with a minimum of repetitiveness. We investigate the patterns of genetic diversity and population structure in a collection of 346 inbred lines representing the breadth of naturally occurring diversity in the Legume plant model Medicago truncatula using 13 microsatellite loci distributed throughout the genome. RESULTS: We confirm the uniqueness of all these genotypes and reveal a large amount of genetic diversity and allelic variation within this autogamous species. Spatial genetic correlation was found only for individuals originating from the same population and between neighbouring populations. Using a model-based clustering algorithm, we identified four main genetic clusters in the set of individuals analyzed. This stratification matches broad geographic regions. We also identified a set of "admixed" individuals that do not fit with this population structure scheme. CONCLUSION: The stratification inferred is discussed considering potential historical events like expansion, refuge history and admixture between neighbouring groups. Information on the allelic richness and the inferred population structure are used to build a nested core-collection. The set of inbred lines and the core collections are publicly available and will help coordinating efforts for the study of naturally occurring variation in the growing Medicago truncatula community

Multi-scale high-throughput phenotyping of apple architectural and functional traits in orchard reveals genotypic variability under contrasted watering regimes

Despite previous reports on the genotypic variation of architectural and functional traits in fruit trees, phenotyping large populations in the field remains challenging. In this study, we used high-throughput phenotyping methods on an apple tree core-collection (1000 individuals) grown under contrasted watering regimes. First, architectural phenotyping was achieved using T-LiDAR scans for estimating convex and alpha hull volumes and the silhouette to total leaf area ratio (STAR). Second, a semi-empirical index (IPL) was computed from chlorophyll fluorescence measurements, as a proxy for leaf photosynthesis. Last, thermal infrared and multispectral airborne imaging was used for computing canopy temperature variations, water deficit, and vegetation indices. All traits estimated by these methods were compared to low-throughput in planta measurements. Vegetation indices and alpha hull volumes were significantly correlated with tree leaf area and trunk cross sectional area, while IPL values showed strong correlations with photosynthesis measurements collected on an independent leaf dataset. By contrast, correlations between stomatal conductance and canopy temperature estimated from airborne images were lower, emphasizing discrepancies across measurement scales. High heritability values were obtained for almost all the traits except leaf photosynthesis, likely due to large intra-tree variation. Genotypic means were used in a clustering procedure that defined six classes of architectural and functional combinations. Differences between groups showed several combinations between architectural and functional traits, suggesting independent genetic controls. This study demonstrates the feasibility and relevance of combining multi-scale high-throughput methods and paves the way to explore the genetic bases of architectural and functional variations in woody crops in field conditions

Western European Populations of the Ichneumonid Wasp Hyposoter didymator Belong to a Single Taxon

Hyposoter didymator (Hymenoptera, Ichneumonidae) is a generalist solitary endoparasitoid of noctuid larvae. In the present work, we tested whether populations of H. didymator were divided in several genetically distinct taxa as described for many other generalist parasitoid species, and whether differences in H. didymator parasitism rates were explained by the insect host species and/or by the plant on which these hosts were feeding on. The genetic analysis of natural populations collected in different regions in France and Spain on seven different insect hosts and seven different host plants (775 individuals) showed that H. didymator populations belong to a unique single taxon. However, H. didymator seems to be somewhat specialized. Indeed, in the fields it more often parasitized Helicoverpa armigera compared to the other host species collected in the present work. Also, H. didymator parasitism rates in field conditions and semi-field experimental studies were dependent on the host plants on which H. armigera larvae are feeding. Still, H. didymator can occur occasionally on non-preferred noctuid species. One hypothesis explaining the ability of H. didymator to switch hosts in natura could be related to fluctuating densities of the preferred host over the year; this strategy would allow the parasitoid to avoid seasonal population collapses

Enherbement du vignoble Méditerranéen avec des luzernes annuelles

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How can a dry forage database be used to predict fresh grass composition by NIR spectroscopy? Data transfer vs spectra transfer

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Unravelling the responses of different apple varieties to water constraints by continuous field thermal monitoring

This research aimed at analyzing the response of apple tree varieties subjected to soil water deficit and atmospheric drought in a field phenotyping platform located in the Mediterranean area. The main assumption of the study was that seasonal and daily stomatal behavior can be monitored by continuous measurement of canopy surface temperature (Ts) as a proxy of stomatal closure. To achieve the study objectives, thermal monitoring of 6 pre-commercial apple varieties was simultaneously carried out throughout one season by nadir-oriented thermo-radiometers placed 1.50 m over the tree top canopy. Two water regimes were applied to each variety during a 4-week summer period: normal irrigation (WW) vs progressive water deficit (WS). The maximum difference in Ts between water regimes was recorded daily between 11:00 and 14:20 GMT, with an earlier closure of stomata in WS trees. During the day, a more negative stem water potential (Ψstem) and a higher diurnal Ts (+1° to +2 °C) were observed on WS trees, resulting in a significant limitation of fruit growth. Tree water stress was caused by both edaphic and atmospheric droughts, in the medium and short terms respectively, with inter-varietal and inter-regime differences highlighting distinct stomatal closure behaviors. Results suggest that some of the varieties studied are well adapted to stressful summer conditions, as long as irrigation needs are met, while other varieties show a particular sensitivity to the mid-day evaporative demand, which may limit their extension. Although these results are not comprehensive enough to predict the optimal performance of varieties under different stress scenarios, the proposed methodology allows to assess the dynamics of tree response to water constraints using non-invasive thermal sensors. It opens up new perspectives for the phenotyping of apple cultivars under abiotic stress, achievable through the quantified study of their transpiration flux in response to stress scenarios. These prospects will require further in planta measurements to dissect varietal differences.info:eu-repo/semantics/acceptedVersio

Unravelling the responses of different apple varieties to water constraints by continuous field thermal monitoring

International audienceThis research aimed at analyzing the response of apple tree varieties subjected to soil water deficit and atmo-spheric drought in a field phenotyping platform located in the Mediterranean area. The main assumption of the study was that seasonal and daily stomatal behavior can be monitored by continuous measurement of canopy surface temperature (Ts) as a proxy of stomatal closure. To achieve the study objectives, thermal monitoring of 6 pre-commercial apple varieties was simultaneously carried out throughout one season by nadir-oriented thermo-radiometers placed 1.50 m over the tree top canopy. Two water regimes were applied to each variety during a 4-week summer period: normal irrigation (WW) vs progressive water deficit (WS). The maximum difference in Ts between water regimes was recorded daily between 11:00 and 14:20 GMT, with an earlier closure of stomata in WS trees. During the day, a more negative stem water potential (psi stem) and a higher diurnal Ts (+1 & nbsp; to +2 C) were observed on WS trees, resulting in a significant limitation of fruit growth. Tree water stress was caused by both edaphic and atmospheric droughts, in the medium and short terms respectively, with inter-varietal and inter-regime differences highlighting distinct stomatal closure behaviors. Results suggest that some of the vari-eties studied are well adapted to stressful summer conditions, as long as irrigation needs are met, while other varieties show a particular sensitivity to the mid-day evaporative demand, which may limit their extension. Although these results are not comprehensive enough to predict the optimal performance of varieties under different stress scenarios, the proposed methodology allows to assess the dynamics of tree response to water constraints using non-invasive thermal sensors. It opens up new perspectives for the phenotyping of apple cultivars under abiotic stress, achievable through the quantified study of their transpiration flux in response to stress scenarios. These prospects will require further in planta measurements to dissect varietal differences

Adaptation of alfalfa ecotypes to climate change

National audienceThe availability of forage resources in European Mediterranean areas, subject to cyclical droughts and changing climatic conditions (temperature increase of + 0.6C°/decade, evapotranspiration + 50 mm/decade), has become a major challenge for livestock farming. Following professional organizations seeking INRA and CIRAD’s expertise to search for alfalfa ecotypes capable of adaptation, we have been investigating the diversity of behaviors of 100 alfalfa ecotypes from 26 countries according to climatic constraints for the last three years. Key assumptions related to the response diversity in terms of i) survival, ii) productivity, and iii) nutritive composition. Tests were carried out without inputs or irrigation. Ecotypes of three different environments were pre-selected from a previous project with a total of 65 industrial, 25 farm and 10 wild ecotypes. The results obtained depending on rainfall amounts – i.e. favorable in 2012 with > 30 mm/month, and unfavorable in 2013 and 2014 with < 30 mm/month during the plant growth period –, can help us make selections based on biomass and total nitrogen content. Under rainfall deficit conditions results show: • A marked drop in the productivity of industrial ecotypes due to their sensitivity, the variation of the dry matter is, in 2012-2013: - 25% ± 0.024; in 2012-2014: - 62% ± 0.015; in 2013-2014: - 46% ± 0.044; • Resilience of farm and wild ecotypes highlighting a more interesting genetic variability for selection purposes; • Changes in the earliness/maturity of the various ecotypes, which revealed opportunities to improve animal feed production (grazing periods, cutting dates...); • An opportunity to integrate some ecotypes in multi-specific mixtures

Contribution of High-Resolution Multispectral and Thermal-Infrared Airborne Imagery to Assess the Behavior of Fruit Trees Facing Water Stress: Proof of the Concept and First Results in an Apple Variety Field Trial

UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitièresA combined airborne thermal and multispectral imagery campaign was performed by UAV in two apple variety trials (flights at 40m elevation) located in South France. Both experimental orchards were dedicated to the assessment of various tree traits, including the response to water deficit. Subplots of each variety were submitted either to normal irrigation (WW), scheduled on the basis of soil hydric potential, or to water restriction (WS) during summer period (July 2015). In planta measurements performed in these 'genotype by environment' experiments comprised the monitoring of fruit diameter increase, the assessment of tree water status by stem or predawn leaf hydric potential, while local microclimatic data were also collected. Thanks to remotely-sensed thermal imagery, significantly higher canopy temperatures were found in WS trees compared to WW ones (average of 3 trees), and also significant differences in narrow-range spectral wavebands (multispectral images), and the vegetation indices calculated (NDVI, GNDVI and PRI). Differences were linked to the severity of water deficit reached, assessed by hydric potential, which varied significantly according to the genotype. Two varieties -more water spending- experienced a characteristic water stress while two others -more water saving- were less affected by water deficit, as revealed by image- and tree-based variables. The experiment thus demonstrated the potential of multispectral and thermal high resolution imagery to non-invasive phenotyping of fruit trees cover