A5005899389- Genetics and Plant Breeding
- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Wheat and Barley Genetics and Pathology
- Crop Yield and Soil Fertility
- Spectroscopy and Chemometric Analyses
- Horticultural and Viticultural Research
- Plant nutrient uptake and metabolism
- Bayesian Methods and Mixture Models
- Statistical Methods and Bayesian Inference
- Gene expression and cancer classification
- Plant Physiology and Cultivation Studies
- Agriculture and Rural Development Research
- Berry genetics and cultivation research
- Plant Disease Resistance and Genetics
- Agriculture, Soil, Plant Science
- Regional Economic and Spatial Analysis
- Evolution and Genetic Dynamics
- Banana Cultivation and Research
- Evolutionary Algorithms and Applications
- Genetic Associations and Epidemiology
- Chromosomal and Genetic Variations
- Agricultural Productivity and Crop Improvement
- Regional Development and Policy
- Insect-Plant Interactions and Control
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2016-2025
Université Paris-Saclay
2022-2025
Génétique Quantitative et Évolution Le Moulon
2013-2025
AgroParisTech
2014-2025
Centre National de la Recherche Scientifique
2012-2025
Université Clermont Auvergne
2020-2024
Génétique, Diversité, Écophysiologie des Céréales
2015-2023
Clermont Université
2022
Limagrain (France)
2012-2014
Université Paris-Sud
2012-2014
Abstract Genomic selection refers to the use of genotypic information for predicting breeding values candidates. A prediction formula is calibrated with genotypes and phenotypes reference individuals constituting calibration set. The size composition this set are essential parameters affecting reliabilities. objective study was maximize reliabilities by optimizing Different criteria based on diversity or error variance (PEV) derived from realized additive relationship matrix–best linear...
In sexually reproducing organisms, meiotic crossovers ensure the proper segregation of chromosomes and contribute to genetic diversity by shuffling allelic combinations. Such reassortment is exploited in breeding combine favorable alleles, research identify factors underlying traits interest via linkage or association-based approaches. Crossover numbers distributions along vary between species, but little known about their intraspecies variation. Here, we report on variation recombination...
Genomic selection - the prediction of breeding values using DNA polymorphisms is a disruptive method that has widely been adopted by animal and plant breeders to increase productivity. It was recently shown other sources molecular variations such as those resulting from transcripts or metabolites could be used accurately predict complex traits. These endophenotypes have advantage capturing expressed genotypes consequently regulatory networks occur in different layers between genome...
Abstract Classical genomic prediction approaches rely on statistical associations between traits and markers rather than their biological significance. Biologically informed selection of regions can help prioritize polymorphisms by considering underlying processes, making models robust accurate. Gene ontology (GO) terms be used for this purpose, the information integrated into through marker categorization. It allows likely causal to account a certain portion genetic variance independently...
Abstract Association mapping has permitted the discovery of major QTL in many species. It can be applied to existing populations and, as a consequence, it is generally necessary take into account structure and relatedness among individuals statistical model control false positives. We analytically studied power association studies by computing noncentrality parameter tests its relationship with parameters characterizing diversity (genetic differentiation between groups allele frequencies)...
Breeding for cold tolerance in maize promises to allow increasing growth area and production temperate zones. The objective of this research was conduct genome-wide association analyses (GWAS) inbred lines find strategies pyramiding genes tolerance. Two panels 306 dent 292 European flint were evaluated per se testcrosses under control conditions a chamber. We recorded indirect measures as the traits number days from sowing emergence, relative leaf chlorophyll content or quantum efficiency...
Plant breeders evaluate their selection candidates in multi-environment trials to estimate performance contrasted environments. The number of genotype/environment combinations that can be evaluated is strongly constrained by phenotyping costs and the necessity limit evaluation a few years. Genomic prediction models taking genotype environment interactions (GEI) into account help identify combination (possibly unphenotyped) genotypes target environments optimizing traits under selection. We...
We propose a criterion to predict genomic selection efficiency for structured populations. This is useful define optimal calibration set and estimate prediction reliability multiparental Genomic refers the use of genotypic information predicting performance candidates. It has been shown that accuracy depends on various parameters including composition (CS). Assessing level given scenario highest importance because it can be used optimize CS sampling before collecting phenotypes, once...
We developed an integrated R library called BWGS to enable easy computation of Genomic Estimates Breeding values (GEBV) for genomic selection. BWGS, BreedWheat selection, was in the framework a cooperative private-public partnership project Breedwheat (https://breedwheat.fr) and relies on existing R-libraries, all freely available from CRAN servers. The two main functions run 1) replicated random cross validations within training set genotyped phenotyped lines 2) GEBV prediction,...
We propose a statistical criterion to optimize multi-environment trials predict genotype × environment interactions more efficiently, by combining crop growth models and genomic selection models. Genotype (GEI) are common in plant (METs). In this context, developed for (GS) that refers the use of genome-wide information predicting breeding values candidates need be adapted. One promising way increase prediction accuracy various environments is combine ecophysiological genetic modelling...
To enable a scalable sparse testing genomic selection (GS) strategy at preliminary yield trials in the CIMMYT maize breeding program, optimal approaches to incorporate genotype by environment interaction (GEI) prediction models are explored. Two cross-validation schemes were evaluated: CV1, predicting genetic merit of new bi-parental populations that have been evaluated some environments and not others, CV2, half population has phenotyped others using coefficient determination (CDmean)...
Roots are essential for water and nutrient uptake but rarely the direct target of breeding efforts. To characterize genetic variability wheat root architecture, shoot traits 200 durum 715 bread varieties were measured at a young stage on high-throughput phenotyping platform. Heritability platform ranged from 0.40 biomass in to 0.82 number tillers. Field data yield components SNP genotyping already available all genotypes. Taking differences earliness into account, several significant...
Elucidating the genetic components of plant genotype-by-environment interactions is key importance in context increasing climatic instability, diversification agricultural practices and pest pressure due to phytosanitary treatment limitations. The genotypic response environmental stresses can be investigated through multi-environment trials (METs). However, genome-wide association studies (GWAS) MET data are significantly more complex than that single environments. In this context, we...
Abstract Key message Phenomic selection based on parental spectra can be used to predict GCA and SCA in a sparse factorial design. Prediction approaches such as genomic game changers hybrid breeding. They allow predicting the genetic values of hybrids without need for their physical production. This leads significant reductions breeding cycle length, so increase progress. However, these methods are often underutilized programs due substantial cost involved genotyping thousands candidate...
Abstract Phenotypic plasticity can contribute to crop adaptation challenging environments. Plasticity indices are potentially useful identify the genetic basis of phenotypic plasticity. Numerous methods exist measure However, their ability capture QTL with environmental effects remains elusive. Here, we analyzed a published multi-trial maize phenotyping dataset that examined water stress response leaf area, shoot biomass and use efficiency, calculating for these traits using seven different...
Genomic prediction is a useful tool for plant and animal breeding programs starting to be used predict human diseases as well. A shortcoming that slows down the genomic selection deployment accuracy of not known priori. We propose EthAcc (Estimated THeoretical ACCuracy) method estimating given training set genotyped phenotyped. based on causal quantitative trait loci model estimated by genome-wide association study. This crucial; therefore, we compared different methods find one yielding...