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[hal-04799829] Identification of metabolic and protein markers representative of the impact of mild nitrogen deficit on agronomic performance of maize hybrids
IntroductionA better understanding of the physiological response of silage maize to a mild reduction in nitrogen (N) fertilization and the identification of predictive biochemical markers of N utilization efficiency could contribute to limit the detrimental effect of the overuse of N inputs.ObjectivesWe integrated phenotypic and biochemical data to interpret the physiology of maize in response to a mild reduction in N fertilization under agronomic conditions and identify predictive leaf metabolic and proteic markers that could be used to pilot and rationalize N fertilization.MethodsEco-physiological, developmental and yield-related traits were measured and complemented with metabolomic and proteomic approaches performed on young leaves of a core panel of 29 European genetically diverse dent hybrids cultivated in the field under non-limiting and reduced N fertilization conditions.ResultsMetabolome and proteome data were analyzed either individually or in an integrated manner together with eco-physiological, developmental, phenotypic and yield-related traits. They allowed to identify (i) common N-responsive metabolites and proteins that could be used as predictive markers to monitor N fertilization, (ii) silage maize hybrids that exhibit improved agronomic performance when N fertilization is reduced.ConclusionsAmong the N-responsive metabolites and proteins identified, a cytosolic NADP-dependent malic enzyme and four metabolite signatures stand out as promising markers that could be used for both breeding and agronomic purposes.
ano.nymous@ccsd.cnrs.fr.invalid (Maria Urrutia) 24 Dec 2024
https://hal.inrae.fr/hal-04799829v1
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[hal-05034220] Reducing the use of plant protection products and greenhouse gas emissions in arable farming systems in northern France (System-Eco+)
Crop protection and nitrogen fertilizers uses are the mainstays of large-scale cereal and industrial cropping systems in northern France. Biological and climatic effects call to design and evaluate cropping systems that cut the use of plant protection products by implementing counterbalancing agronomic levers aiming to maintain yields. An experimental set-up composed of 7 cropping systems located at the Estrées-Mons agronomic station (France) was monitored from 2018 to 2024. The experiment combined decrease in the use of plant protection products while improving the greenhouse gas (GHG) balance by reducing synthetic fertilization. The introduction of cropping systems designed to reduce the use of pesticides made it possible to achieve treatment frequency index (TFI) reductions of 70 to 100% without significantly affecting yields and while ensuring weed control. This also resulted in a significant reduction in fungicide and herbicide residues in the soil. The levers used to reduce the use of plant protection products have a neutral effect on greenhouse gas emissions, or even a favourable effect when leguminous crops are introduced into the succession to provide soil cover and balance the nitrogen balance.
ano.nymous@ccsd.cnrs.fr.invalid (Célestin Valentin) 15 Apr 2025
https://hal.inrae.fr/hal-05034220v1
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[hal-04057470] Combining a multi-environment trial and a diagnosis method to assess potential yield and main limiting factors of three highly different pea types
The evaluation of varieties of cultivated species is based on the implementation of multi-environmental trials that show high performances or strong limitations in some environments. To know the cause of these limitations, and to reason the adaptation of varieties to different environments, we propose a combined approach between the classical analysis of experimental results and a diagnostic approach using the DiagVar tool, which allows to assess the impact of limiting factors in each trial, the potential yield and the sensitivity of cultivars to those factors. This procedure is applied in a large and diversified field trial network including eight locations and three years to the comparison of two to four cultivars of the three agronomical pea types: spring peas, hr-winter peas (non-reactive to photoperiod) and Hr-winter peas (reactive to photoperiod). Estimates of potential yields from DiagVar for the three pea types were consistent with the experimental results, with higher values for hr-winter cultivars than for spring and Hr-winter ones. We shed light on specific limiting factors for each type, some of them being rarely quantified previously, which allows us to better target specific regions or environments for each pea type. Thus, spring types were more impacted by early limiting factors (loss of plants, low temperatures and radiation, lack of water, leading to reduced growth) and end-ofcycle stresses (high temperatures, water stress). Diseases had higher impacts on both winter types. Here we show for the first time that the lack of solar radiation affected particularly hr-winter type and the low crop nitrogen status affected more frequently spring peas. These results highlight the interest of carrying out an agronomic diagnosis in the analysis of varietal multi-environment trials, revealing the most important limiting factors to take into account while breeding new pea cultivars, particularly limiting factors that are difficult to directly observe. This method proves to be reliable and informative for breeders, technicians and agricultural advisors to discuss the adaptation of varieties to specific environment.
ano.nymous@ccsd.cnrs.fr.invalid (Christophe Lecomte) 04 Apr 2023
https://hal.inrae.fr/hal-04057470v1
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[hal-05041858] Bottom and Top Internodes Subjected to Interactions with Genotype in Miscanthus: Impact of Biochemical Composition and Anatomy on Stem-Based Composites Mechanical Properties
Miscanthus (Miscanthus Andersson) is a perennial grass for which biomaterials market has taken growing interest. Our objective was to evaluate the effect of stem internode position in Miscanthus × giganteus and Miscanthus sinensis and the impact of its anatomy and biochemical composition on internode-based composites' mechanical properties. Stems' bottom and top internodes were sampled for two genotypes of each species in two different years and separately added to a polypropylene matrix, and the mechanical properties of the internode-reinforced composites were measured. Before composite production, the internodes were extensively phenotyped for biochemical composition and anatomy. Stems' bottom and top internode-based composites yielded different modulus (3203 and 2988 MPa, respectively), while tensile strength was similar (36.4 and 36.5 MPa, respectively). Significant genotype × internode interactions occurred for most variables, mainly due to differences among species, since both Miscanthus sinensis clones proved to be more stable than both Miscanthus × giganteus clones for modulus (4% and 10.2%, respectively). Regarding tensile strength, the species showed small but opposite differences between internodes. Tensile strength and modulus were rather close only in the top internodes, where good mechanical properties were associated with the lowest values of vascular bundles number and section area and highest parenchyma tissue, while opposite results were obtained in the bottom ones, only for tensile strength. Miscanthus sinensis species proved to be interesting for the stability improvement of composite mechanical properties. It appears essential for experimental purposes to stratify the sampling by internode in order to be representative of the whole stem.
ano.nymous@ccsd.cnrs.fr.invalid (Maryse Brancourt-Hulmel) 22 Apr 2025
https://hal.inrae.fr/hal-05041858v1
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[hal-04623306] Trends and seasonal variability of atmospheric NO2 and HNO3 concentrations across three major African biomes inferred from long-term series of ground-based and satellite measurements
[...]
ano.nymous@ccsd.cnrs.fr.invalid (M. Ossohou) 25 Jun 2024
https://hal.science/hal-04623306v1
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[hal-03671280] PeaMUST (Pea MultiStress Tolerance), a multidisciplinary French project uniting researchers, plant breeders, and the food industry
The French government has supported as part of its "Investments for the Future" program a 9-year research project, PeaMUST, devoted to pea and to a lesser extent, faba bean improvement. Focusing on the main causes of yield irregularity that limit pea and faba bean cultivation, an integrated approach, including molecular exploitation of the pea genome sequence, was applied to identify and incorporate favorable alleles and allele combinations in prebreeding material.
ano.nymous@ccsd.cnrs.fr.invalid (Judith Burstin) 18 May 2022
https://hal.inrae.fr/hal-03671280v1
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[hal-01989858] Projet SYSTEM-ECO4 : Evaluation de systèmes de grandes cultures à faible usage de pesticides
19 prototypes de systèmes de culture ont été testés sur quatre sites contrastés (Picardie, Bourgogne et deux sites dans la région de Toulouse). Ces systèmes de grandes cultures ont été conçus selon les principes de Protection Intégrée pour limiter l'usage des pesticides en général et des herbicides en particulier. Les combinaisons de leviers alternatifs ont permis de gérer durablement la flore adventice avec peu d'herbicides, et de baisser l'usage de l'ensemble des pesticides. Certains systèmes permettent de concilier faible IFT et bonne performance économique. Trois sites ont été instrumentés pour collecter des eaux de drainage et mesurer les transferts de substances actives. Ces dispositifs ont permis d'établir un lien entre les IFT cumulés et les quantités de substance transférées dans les eaux, à l'échelle d'un site et sur trois années de mesure, confirmant ainsi le lien entre l'usage de pesticides et leur impact. Les prototypes fondés sur le semis direct ont été décevants : ils ont nécessité beaucoup d'herbicides pour maîtriser les adventices, les quantités de substances actives transférées sous ces parcelles ont été importantes, et les performances économiques ont été moyennes.
ano.nymous@ccsd.cnrs.fr.invalid (Nicolas Munier-Jolain) 22 Jan 2019
https://hal.inrae.fr/hal-01989858v1
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[hal-04353481] Genome-wide hypermethylation of TEs following low temperature exposure in maize
Transposable elements (TEs) are major players in shaping genome structure. TE sequences are transcriptionally silenced by epigenomic modifications to limit the mutagenic potential of their transpositional activity. In particular, several DNA methylation pathways are responsible for TE silencing in the various chromosomal locations where TE reside. While DNA methylation is known to be modified by abiotic constraints, the extent to which it can be remodeled remains to be fully elucidated. We show that low temperature triggers genome-wide hypermethylation in maize, mainly at transposable elements and centromeres. This hypermethylation is mediated by the parallel activation of multiple methylation pathways across chromosomes, to actively hypermethylate TEs in the various chromatin locations where they reside. This likely reflects the importance of taming transposable elements following an abiotic stress in maize, a species for which over 85% of the genome is constituted of transposable elements.
ano.nymous@ccsd.cnrs.fr.invalid (Zeineb Achour) 19 Dec 2023
https://hal.science/hal-04353481v1
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[hal-04305927] Low temperature triggers genome-wide hypermethylation of transposable elements and centromeres in maize
ABSTRACT Characterizing the molecular processes developed by plants to respond to environmental cues is a major task to better understand local adaptation. DNA methylation is a chromatin mark involved in the transcriptional silencing of transposable elements (TEs) and gene expression regulation. While the molecular bases of DNA methylation regulation are now well described, involvement of DNA methylation in plant response to environmental cues remains poorly characterized. Here, using the TE-rich maize genome and analyzing methylome response to prolonged cold at the chromosome and feature scales, we investigate how genomic architecture affects methylome response to stress in a cold-sensitive genotype. Interestingly, we show that cold stress induces a genome-wide methylation increase through the hypermethylation of TE sequences and centromeres. Our work highlights a cytosine context-specific response of TE methylation that depends on TE types, chromosomal location and proximity to genes. The patterns observed can be explained by the parallel transcriptional activation of multiple DNA methylation pathways that methylate TEs in the various chromatin locations where they reside. Our results open new insights into the possible role of genome-wide DNA methylation in phenotypic response to stress.
ano.nymous@ccsd.cnrs.fr.invalid (Zeineb Achour) 24 Nov 2023
https://hal.science/hal-04305927v1
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[hal-04353514] Genome-wide hypermethylation of TEs and centromeres following low temperature exposure in B73
Transposable elements (TEs) are major players in shaping genome structure. TE sequences are transcriptionally silenced by epigenomic modifications to limit the mutagenic potential of their transpositional activity. In particular, several DNA methylation pathways are responsible for TE silencing in the various chromosomal locations where TE reside. While DNA methylation is known to be modified by abiotic constraints, the extent to which it can be remodeled remains to be fully elucidated. We show that low temperature triggers genome-wide hypermethylation in maize, mainly at transposable elements and centromeres. This hypermethylation is mediated by the parallel activation of multiple methylation pathways across chromosomes, to actively hypermethylate TEs in the various chromatin locations where they reside. This likely reflects the importance of taming transposable elements following an abiotic stress in maize, a species for which over 85% of the genome is constituted of transposable elements.
ano.nymous@ccsd.cnrs.fr.invalid (Zeineb Achour) 19 Dec 2023
https://hal.science/hal-04353514v1
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[hal-02955226] Transcriptome analysis of a chilling tolerance strategy in European maize dent germplasm.
Maize has become an extensively cultivated crop in high latitudes like Northern Europe thanks to historical improvements of cold tolerance. However, earlier sowing increase the risk of exposure to longer chilling periods, affecting early growth and frequently plant performance and final yield. Understanding how maize responds to chilling periods is therefore a major task to both better understand maize local adaptation and improve agriculture. Here, we evaluated two sister double-haploid dent maize lines sharing 82% of their genome and displaying a contrasted tolerance to chilling. Using an Illumina stranded and paired-end mRNA-seq dataset from leaves of both sister lines grown under control and chilling conditions, we captured the allelic variation consequences at the transcript level. Clustering of differentially expressed gene profiles let us identify 574 genes differentially expressed, 513 and 61 being up- and down-expressed in the chilling-tolerant line compared to the chilling-sensitive line. We then explored how the variation in gene expression contributes to the variation in phenotypic traits. Genes associated with these traits were identified, paving the way for pinpointing candidate genes for chilling tolerance in future follow-up studies.
ano.nymous@ccsd.cnrs.fr.invalid (Catalina Durand Garzon) 01 Oct 2020
https://hal.inrae.fr/hal-02955226v1
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[hal-04787329] Analyse de la durabilité socio-économique et environnementale d'un réseau de systèmes de culture zéro-pesticides (Rés0Pest) après 10 ans d'expérimentation
Réduire la dépendance aux pesticides des systèmes agricoles est une priorité en raison de leurs impacts négatifs démontrés sur la santé des agroécosystèmes et la santé humaine. Nous présentons les résultats de dix ans d'expérimentation (2013-2022), évaluant la durabilité 1 de huit systèmes de culture sans pesticides en grande culture et en polyculture-élevage, dans différents contextes pédoclimatiques et socio-économiques en France. La contribution au développement durable des huit systèmes testés varie de « Moyenne à élevée » à « Très élevée ». La durabilité environnementale est « Très élevée » pour tous les systèmes. La rentabilité montre de fortes différences entre les systèmes, allant de « Très faible » à « Très élevée », dans un contexte où aucune valorisation économique particulière des récoltes produites sans pesticides n'a été prise en compte. Aucune dégradation de la capacité productive ou de la qualité sanitaire des récoltes n'a été observée à long terme et on montre qu'il est possible de se passer des pesticides si la préservation de l'environnement et de la santé humaine est compensée par une plusvalue dans le prix de vente des récoltes obtenues. Ces résultats confirment que la diversification des cultures et des pratiques culturales sont des leviers efficaces pour assurer la durabilité des systèmes de culture.
ano.nymous@ccsd.cnrs.fr.invalid (Vincent Cellier) 15 Apr 2025
https://hal.inrae.fr/hal-04787329v2
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[hal-05033805] Analysis of the socio-economic and environmental sustainability of a network of zero-pesticide cropping systems (Rés0Pest) after 10 years of experimentation
Reducing dependence on pesticides in agricultural systems is a priority due to their proven negative impacts on agroecosystems and human health. We present here the results of a ten years of experimental network (2013-2022), assessing the sustainability 1 of eight pesticide-free cropping systems in field and mixed cropping, in different pedoclimatic and socio-economic contexts in France. The contribution to sustainable development of the eight systems tested ranges from "medium to high" to "very high". Environmental sustainability is "very high" for all systems. Profitability varies widely from "very low" to "very high", in a context where no specific economic reward was considered for pesticide-free cropping systems preserving the environment and human health. No deterioration in the production capacity or sanitary quality of the crops was observed over the long term, and we show that it is possible to produce without pesticides if there is added value for harvest sold. These results confirm that crop diversification and cultivation practices are effective levers for ensuring the sustainability of cropping systems.
ano.nymous@ccsd.cnrs.fr.invalid (Vincent Cellier) 14 Apr 2025
https://hal.inrae.fr/hal-05033805v1
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[hal-02620164] Regulation of carbon metabolism in two maize sister lines contrasted for chilling tolerance
Maize can grow in cool temperate climates but is often exposed to spring chilling temperatures that can affect early seedling growth. Here, we used two sister double-haploid lines displaying a contrasted tolerance to chilling to identify major determinants of long-term chilling tolerance. The chilling-sensitive (CS) and the chilling-tolerant (CT) lines were grown at 14°C day/10°C night for 60 days. CS displayed a strong reduction in growth and aerial biomass compared to CT. Photosynthesis efficiency was affected with an increase in energy dissipation in both lines. Chilling tolerance in CT was associated with higher chlorophyll content, glucose-6-phosphate dehydrogenase activity and sucrose-to-starch ratio. Few changes in cell wall composition were observed in both genotypes. There was no obvious correlation between nucleotide sugar content and cell wall polysaccharide composition. Our findings suggest that the central starch-sucrose metabolism is one major determinant of the response to low temperature, and its modulation accounts for the ability of chilling-tolerant plants to cope with low temperature. This modulation seemed to be linked to a strong alteration in the biosynthesis of nucleotide sugars which at a high level, could reflect the remobilization of carbon in response to chilling.
ano.nymous@ccsd.cnrs.fr.invalid (Catalina Duran Garzon) 25 May 2020
https://hal.inrae.fr/hal-02620164v1
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[hal-02928007] Complementary approaches towards the discovery of genes controlling yield in pea
Pea is one of the most important grain legumes in the world. Improving pea yield is a critical breedingtarget in the current context of consumers’ increasing demand for plant proteins for food and feed. Becauseof its polygenic nature and the impact of the environment, breeding for higher yield is challenging. Weinvestigated the genetic determinism of yield (SW), seed number (SN) and thousand seed weight (TSW) usingboth linkage and linkage-disequilibrium approaches.Nine interconnected mapping populations, representing a total of 1,213 recombinant inbred lineswere phenotyped for SW, SN and TSW in six different field environments. These lines were genotyped usingthe GenoPea 13.2K SNP Array [1]. A multi-population quantitative trait loci (QTL) analysis [2] identified 19 QTLfor SW, 18 QTL for SN and 36 QTL for TSW. From this first QTL analysis, a metaQTL analysis [3] detected 27metaQTL and reduced confidence intervals.In addition, two panels of conventional winter pea (376 accessions) and spring pea (300 accessions)were phenotyped for the same traits in seven different field environments. These accessions were genotypedby re-sequencing after exome capture [4]. A Genome Wide Association analysis [5] detected markerssignificantly associated with the 3 traits.The combination of these two genetic approaches highlighted common regions on the pea genomethat represent genomic regions consistently involved in controling yield and its components in pea. Theseresults represent an important step towards marker assisted breeding programs for yield improvement.
ano.nymous@ccsd.cnrs.fr.invalid (Anthony Klein) 02 Sep 2020
https://hal.science/hal-02928007v1
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[hal-02737028] Projets IVD INRA-AgriObtentions variétales pour les légumineuses à graines
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Nathalie Moutier) 02 Jun 2020
https://hal.inrae.fr/hal-02737028v1
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[hal-03718343] Mixing Ability of Intercropped Wheat Varieties: Stability Across Environments and Tester Legume Species
Cereal-legume intercrops are developed mainly in low input or organic farming systems because of the overyielding and numerous ecosystem services they provide. For this management, little advice is available for varietal choice and there are almost no specific breeding programs. Our study aimed to evaluate the mixing ability of a panel of bread wheat genotypes in intercropping and to assess the impact of environment and legume tester choice on this ability. We used partial land equivalent ratios (LERs) to assess the mixing ability of a genotype defined as the combination of its ability to maintain its own yield in intercropping (producer effect, LERw) and to let the mixed species produce (associate effect, LERl). Eight wheat genotypes and 5 legume testers (3 pea and 2 faba bean varieties) were grown in sole crop and in all possible binary intercrops in nine contrasting environments. A mixed model was used to evaluate the effects of wheat genotypes, legume testers, environments, and all the interactions among these 3 factors on LERw and LERl. The chosen wheat genotypes presented contrasting mixing ability, either in terms of producer effect (LERw) or associate effect (LERl). A strong negative correlation was observed between these two components of genotype mixing ability, with an increase in producer effect being generally associated with similar decrease in associate effect, except for three genotypes. The impact of environment on the producer and associate effects was limited and similar between genotypes. Legume tester had a significant effect on both LERw and LERl, making the choice of tester a major issue to reveal the producer or associate effects of wheat genotype. Although the 5 testers showed no significant differences in wheat genotype order for both producer or associate effects, they showed different competitiveness and ability to discriminate genotypes: faba bean was very competitive, resulting in low LERt and low capacity to discriminate wheat genotypes for their mixing ability. On the contrary, pea was less competitive, resulting in higher LERt and better capacity to discriminate wheat genotypes. In particular, the Hr varieties (Geronimo and Spencer) discriminated best the wheat genotypes. Consequences on the implementation of breeding programs for wheat varieties adapted to intercropping are discussed.
ano.nymous@ccsd.cnrs.fr.invalid (Nathalie Moutier) 20 Jan 2023
https://hal.science/hal-03718343v1
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[hal-01607194] Bread wheat milling behavior: effects of genetic and environmental factors, and modeling using grain mechanical resistance traits
Genetic (Pinb-D1 alleles) and environment (through vitreousness) have important effects on bread wheat milling behavior. SKCS optimal values corresponding to soft vitreous or hard mealy grains were defined to obtain the highest total flour yield.Near-isogenic lines of bread wheat that differ in hardness, due to distinct puroindoline-b alleles (the wild type, Pinb-D1a, or the mutated forms, Pinb-D1b or Pinb-D1d), were grown in different environments and under two nitrogen fertilization levels, to study genetic and environmental effects on milling behavior. Milling tests used a prototype mill, equipped with two break steps, one sizing step, and two reduction steps, and this enabled 21 individual or aggregated milling fractions to be collected. Four current grain characters, thousand grain weight, test weight, grain diameter, and protein content, were measured, and three characters known to influence grain mechanical resistance, NIRS hardness, SKCS hardness index, and grain vitreousness (a character affecting the grain mechanical behavior but generally not studied). As expected, the wild type or mutated forms of Pinb-D1 alleles led to contrasted milling behavior: soft genotypes produced high quantities of break flour and low quantities of reduction flour, whereas reverse quantities were observed for hard genotypes. This different milling behavior had only a moderate influence on total flour production. NIRS hardness and vitreousness were, respectively, the most important and the second most important grain characters to explain milling behavior. However, contrary to NIRS hardness, vitreousness was only involved in endosperm reduction and not in the separation between the starchy endosperm and the outer layers. The highest flour yields were obtained for SKCS values comprised between 30 and 50, which corresponded either to soft vitreous or hard mealy grains. Prediction equations were defined and showed a good accuracy estimating break and reduction flours portions, but should be used more cautiously for total flour.
ano.nymous@ccsd.cnrs.fr.invalid (Francois-Xavier Oury) 30 Jul 2024
https://hal.science/hal-01607194v1
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[hal-02737297] Sélection pour les associations blé-pois : les caractéristiques des variétés de pois en culture pure sont-elles prédictives de leur comportement en culture associé
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Nathalie Moutier) 02 Jun 2020
https://hal.inrae.fr/hal-02737297v1
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[hal-02553534] Economical optimization of a breeding scheme by selective phenotyping of the calibration set in a multi-trait context: application to bread making quality
Trait-assisted genomic prediction approach is a way to improve genetic gain by cost unit, by reducing budget allocated to phenotyping or by increasing the program's size for the same budget. This study compares different strategies of genomic prediction to optimize resource allocation in breeding schemes by using information from cheaper correlated traits to predict a more expensive trait of interest. We used bread wheat baking score (BMS) calculated for French registration as a case study. To conduct this project, 398 lines from a public breeding program were genotyped and phenotyped for BMS and correlated traits in 11 locations in France between 2000 and 2016. Single-trait (ST), multi-trait (MT) and trait-assisted (TA) strategies were compared in terms of predictive ability and cost. In MT and TA strategies, information from dough strength (W), a cheaper trait correlated with BMS (r = 0.45), was evaluated in the training population or in both the training and the validation sets, respectively. TA models allowed to reduce the budget allocated to phenotyping by up to 65% while maintaining the predictive ability of BMS. TA models also improved the predictive ability of BMS compared to ST models for a fixed budget (maximum gain: + 0.14 in cross-validation and + 0.21 in forward prediction). We also demonstrated that the budget can be further reduced by approximately one fourth while maintaining the same predictive ability by reducing the number of phenotypic records to estimate BMS adjusted means. In addition, we showed that the choice of the lines to be phenotyped can be optimized to minimize cost or maximize predictive ability. To do so, we extended the mean of the generalized coefficient of determination (CD) criterion to the multi-trait context (CD).
ano.nymous@ccsd.cnrs.fr.invalid (S. Ben-Sadoun) 14 Dec 2020
https://hal.inrae.fr/hal-02553534v1
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[hal-04786067] Pesticide-free agriculture: is a third way possible aside organic agriculture and conventional agriculture?
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Diana Ortiz-Vallejo) 15 Nov 2024
https://hal.science/hal-04786067v1
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[hal-03480325] Identification of factors influencing predictive ability of phenomic selection and comparison to genomic selection in wheat breeding programs
In plant breeding, the selection of the best individuals is mainly based on phenotyping records. Because phenotyping is costly and time consuming, predictive tools such as Genomic selection (GS) have been developed in order to select among unphenotyped candidates. GS allows predicting the target traits for the selection candidates using the phenotypes of a training set and genotypic information collected on the training set and the selection candidates. Despite a good potential of the method to assist breeders in their selection choices, the cost of the genotyping still remains expensive, as GS requires to genotype each year the new selection candidates. In 2018, Rincent et al. developed a new, low cost, and high throughput method to predict the target trait of unobserved selection candidates. This method called phenomic selection (PS) is similar to GS, but genotyping is replaced by near infrared spectroscopy (NIRS). NIRS has the main advantage of being affordable, and already routinely applied on the selection candidates for many species such as wheat. GS has been well studied for twenty years, and many factors influencing its predictive ability are well understood. In PS, little is known about the factors influencing the predictive abilities, and about its performance relative to GS. We conducted the analyses on several datasets, corresponding to breeding lines drawn from the first or second years of trial evaluation from two breeding companies and one research institute in France. We evaluated several factors affecting PS predictive abilities including the possibility of combining spectra collected in different environments or at different steps of the breeding program. Contrary to genotypic data, near infrared spectra are indeed influenced by both the genotype and the environment. Thus, a selection candidate can be characterised by a multitude of spectra measured in different environments. The statistical model used was a simple H-BLUP model, reaching prediction ability from 0.26 to 0.62.Our results showed that the environment in which the NIR spectra was collected had an impor-tant impact on predictive ability and this impact was specific to the trait considered. Among all the models tested, combining NIR spectra from different environments were the best PS models and were at least as accurate as GS in most of the datasets. We finally tested a model which gathered NIRS and molecular marker effects. This model, GH-BLUP, was the best model of all, regardless of the trait or dataset, with prediction abilities reaching 0.31 to 0.73. In this study we showed that PS could be a great support tool for breeders to improve wheat breeding programs and could efficiently replace or complement GS..
ano.nymous@ccsd.cnrs.fr.invalid (P Robert) 14 Dec 2021
https://hal.inrae.fr/hal-03480325v1
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[hal-03517627] A Comparative Study of Maize and Miscanthus Regarding Cell-Wall Composition and Stem Anatomy for Conversion into Bioethanol and Polymer Composites
Due to an increasing demand for environmentally sustainable products, miscanthus and maize stover represent interesting lignocellulosic resources for conversion into biofuels and biomaterials. The overall purpose was to compare miscanthus and maize regarding cell-wall composition and stem anatomy for conversion into bioethanol and polymer composites using partial least squares regressions. For each of the two crops, six contrasted genotypes were cultivated in complete block design, and harvested. Internodes below the main cob for maize, and on the first aboveground internode for miscanthus, were analyzed for biochemistry and anatomy. Their digestibility was predicted using crop-specific near infrared calibrations, and the mechanical properties were evaluated in stem-based composites. On average, the internode cross-section of miscanthus anatomy was characterized by a thick rind (26.2 %) and few but dense pith-bundles (3.5 nb/mm²), while cell-wall constituted 95.2 % of the dry matter with high lignin (243.2 mg/g) and cellulose concentrations (439.7 mg/g). Maize internode-anatomy showed large cross-sections (397.5 mm²), pith with the presence of numerous bundles and non-lignified-pith fractions (22.3 % of the section). Its cellwall biochemistry displayed high concentrations of hemicelluloses, galactose, arabinose, xylose and ferulic acid. Cell-wall, lignin and cellulose concentrations were positively correlated with rind-fraction and pith-bundle-density, which explained strong mechanical properties as shown in miscanthus. Hemicelluloses, galactose, arabinose and ferulic acid concentrations were positively correlated with pith fraction and stem cross-section, revealing high digestibility as shown in maize. This underlines interesting traits for further comparative genetic studies, as maize represents a good model for digestibility and miscanthus for composites.
ano.nymous@ccsd.cnrs.fr.invalid (M. Brancourt-Hulmel) 07 Jan 2022
https://hal.science/hal-03517627v1
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[hal-03524817] Phenomic selection in wheat breeding: identification and optimisation of factors influencing prediction accuracy and comparison to genomic selection
Phenomic selection is a promising alternative or complement to genomic selection in wheat breeding. Models combining spectra from different environments maximise the predictive ability of grain yield and heading date of wheat breeding lines. Phenomic selection (PS) is a recent breeding approach similar to genomic selection (GS) except that genotyping is replaced by near-infrared (NIR) spectroscopy. PS can potentially account for non-additive effects and has the major advantage of being low cost and high throughput. Factors influencing GS predictive abilities have been intensively studied, but little is known about PS. We tested and compared the abilities of PS and GS to predict grain yield and heading date from several datasets of bread wheat lines corresponding to the first or second years of trial evaluation from two breeding companies and one research institute in France. We evaluated several factors affecting PS predictive abilities including the possibility of combining spectra collected in different environments. A simple H-BLUP model predicted both traits with prediction ability from 0.26 to 0.62 and with an efficient computation time. Our results showed that the environments in which lines are grown had a crucial impact on predictive ability based on the spectra acquired and was specific to the trait considered. Models combining NIR spectra from different environments were the best PS models and were at least as accurate as GS in most of the datasets. Furthermore, a GH-BLUP model combining genotyping and NIR spectra was the best model of all (prediction ability from 0.31 to 0.73). We demonstrated also that as for GS, the size and the composition of the training set have a crucial impact on predictive ability. PS could therefore replace or complement GS for efficient wheat breeding programs.
ano.nymous@ccsd.cnrs.fr.invalid (Pauline Robert) 23 Apr 2022
https://hal.inrae.fr/hal-03524817v1
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[hal-04816605] Réduction d'usage des phytosanitaires et émissions de gaz à effet de serre en systèmes de grande culture du Nord de la France (System-Eco+)
En contexte de grandes cultures céréalières et industrielles du nord de la France, 7 systèmes de culture mis en place sur la station agronomique d'Estrées-Mons (80) ont été suivis de 2018 à 2024 afin d'évaluer un gradient de réduction de la protection phytosanitaire via le recours à des leviers agronomiques compensateurs. L'expérimentation mise en place propose une approche transversale combinant la réduction de l'usage des produits phytosanitaires et l'amélioration du bilan des gaz à effet de serre (GES), notamment par la réduction de la fertilisation azotée. Les systèmes de culture conçus pour réduire l'usage des pesticides ont permis de réduire l'indicateur de fréquence de traitement (IFT) de 70 à 100% sans nuire de façon significative aux rendements tout en assurant la maîtrise des adventices. Une réduction des résidus de fongicides et herbicides dans les sols a aussi été mesurée. Les leviers mobilisés pour réduire l'usage des produits phytosanitaires ont un effet neutre sur les émissions de GES, voire favorable lorsque des légumineuses ayant pour objectifs la couverture du sol et l'équilibrage du bilan azoté sont introduites dans la succession.
ano.nymous@ccsd.cnrs.fr.invalid (Célestin Valentin) 03 Dec 2024
https://hal.inrae.fr/hal-04816605v1
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[hal-04454441] The maize low-lignin mutant F2bm3 shows pleiotropic effects on photosynthetic and cell wall metabolisms in response to chilling
Maize (Zea mays L.) is one of the major crops in the world and is highly sensitive to low temperature due to its tropical origin. Chilling may particularly affect maize during early seedling growth by altering physiological processes including photosynthesis and cell wall properties, leading to biomass reduction. Changes in photosynthetic and cell wall metabolisms were investigated during a long chilling exposure in a low-lignin maize mutant, brown midrib3 (bm3), which contains a null-mutation in the gene encoding caffeic acid O-methyltransferase (COMT). Wild-type F2 plants and the near-isogenic F2 bm3 mutant were grown during 60 days with a day/night temperature regime of 15°C/11°C in a greenhouse. Photosynthetic pigments, non-structural sugars, cell wall sugars, lignin, cell wall bound hydroxycinnamic acids (HCA) contents and phenylpropanoid pathway enzyme activities were determined when the 4th leaf had fully emerged. Results showed that the plants were smaller in response to chilling and this was more pronounced in the mutant. However, both genotypes showed good vigor. F2bm3 contained a two-fold increase in the level of chlorophyll a and accumulated zeaxanthin in response to chilling compared to F2, indicating an alternative photoprotection mechanism. Unlike the wild-type F2 line, the starch content was reduced in the F2bm3 mutant and the sucrose/starch partitioning was increased in F2bm3. Few changes in the non-cellulosic cell wall sugars composition could be detected, except a higher degree of substitution of glucuronoarabinoxylan and a higher content of β-glucan in both lines in response to chilling. The lignin content in leaves did not significantly change. But the concentration of HCAs was increased in F2bm3 while it decreased in F2. Furthermore, the concentration of esterified ferulic acid (FA) was greater in F2bm3, suggesting a higher degree of cross-linking between GAX and FA under chilling treatment. Thus, the increase in arabinose substitution on the xylan backbone and the abundance of HCA in F2bm3 could increase cell wall extensibility, thereby maintaining the hydration status of the cell wall in response to chilling. In addition, the higher concentrations of HCA and chlorophyll observed in F2bm3 suggest that HCAs could function as photoprotectors, thus enhancing chilling tolerance.
ano.nymous@ccsd.cnrs.fr.invalid (Catalina Duran Garzon) 13 Feb 2024
https://u-picardie.hal.science/hal-04454441v1
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[hal-03686646] The maize low-lignin $brown\ midrib3$ mutant shows pleiotropic effects on photosynthetic and cell wall metabolisms in response to chilling
Maize (Zea mays L.) is one of the major cereal crops in the world and is highly sensitive to low temperature. Here, changes in photosynthetic and cell wall metabolisms were investigated during a long chilling exposure in inbred line F2 and a low-lignin near-isogenic brown midrib3 mutant (F2bm3), which has a mutation in the caffeic acid O-methyltransferase (COMT) gene. Results revealed that the plant biomass was reduced, and this was more pronounced in F2bm3. Photosynthesis was altered in both lines with distinct changes in photosynthetic pigment content between F2bm3 and F2, indicating an alternative photoprotection mechanism between lines under chilling. Starch remobilization was observed in F2bm3 while concentrations of sucrose, fructose and starch increased in F2, suggesting a reduced sugar partitioning in F2. The cell wall was altered upon chilling, resulting in changes in the composition of glucuronorabinoxylan and a reduced cellulose level in F2. Chilling shifted lignin subunit composition in F2bm3 mutant to a higher proportion of p-hydroxyphenyl (H) units, whereas it resulted in lignin with a higher proportion of syringyl (S) residues in F2. On average, the total cell wall ferulic acid (FA) content increased in both genotypes, with an increase in ether-linked FA in F2bm3, suggesting a greater degree of cross-linking to lignin. The reinforcement of the cell wall with lignin enriched in H-units and a higher concentration in cell-wall-bound FA observed in F2bm3 as a response to chilling, could be a strategy to protect the photosystems.
ano.nymous@ccsd.cnrs.fr.invalid (Catalina Duran Garzon) 22 Jul 2024
https://u-picardie.hal.science/hal-03686646v1
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[hal-03270992] Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea
Frost is a limiting abiotic stress for the winter pea crop (Pisum sativum L.) and identifying the genetic determinants of frost tolerance is a major issue to breed varieties for cold northern areas. Quantitative trait loci (QTLs) have previously been detected from bi-parental mapping populations, giving an overview of the genome regions governing this trait. The recent development of high-throughput genotyping tools for pea brings the opportunity to undertake genetic association studies in order to capture a higher allelic diversity within large collections of genetic resources as well as to refine the localization of the causal polymorphisms thanks to the high marker density. In this study, a genome-wide association study (GWAS) was performed using a set of 365 pea accessions. Phenotyping was carried out by scoring frost damages in the field and in controlled conditions. The association mapping collection was also genotyped using an Illumina Infinium® BeadChip, which allowed to collect data for 11,366 single nucleotide polymorphism (SNP) markers.
ano.nymous@ccsd.cnrs.fr.invalid (Sana Beji) 23 Jan 2024
https://hal.inrae.fr/hal-03270992v1
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[hal-01604094] Genome-Wide association mapping of frost tolerance in Pisum sativum
Genome Wide Association Mapping was performed in pea. Accessions from the pea reference collection where phenotyped for frost in field and controlled conditions, and genotyped using Infinium®BeadChip 15K SNPs (Tayeh et al., 2015). After applying filters of quality control, we obtained 363 accessions and 10739 loci for GWA study. Association analyses were conducted with FaST-LMM software using a mixed model that included a relatedness kinship matrix (K) and a population structure matrix (Q) to control for false positives. The K matrix was generated using two approaches. In the first one, the kinship matrix was estimated with all the 10739 markers. In the second approach, we estimated the kinship, called “K-chr”, with all the markers other than those located on the same chromosome as the marker being tested (Rincent et al., 2014). Simulations revealed that Rincent’s approach was more powerful than the mixed model taking into account a general kinship (estimated for all chromosomes). The GWA study identified 8 loci distributed over different chromosomes comprising 61 SNPs significantly associated with frost tolerance. Results confirmed 3 QTLs that were previously mapped using bi-parental populations and identified 3 novel tolerance loci. Several potential-candidate genes were found corresponding to these SNPs. Additionally, the analyses allowed to identify haplotypes with increased frost tolerance and accessions with favourable alleles for this trait.
ano.nymous@ccsd.cnrs.fr.invalid (Sana Beji) 03 Jun 2020
https://hal.science/hal-01604094v1
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[hal-02741945] Towards genome-wide breeding for yield stability in spring pea
Field pea (<em>Pisum sativum</em> L.) is an attractive crop for human and livestock nutrition and an important contributor to low-input farming systems. Multiple environmental challenges face field pea production and penalize yield regularity. The work-package 1 of the French National ANR project PeaMUST aims at identifying efficient gene combinations for yield stability in low-input cropping systems through genomic selection. Genomic selection is a new breeding method that uses increasingly abundant genomic information and statistical modelling to select superior genotypes based on genomic estimated breeding values (GEBVs). The main goals are: 1- to build a genomic selection prediction equation for yield stability in low-input cropping systems, 2- to implement a genomic selection program and, 3- to evaluate the genetic progress obtained after one and two genomic selection cycles.
ano.nymous@ccsd.cnrs.fr.invalid (Anthony Klein) 03 Jun 2020
https://hal.inrae.fr/hal-02741945v1
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[hal-02743637] Nouveautés variétales de Pois Hr, adaptation au changement climatique
Contexte et problématique. Dans un contexte de fluctuation des surfaces cultivées de pois en France, les pois sont de plus en plus localisés dans la zone intermédiaire (22 départements du centre de la France situés entre le Poitou-Charente et la Lorraine). Pour la Bourgogne, les pois sont surtout cultivés dans les zones à vocation « grandes cultures », et notamment sur les plateaux et terres calcaires. En même temps, on constate que les pois d’hiver occupent une part croissante de ces surfaces. Ces évolutions s’expliquent par la volonté de minimiser un certain nombre de risques plus importants en sol profond et sur pois de printemps (Aphanomycès, stress de fin de cycle) et par l’arrivée de variétés de pois d’hiver de plus en plus performantes. La stagnation apparente des rendements sur le pois s’explique pour une part par ces évolutions. Pois d’hiver Hr. Les pois d’hiver Hr sont réactifs à la photopériode, c’est-à-dire que leur initiation florale ne peut avoir lieu pour des durées du jour inférieures à une certaine valeur, et donc pas avant une date calendaire relativement précise au printemps. Cela permet de les semer plus tôt à l’automne, dans le même créneau que le blé, sans courir le risque que l’initiation florale ait lieu trop tôt, ce qui exposerait les bourgeons floraux à des gels tardifs de fin d’hiver. Ces pois ont encore un caractère indéterminé (nombre d’étage florifères non fixé et pouvant être important), lié à une tardiveté qui positionne leur fin de cycle en même temps que les pois de printemps. Mais des progrès significatifs ont été obtenus pour avancer leurs dates de floraison et de maturité, ainsi que pour améliorer leur tolérance au gel, aux maladies et à la verse. En terme de productivité, ils peuvent donner des résultats comparables ou supérieurs aux autres pois d’hiver, mais la production reste plus soumise à des aléas. Deux variétés de pois d’hiver Hr sont inscrites pour la production de graines mais ne font pas l’objet de multiplications. La culture du pois en association avec une céréale présente plusieurs intérêts dans le contexte actuel (réduction des intrants, maintien de la teneur en protéines du blé, maîtrise des adventices…) et c’est une utilisation intéressante des pois Hr, qui donnent des performances comparables à celles des pois d’hiver classiques, tout en étant mieux synchronisés avec la céréale (en particulier dans le cas du blé). Adaptation au changement climatique. Le changement climatique en cours est attesté par les observations d’élévation de températures à toutes les saisons, depuis l’année 1987. Ceci se traduit par une évolution des risques climatiques sur la culture du pois que l’on peut partiellement anticiper. 2 Concernant le gel hivernal, les observations réalisées depuis 1987 et l’utilisation d’un modèle de calcul de la résistance au gel du pois indiquent qu’on a paradoxalement une augmentation du nombre de jours avec des dégâts de gel, mais une diminution de l’intensité moyenne du gel. L’élévation des températures entraîne une moindre acclimatation des plantes au froid, ce qui les rend plus vulnérables à des coups de gel brutaux comme en février 2012. Ceci est d’autant plus marqué avec des plantes à endurcissement lent, ce qui est le cas des types Hr actuels. Mais nous exploitons actuellement des ressources génétiques qui apportent un endurcissement rapide en même temps qu’une plus grande précocité. L’exposition du pois à des fortes températures en fin de cycle (en phase de remplissage des graines), s’accompagne d’une diminution du rendement, d’une élévation de la teneur en protéines des graines, et d’une diminution de la qualité germinative des semences. On s’attend également à ce que le changement climatique s’accompagne d’une augmentation de l’évapotranspiration des cultures, d’une augmentation de la nébulosité, et donc à une diminution du rapport éclairement / températures, qui peut avoir des conséquences sur la fertilité des plantes et le remplissage des graines. Conséquences sur les types variétaux à rechercher. Ces évolutions ont des conséquences sur les types variétaux à rechercher pour l’avenir : cycle de développement plus court, notamment pour les pois d’hiver Hr, adaptation à la culture en association, résistance au gel et vitesse d’endurcissement accrue, tolérance à la diminution de l’éclairement, aux fortes températures et au stress hydrique en fin de cycle. Pour ce dernier point, nous souhaitons exploiter les nouvelles connaissances acquises en terme de variabilité du développement du système racinaire et des interactions avec les micro-organismes du sol. D’autres travaux sont en cours, ou vont démarrer pour estimer l’effet des facteurs climatiques sur la production, leur évolution dans le contexte du changement climatique, ainsi que pour identifier des sources de résistance qui pourront être exploitées en création variétale.
ano.nymous@ccsd.cnrs.fr.invalid (Christophe Lecomte) 03 Jun 2020
https://hal.inrae.fr/hal-02743637v1
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[hal-04989185] Plan de Gestion de Données de l' Entité Unité Expérimentale Grandes Cultures Innovation Environnement (UE 0972 GCIE)
Ce Plan de Gestion des Données explicite la manière dont sont obtenues, documentées, analysées, stockées et partagées les données produites par l'UE GCIE. Ce document est conçu comme un outil pour gérer les données. Il a vocation à servir de base et à être adapté pour la rédaction des PGD de projets scientifiques.
ano.nymous@ccsd.cnrs.fr.invalid (Stéphanie Arnoult) 13 Mar 2025
https://hal.inrae.fr/hal-04989185v2
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[hal-02742488] Cold treatment affects the metabolite profiles of maize leaves
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Nadia Lamari) 03 Jun 2020
https://hal.inrae.fr/hal-02742488v1
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[hal-03125712] Combined metabolomic and proteomic profiling of maize leaf to reveal metabolic responses to cold temperatures
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Maria Urrutia) 29 Jan 2021
https://hal.inrae.fr/hal-03125712v1
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[hal-02742089] Combining LCMS data from two years for plant performance biomarkers discovery
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Maria Urrutia Rosauro) 03 Jun 2020
https://hal.inrae.fr/hal-02742089v1
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[hal-02799732] Determining a critical nitrogen dilution curve in Miscanthus x giganteus
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Marion Zapater) 05 Jun 2020
https://hal.inrae.fr/hal-02799732v1
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[hal-02800986] Rhizome filling seems to be triggered by climatic events in Miscanthus x giganteus
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Marion Zapater) 05 Jun 2020
https://hal.inrae.fr/hal-02800986v1
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[hal-02539641] Metabotyping of 30 maize hybrids under early-sowing conditions reveals potential marker-metabolites for breeding
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Nadia Lamari) 02 Feb 2024
https://hal.science/hal-02539641v1
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[hal-02801159] Miscanthus genetics and agronomy for bioenergy feedstock
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Maryse Brancourt Hulmel) 05 Jun 2020
https://hal.inrae.fr/hal-02801159v1
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[hal-02793860] Transfer of a miniaturized method for high-throughput screeninig of biomass pretreatment and saccharification and application on poplar and miscanthus clones
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Nassim Belmokhtar) 05 Jun 2020
https://hal.inrae.fr/hal-02793860v1
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[hal-02801880] Gérer les adventices sans herbicides
systèmes de culture innovants minimisant le recours aux pesticides, en combinant des leviers agronomiques et en valorisant les régulations biologiques, en grande culture et polyculture-élevage. Il a vu le jour en 2012 et regroupe 8 dispositifs expérimentaux (INRA et lycée agricole d’Auzeville) dans lesquels sont testés des systèmes de culture ayant en commun de ne pas recourir aux pesticides. Ses objectifs sont de : - concevoir et expérimenter des systèmes de culture sans pesticide dans différentes situations de production ; d’en évaluer les performances agronomiques, économiques, environnementales et sociales ; - analyser l’effet de ces systèmes sur l’évolution des communautés, notamment les bioagresseurs, et les régulations biologiques. Outre l’interdiction du recours aux pesticides, les systèmes testés doivent chercher à maximiser une production respectueuse des exigences des filières locales (les cultures de vente représentatives de la région doivent être maintenues et les critères de qualité des productions sont recherchés) et à maintenir le revenu de l’agriculteur. Les successions de cultures sont donc différentes selon les sites. Les systèmes de culture sont construits selon les principes de la protection intégrée en combinant des techniques alternatives, éprouvées ou suggérées par la bibliographie et les connaissances actuelles sur les bioagresseurs, en vue de réduire les risques de développement des bioagresseurs et de favoriser la mise en place de régulations biologiques. Bien qu’ils aient été conçus indépendamment les uns des autres, les systèmes de culture Rés0Pest utilisent des techniques communes pour la lutte contre les adventices, certaines étant raisonnées au niveau de la rotation (allongement de la rotation, diversification des cultures et des périodes de semis, alternance labour/non-labour, implantation de CIPAN, …), d’autres au niveau de l’itinéraire technique de chaque culture (faux-semis, désherbage mécanique, date et densité de semis…). Malgré son positionnement « zéro pesticide » très en rupture avec l’agriculture conventionnelle, Rés0Pest se distingue de l’Agriculture Biologique par l’alimentation azotée des cultures. En effet, la fertilisation minérale chimique est utilisée pour viser un rendement plus élevé, ce qui n'est pas sans conséquence sur le développement des adventives et des autres bioagresseurs. Rés0Pest permet donc d’obtenir des références originales intéressantes tant pour l’agriculture dite conventionnelle que pour l’Agriculture Biologique. Un tronc commun de mesures et d’observations a été mis en place sur le réseau dans le but de conduire un diagnostic agronomique et en particulier de suivre l’évolution de la flore adventice. Les trois premières campagnes expérimentales ont déjà permis de tirer des premiers enseignements sur la faisabilité et la maitrise de certaines combinaisons de techniques. Les expérimentations seront maintenues à minima pour les 3 prochaines campagnes culturales de manière à rendre possible l’étude des effets cumulatifs sur le long terme, en particulier sur la flore adventice.
ano.nymous@ccsd.cnrs.fr.invalid (Antoine Savoie) 05 Jun 2020
https://hal.inrae.fr/hal-02801880v1
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[hal-02744241] Searching for marker metabolites of crop performance
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Annick Moing) 03 Jun 2020
https://hal.inrae.fr/hal-02744241v1
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[hal-04154541] Magnitude, change over time, demographic characteristics and geographic distribution of excess deaths among nursing home residents during the first wave of COVID-19 in France: a nationwide cohort study
Abstract Background The objectives were to assess the excess deaths among Nursing Home (NH) residents during the first wave of the COVID-19 pandemic, to determine their part in the total excess deaths and whether there was a mortality displacement. Methods We studied a cohort of 494,753 adults in 6,515 NHs in France exposed to COVID-19 pandemic (from 1 March to 31 May 2020) and compared with the 2014–2019 cohorts using data from the French National Health Data System. The main outcome was death. Excess deaths and standardized mortality ratios (SMRs) were estimated. Result There were 13,505 excess deaths. Mortality increased by 43% (SMR: 1.43). The mortality excess was higher among males than females (SMR: 1.51 and 1.38) and decreased with increasing age (SMRs in females: 1.61 in the 60–74 age group, 1.58 for 75–84, 1.41 for 85–94 and 1.31 for 95 or over; males: SMRs: 1.59 for 60–74, 1.69 for 75–84, 1.47 for 85–94 and 1.41 for 95 or over). No mortality displacement effect was observed up until 30 August 2020. By extrapolating to all NH residents nationally (N = 570,003), we estimated that they accounted for 51% of the general population excess deaths (N = 15,114 out of 29,563). Conclusion NH residents accounted for half of the total excess deaths in France during the first wave of the COVID-19 pandemic. The excess death rate was higher among males than females and among younger than older residents.
ano.nymous@ccsd.cnrs.fr.invalid (Florence Canouï-Poitrine) 06 Jul 2023
https://hal.u-pec.fr/hal-04154541v1
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[hal-03107184] Maize metabolome and proteome responses to controlled cold stress partly mimic early‐sowing effects in the field and differ from those of Arabidopsis
In Northern Europe, sowing maize one-month earlier than current agricultural practices may lead to moderate chilling damage. However, studies of the metabolic responses to low, non-freezing, temperatures remain scarce. Here, genetically-diverse maize hybrids (Zea mays, dent inbred lines crossed with a flint inbred line) were cultivated in a growth chamber at optimal temperature and then three decreasing temperatures for two days each, as well as in the field. Leaf metabolomic and proteomic profiles were determined. In the growth chamber, 50% of metabolites and 18% of proteins changed between 20 and 16°C. These maize responses, partly differing from those of Arabidopsis to short-term chilling, were mapped on genome-wide metabolic maps. Several metabolites and proteins varied similarly for all temperature decreases: seven MS-based metabolite signatures and two proteins involved in photosynthesis decreased continuously. Several metabolites or proteins increasing in the growth-chamber chilling conditions showed similar trends in the early-sowing field experiment, including trans-aconitate, three hydroxycinnamate derivatives, a benzoxazinoid, a sucrose synthase, lethal leaf-spot 1 protein, an allene oxide synthase, several glutathione transferases and peroxidases. Hybrid groups based on field biomass were used to search for the metabolite or protein responses differentiating them in growth-chamber conditions, which could be of interest for breeding. This article is protected by copyright. All rights reserved.
ano.nymous@ccsd.cnrs.fr.invalid (Maria Urrutia) 22 Apr 2021
https://hal.inrae.fr/hal-03107184v1
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[hal-03766083] Estimation of Genetic Parameters of Biomass Production and Composition Traits in Miscanthus sinensis Using a Staggered-Start Design
Traits for biomass production and composition make Miscanthus a promising bioenergy crop for different bioconversion routes. They need to be considered in miscanthus breeding programs as they are subjected to genetic and genetic x environment factors. The objective was to estimate the genetic parameters of an M. sinensis population grown during 4 years in two French locations. In each location, the experiment was established according to a staggered-start design in order to decompose the year effect into age and climate effects. Linear mixed models were used to estimate genetic variance, genotype x age, genotype x climate interaction variances, and residual variances. Individual plant broad-sense heritability means ranged from 0.42 to 0.62 for biomass production traits and were more heritable than biomass composition traits with means ranging from 0.26 to 0.47. Heritability increased through age for most of the biomass production and composition traits. Low genetic variance along with large genotype x age and genotype x climate interaction variances tended to decrease the heritability of biomass production traits for young plant ages. Most of the production traits showed large interaction variances for age and climate in both locations, while biomass composition traits highlighted large interaction variances due to climate in Orleans. The genetic and phenotypic correlations between biomass production and composition traits were positive, while hemicelluloses were negatively correlated with all traits. Selection is difficult on young plants as the heritability is too low. The joint improvement of biomass production and composition traits would help provide a better response of miscanthus to selection.
ano.nymous@ccsd.cnrs.fr.invalid (Raphaël Raverdy) 31 Aug 2022
https://hal.inrae.fr/hal-03766083v1
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[hal-04000204] Impact of miscanthus lignin and arabinoxylan on Portland cement
Miscanthus biomass can be used to produce lightweight concrete. However, cell wall polymers leached in the alkaline cementitious medium can disturb cement setting. This is the case for grass lignin and grass arabinoxylan due to their specific alkali solubility. The main objective of this paper was to study the impact of lignin and of arabinoxylan from miscanthus biomass on the hydration of Portland cement and by electrical conductivity. To this end, dioxan lignin (DL) and arabinoxylan (AX) were extracted from miscanthus by methods preserving the main structural specificities of the native polymers. These DL and AX fractions were added to Portland cement (1-5% w/w in cement) and their impact on the electrical conductivity of cement/water mixtures was time-monitored. The novelty of this study lies in using polymers structurally similar to those of miscanthus fibers rather than commercially available ones, such as kraft lignin (KL). The addition of DL or of KL to cement/water mixture differently affected the electrical conductivity, which is most likely assignable to the severe structural degradation of KL during kraft process. The conductivity curves suggested that cement hydration was substantially delayed when DL % in cement was 3% or more while lower values had no impact. The results support the hypothesis that the access of water to cement grains was impeded by the adsorption of ionized lignin entities at their surface. When co-added to the cement (1.6 wt% each), the DL and AX fraction delayed cement hydration more substantially than when the same amounts were separately added. This unexpected synergy suggests that the miscanthus lignin and arabinoxylan polymers form lignin-carbohydrate complexes efficiently adsorbed on cement grains.
ano.nymous@ccsd.cnrs.fr.invalid (Jordi Girones) 22 Feb 2023
https://hal.science/hal-04000204v1
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[hal-03103076] Polysaccharides and phenolics of miscanthus belowground cell walls and their influence on polyethylene composites
Belowground materials from two miscanthus species were ground into fragments for preparing polyethylene composites. Both species show a lot of similarities in terms of polysaccharides, lignin and cell wall-linked p-coumaric and ferulic acids contents. The structures of polysaccharides and of lignins are markedly different in the miscanthus belowground and aboveground biomass. The non-cellulosic fraction of the samples comprises a high level of xylose, with the arabinose to xylose ratio about twice as high as that observed for analogous stem samples, suggesting that belowground arabinoxylans are more substituted than stem ones. The mechanical properties of the belowground miscanthus-polyethylene composites correlate with several of their compositional traits, with similar trends as for plant stem-polyethylene composites with positive correlations for lignin and p-coumaric acid contents and negative correlations for most non-cellulosic sugars.
ano.nymous@ccsd.cnrs.fr.invalid (Erika Di Giuseppe) 07 Jan 2021
https://minesparis-psl.hal.science/hal-03103076v1
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[hal-02921257] Thermal and dynamic mechanical characterization of miscanthus stem fragments: Effects of genotypes, positions along the stem and their relation with biochemical and structural characteristics
The thermal and dynamic mechanical properties of miscanthus stem fragments and differences between genotypes and positions along the stem are studied in relation with their biochemical and structural characteristics. The starting degradation temperature does not correlate to the biochemical composition. However, the first DTG peak temperature is negatively correlated to hemicelluloses content and positively correlated to lignin and p-coumaric contents. A pronounced genotypic effect is evidenced on fragments elastic moduli while limited effect of the position along the stem is found. This is mostly related to ferulic and p-coumaric acid contents of stem fragments for which a strong correlation to elastic moduli is evidenced. Our results highlight that genotypic effect, position along the stem, stem fragment dimensions and mechanical properties of miscanthus stem fragments are strongly interconnected in relation with their respective biochemical and structural characteristics. This opens interesting perspectives for identifying key biological traits that need to be optimized for a better selection of performing miscanthus genotypes targeted to polymer composite applications.
ano.nymous@ccsd.cnrs.fr.invalid (Lucie Chupin) 01 Sep 2020
https://imt-mines-ales.hal.science/hal-02921257v1
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[hal-03766074] One-step preparation procedure, mechanical properties and environmental performances of miscanthus-based concrete blocks
Concrete blocks prepared with Portland cement and miscanthus-based aggregates were prepared in order to check if the miscanthus genotype may influence their mechanical properties and to perform an environmental assessment. To produce lightweight, load-bearing concrete blocks using miscanthus stem fragments as aggregates in a single mixing method turned out to be impossible, although trying to optimize the concrete formulation. The results show that genotypes and size of miscanthus fragments controlled the mechanical properties of the final blocks. The lower was the amount of light elements such as leaves and sheath, the better were the mechanical properties of the blocks. When comparing genotypes with the same leaf/stem ratio, it was not possible to see a correlation between the biochemical composition of the stem and the compressive strength of the blocks. A probable explanation is the small variation of biochemical composition between genotypes. Using life cycle analysis tools, miscanthus block were not found to be competitive with conventional alternatives (concrete block and lightweight pumice block) when trying to increase compressive strength above 3 MPa. However, compared to non-load bearing alternatives (light clay brick), blocks integrating miscanthus had a better global environmental performance mainly due to a favorable climate change impact. The present work also points out the risk of decreasing the environmental performances when cultivating the crop on land in competition with food, because of the impacts of indirect consequences of Land Use Change.
ano.nymous@ccsd.cnrs.fr.invalid (Colin Jury) 22 Jul 2024
https://hal.inrae.fr/hal-03766074v1
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[hal-03517628] Variability of stem solidness among miscanthus genotypes and its role on mechanical properties of polypropylene composites
Miscanthus (Miscanthus Andersson) is a perennial grass that is attracting growing interest from the biomaterial industry. Our aim was to compare miscanthus genotypes varying in stem solidness, a measure of degree to which pith fills cavity between the outer walls of the stem, and analyze whether this trait influences the mechanical properties of polypropylene composites reinforced with miscanthus particles. Six contrasting genotypes were chosen from a Miscanthus sinensis population to determine morphological variables, stem solidness, and mechanical properties of polypropylene composites including 30% of milled miscanthus particles of two sizes of 100 < × < 200 μm and 200 < × < 300 μm. Although aboveground biomass of miscanthus was closely related to the aboveground volume of the plant, namely stand volume, a few genotypes showed contrasting aboveground biomass production for similar stand volumes. This generated contrasting ratio between aboveground biomass and stand volume, namely plant-specific weights, for similar plant volumes. A principal component analysis showed that fully pith-filled stems, namely solid stems, were explained by a large stand volume and plant-specific weights as well as small stem cross-sections. Genotypes showing partially filled stems were taller with larger stem cross-sections but smaller plant-specific weights. They revealed high lignin and p-coumaric acid contents. Compared to neat-polypropylene, Young's modulus increased significantly by 139% and 134% and tensile strength by 39% and 36% for genotypes with partially filled stems compared to genotypes with fully pith-filled stems, respectively. This difference in reinforcing capacity was similar to that of two particle sizes (139% and 134% for Young's modulus, 41% and 34% for tensile strength, respectively). A good tensile strength was obtained with large cross-stem section, plant height and lignin and p-coumaric acid contents. It decreased with plant-specific weight, hemicellulose and ferulic acid contents. Wider morphological variations in other progenies or Miscanthus species should be explored further using the techniques reported here.
ano.nymous@ccsd.cnrs.fr.invalid (Maryse Brancourt‐hulmel) 07 Jan 2022
https://hal.science/hal-03517628v1
