PUBLICATIONS

Genome-wide association analysis of resistance to wheat spindle streak mosaic virus in bread wheat
D. Hourcade, M. Bogard, M. Bonnefoy, F. Savignard, F. Mohamadi, S. Lafarge, P. Du Cheyron, N. Mangel and J. P. Cohan, 2019
Abstract: Wheat spindle streak mosaic virus (WSSMV) is a major concern for cereal crops in Europe and North America. A strong increase in the occurrence of WSSMV has been observed in each French region where susceptible cultivars are cultivated. Most European bread wheat cultivars are resistant, but assessing the status of newly registered cultivars or breeding lines regarding WSSMV resistance is of importance. This paper describes a genome-wide association study carried out on a panel of 163 cultivars and tested for their resistance to WSSMV. Two regions on chromosomes 5B<br /> and 7D showed minor effects on WSSMV resistance. More importantly, a large genomic region on chromosome 2D explained most of the resistance to WSSMV. More than 99% of the cultivars carrying the AA genotype at the most associated marker (Excalibur_c15426_661) were resistant to WSSMV, while 100% of the cultivars showing the GG genotype were susceptible. This large genomic region of 45.8 Mb was found distal to the centromere and showed very high linkage disequilibrium. It is hypothesized that this region may be an alien introgression originating from a wild<br /> related species. This region contains a total of 2605 predicted genes based on the Chinese Spring IWGSC RefSeq v. 1.0 including genes potentially involved in plant disease resistance. A kompetitive allele-specific PCR (KASP) single nucleotide polymorphism (SNP) marker was designed in order to identify breeding lines or registered cultivars resistant to WSSMV. DOI: https://onlinelibrary.wiley.com/doi/full/10.1111/ppa.12972
Ear density estimation from high resolution RGB imagery using deep learning technique
Simon Madec, Xiuliang Jin, Hao Lu, Benoit De Solan, Shouyang Liu, Florent Duyme, Emmanuelle Heritier, Frédéric Baret - Agricultural and Forest Meteorology, 2019
Abstract: Wheat ear density estimation is an appealing trait for plant breeders. Current manual counting is tedious and inefficient. In this study we investigated the potential of convolutional neural networks (CNNs) to provide accurate ear density using nadir high spatial resolution RGB images. Two different approaches were investigated, either using the Faster-RCNN state-of-the-art object detector or with the TasselNet local count regression network. Both approaches performed very well (rRMSE≈6%) when applied over the same conditions as those prevailing for the calibration of the models. However, Faster-RCNN was more robust when applied to a dataset acquired at a later stage with ears and background showing a different aspect because of the higher maturity of the plants. Optimal spatial resolution for Faster-RCNN was around 0.3 mm allowing to acquire RGB images from a UAV platform for high-throughput phenotyping of large experiments. Comparison of the estimated ear density with in-situ manual counting shows reasonable agreement considering the relatively small sampling area used for both methods. Faster-RCNN and in-situ counting had high and similar heritability (H²≈85%), demonstrating that ear density derived from high resolution RGB imagery could replace the traditional counting method. Keywords: Wheat ear density, Object detection, Object counting, Convolutional neural networks, Phenotyping, Broad-sense heritability. DOI: https://doi.org/10.1016/j.agrformet.2018.10.013
Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies
Zuzana Tulpová, Ming-Cheng Luo, Helena Toegelová, Paul Visendi, Satomi Hayashi, Petr Vojta, Etienne Paux, Andrzej Kilian, Michaël Abrouk, Jan Bartoš, Marián Hajdúch, Jacqueline Batley, David Edwards, Jaroslav Doležel, Hana Šimková - New Biotechnology, 2019
Abstract: Bread wheat (Triticum aestivum L.) is a staple food for a significant part of the world’s population. The growing demand on its production can be satisfied by improving yield and resistance to biotic and abiotic stress. Knowledge of the genome sequence would aid in discovering genes and QTLs underlying these traits and provide a basis for genomics-assisted breeding. Physical maps and BAC clones associated with them have been valuable resources from which to generate a reference genome of bread wheat and to assist map-based gene cloning. As a part of a joint effort coordinated by the International Wheat Genome Sequencing Consortium, we have constructed a BAC-based physical map of bread wheat chromosome arm 7DS consisting of 895 contigs and covering 94% of its estimated length. By anchoring BAC contigs to one radiation hybrid map and three high resolution genetic maps, we assigned 73% of the assembly to a distinct genomic position. This map integration, interconnecting a total of 1713 markers with ordered and sequenced BAC clones from a minimal tiling path, provides a tool to speed up gene cloning in wheat. The process of physical map assembly included the integration of the 7DS physical map with a whole-genome physical map of Aegilops tauschii and a 7DS Bionano genome map, which together enabled efficient scaffolding of physical-map contigs, even in the non-recombining region of the genetic centromere. Moreover, this approach facilitated a comparison of bread wheat and its ancestor at BAC-contig level and revealed a reconstructed region in the 7DS pericentromere. Keywords: Triticum aestivum, BAC, BNG map, Aegilops tauschii, Centromere. DOI: https://doi.org/10.1016/j.nbt.2018.03.003
The bZIP transcription factor SPA Heterodimerizing Protein represses glutenin synthesis in Triticum aestivum
Julie Boudet, Marielle Merlino, Anne Plessis, Jean‐Charles Gaudin, Mireille Dardevet, Sibille Perrochon, David Alvarez, Thierry Risacher, Pierre Martre, Catherine Ravel - Plant Journal, 2019
Summary: The quality of wheat grain is mainly determined by the quantity and composition of its grain storage proteins (GSPs). Grain storage proteins consist of low‐ and high‐molecular‐weight glutenins (LMW‐GS and HMW‐GS, respectively) and gliadins. The synthesis of these proteins is essentially regulated at the transcriptional level and by the availability of nitrogen and sulfur. The regulation network has been extensively studied in barley where BLZ1 and BLZ2, members of the basic leucine zipper (bZIP) family, activate the synthesis of hordeins. To date, in wheat, only the ortholog of BLZ2, Storage Protein Activator (SPA), has been identified as playing a major role in the regulation of GSP synthesis. Here, the ortholog of BLZ1, named SPA Heterodimerizing Protein (SHP), was identified and its involvement in the transcriptional regulation of the genes coding for GSPs was analyzed. In gel mobility shift assays, SHP binds cis‐motifs known to bind to bZIP family transcription factors in HMW‐GS and LMW‐GS promoters. Moreover, we showed by transient expression assays in wheat endosperm that SHP acts as a repressor of the activity of these gene promoters. This result was confirmed in transgenic lines overexpressing SHP, which were grown with low and high nitrogen supply. The phenotype of SHP‐overexpressing lines showed a lower quantity of both LMW‐GS and HMW‐GS, while the quantity of gliadin was unchanged, whatever the nitrogen availability. Thus, the gliadin/glutenin ratio was increased, which suggests that gliadin and glutenin genes may be differently regulated. DOI: https://doi.org/10.1111/tpj.14163
Phenomic Selection Is a Low-Cost andHigh-Throughput Method Based on IndirectPredictions: Proof of Concept on Wheat and Poplar
Renaud Rincent, Jean-Paul Charpentier, Patricia Faivre-Rampant, Etienne Paux, Jacques Le Gouis, Catherine Bastien, and Vincent Segura - G3, 2018
Abstract: Genomic selection - the prediction of breeding values using DNA polymorphisms - is adisruptive method that has widely been adopted by animal and plant breeders to increase productivity. Itwas recently shown that other sources of molecular variations such as those resulting from transcripts ormetabolites could be used to accurately predict complex traits. These endophenotypes have the advantageof capturing the expressed genotypes and consequently the complex regulatory networks that occur in thedifferent layers between the genome and the phenotype. However, obtaining such omics data at very largescales, such as those typically experienced in breeding, remains challenging. As an alternative, weproposed using near-infrared spectroscopy (NIRS) as a high-throughput, low cost and non-destructive toolto indirectly capture endophenotypic variants and compute relationship matrices for predicting complextraits, and coined this new approach”phenomic selection”(PS). We tested PS on two species of economicinterest (Triticum aestivumL. andPopulus nigraL.) using NIRS on various tissues (grains, leaves, wood).We showed that one could reach predictions as accurate as with molecular markers, for developmental,tolerance and productivity traits, even in environments radically different from the one in which NIRS werecollected. Our work constitutes a proof of concept and provides new perspectives for the breeding com-munity, as PS is theoretically applicable to any organism at low cost and does not require any molecularinformation. DOI: 10.1534/g3.118.200760
The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping
Jordan KW, Wang S, He F, Chao S, Lun Y, Paux E, Sourdille P, Sherman J, Akhunova A, Blake NK, Pumphrey MO, Glover K, Dubcovsky J, Talbert L, Akhunov ED - Plant Journal, 2018
Abstract: Recombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence-based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO). Genome-wide recombination rate variation was mostly defined by rare alleles with small effects together explaining up to 48.6% of variation. Most QTL were additive and showed predominantly trans-acting effects. The QTL affecting the proximal COs also acted additively without increasing the frequency of distal COs. We showed that the regions with decreased recombination carry more single nucleotide polymorphisms (SNPs) with possible deleterious effects than the regions with a high recombination rate. Therefore, our study offers insights into the genetic basis of recombination rate variation in wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans-acting additive QTL can be utilized to manipulate CO frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low-recombining pericentromeric regions of chromosomes. DOI: 10.1111/tpj.14009
Impact of transposable elements on genome structure and evolution in bread wheat
Thomas Wicker, Heidrun Gundlach, Manuel Spannagl, Cristobal Uauy, Philippa Borrill, Ricardo H. Ramírez-González, Romain De Oliveira, International Wheat Genome Sequencing Consortium, Klaus F. X. Mayer, Etienne Paux and Frédéric Choulet - Genome Biology, 2018
Abstract: Background: Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes. Results: The overall TE content is very similar between the A, B, and D subgenomes, although we find no evidence for bursts of TE amplification after the polyploidization events. Despite the near-complete turnover of TEs since the subgenome lineages diverged from a common ancestor, 76% of TE families are still present in similar proportions in each subgenome. Moreover, spacing between syntenic genes is also conserved, even though syntenic TEs have<br /> been replaced by new insertions over time, suggesting that distances between genes, but not sequences, are under evolutionary constraints. The TE composition of the immediate gene vicinity differs from the core intergenic regions. We find the same TE families to be enriched or depleted near genes in all three subgenomes. Evaluations at the subfamily level of timed long terminal repeat-retrotransposon insertions highlight the independent evolution of the diploid A, B, and D lineages before polyploidization and cases of concerted proliferation in the AB tetraploid.<br /> Conclusions: Even though the intergenic space is changed by the TE turnover, an unexpected preservation is observed between the A, B, and D subgenomes for features like TE family proportions, gene spacing, and TE enrichment near genes. Keywords: Transposable elements, Wheat genome, Genome evolution, LTR retrotransposons, Polyploidy, Triticum aestivums. DOI: https://doi.org/10.1186/s13059-018-1479-0
Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data
Michael Alaux, Jane Rogers, Thomas Letellier, Raphaël Flores, Françoise Alfama, Cyril Pommier, Nacer Mohellibi, Sophie Durand, Erik Kimmel, Célia Michotey, Claire Guerche, Mikaël Loaec, Mathilde Lainé, Delphine Steinbach, Frédéric Choulet, Hélène Rimbert, Philippe Leroy, Nicolas Guilhot, Jérôme Salse, Catherine Feuillet, International Wheat Genome Sequencing Consortium, Etienne Paux, Kellye Eversole, Anne-Françoise Adam-Blondon and Hadi Quesneville - Genome Biology, 2018
Abstract: The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement. Keywords: Data integration, Information system, Big data, Wheat genomics, genetics and phenomics. DOI: https://doi.org/10.1186/s13059-018-1491-4
Shifting the limits in wheat research and breeding using a fully annotated reference genome
International Wheat Genome Sequencing Consortium (IWGSC) - Science, 2018
Abstract: An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. DOI: 10.1126/science.aar7191
Ferulate and lignin cross-links increase in cell walls of wheat grain outer layers during late development
Anne-Laure Chateigner-Boutina, Catherine Lapierre, Camille Alvarado, Arata Yoshinaga, Cécile Barron, Brigitte Bouchet, Bénédicte Bakan, Luc Saulnier, Marie-Françoise Devaux, Christine Girousse, Fabienne Guillon - Plant Science, 2018
Abstract: Important biological, nutritional and technological roles are attributed to cell wall polymers from cereal grains. The composition of cell walls in dry wheat grain has been well studied, however less is known about cell wall deposition and modification in the grain outer layers during grain development. In this study, the composition of cell walls in the outer layers of the wheat grain (Triticum aestivum Recital cultivar) was investigated during grain development, with a focus on cell wall phenolics. We discovered that lignification of outer layers begins earlier than previously reported and long before the grain reaches its final size. Cell wall feruloylation increased in development. However, in the late stages, the amount of ferulate releasable by mild alkaline hydrolysis was reduced as well as the yield of lignin-derived thioacidolysis monomers. These reductions indicate that new ferulate-mediated cross-linkages of cell wall polymers appeared as well as new resistant interunit bonds in lignins. The formation of these additional linkages more specifically occurred in the outer pericarp.<br /> Our results raised the possibility that stiffening of cell walls occur at late development stages in the outer pericarp and might contribute to the restriction of the grain radial growth. Keywords: cell wall, ferulic acid, grain size, lignins, wheat grain, developing pericarp. DOI https://doi.org/10.1016/j.plantsci.2018.08.022
Coexpression network and phenotypic analysis identify metabolic pathways associated with the effect of warning on grain yield components in wheat
Christine Girousse, Jane Roche, Claire Guerin, Jacques Le Gouis, Sandrine Balzegue, Said Mouzeyar, Mouhamed Fouad Bouzidi - PLOS one, 2018
Abstract: Wheat grains are an important source of human food but current production amounts cannot meet world needs. Environmental conditions such as high temperature (above 30°C) could affect wheat production negatively. Plants from two wheat genotypes have been subjected to two growth temperature regimes. One set has been grown at an optimum daily mean temperature of 19°C while the second set of plants has been subjected to warming at 27°C from two to 13 days after anthesis (daa). While warming did not affect mean grain number per spike, it significantly reduced other yield-related indicators such as grain width, length, volume and maximal cell numbers in the endosperm. Whole genome expression analysis identified 6,258 and 5,220 genes, respectively, whose expression was affected by temperature in the two genotypes. Co-expression analysis using WGCNA (Weighted Gene Coexpression Network Analysis) uncovered modules (groups of co-expressed genes) associated with agronomic traits. In particular, modules enriched in genes related to nutrient reservoir and endopeptidase inhibitor activities were found to be positively associated with cell numbers in the endosperm. A hypothetical model pertaining to the effects of warming on gene expression and growth in wheat grain is proposed. Under moderately high temperature conditions, network analyses suggest a negative effect of the expression of genes related to seed storage proteins and starch biosynthesis on the grain size in wheat. DOI 13(6): e0199434
High throughput SNP discovery and genotyping in hexaploid wheat
Hélène Rimbert, Benoit Darrier, Julien Navarro, Jonathan Kitt, Frederic Choulet, Magalie Leveugle, Jorge Duarte, Nathalie Rivière, Kellye Eversole on behalf of The International Wheat Genome Sequencing Consortium, Jacques Le Gouis on behalf The BreedWheat Consortium, Alessandro Davassi, Francois Balfourier, Marie-Christine Le Paslier, Aurelie Berard, Dominique Brunel, Catherine Feuillet, Charles Poncet, Pierre Sourdille, Etienne Paux - Field Crops Research, 2018
Abstract: Because of their abundance and their amenability to high-throughput genotyping techniques, Single Nucleotide Polymorphisms (SNPs) are powerful tools for efficient genetics and genomics studies, including characterization of genetic resources, genome-wide association studies and genomic selection. In wheat, most of the previous SNP discovery initiatives targeted the coding fraction, leaving almost 98% of the wheat genome largely unexploited. Here we report on the use of whole-genome resequencing data from eight wheat lines to mine for SNPs in the genic, the repetitive and non-repetitive intergenic fractions of the wheat genome. Eventually, we identified 3.3 million SNPs, 49% being located on the B-genome, 41% on the A-genome and 10% on the D-genome. We also describe the development of the TaBW280K high-throughput genotyping array containing 280,226 SNPs. Performance of this chip was examined by genotyping a set of 96 wheat accessions representing the worldwide diversity. Sixty-nine percent of the SNPs can be efficiently scored, half of them showing a diploid-like clustering. The TaBW280K was proven to be a very efficient tool for diversity analyses, as well as for breeding as it can discriminate between closely related elite varieties. Finally, the TaBW280K array was used to genotype a population derived from a cross between Chinese Spring and Renan, leading to the construction a dense genetic map comprising 83,721 markers. The results described here will provide the wheat community with powerful tools for both basic and applied research. DOI 10.1371/journal.pone.0186329
Whole-genome prediction of reaction norms to environmental stress in bread wheat (Triticum aestivum L.) by genomic random regression
Delphine Ly, Sylvie Huet, Arnaud Gauffreteau, Renaud Rincent, Gaëtan Touzy, Agathe Mini, Jean-Luc Janninke, Fabien Cormier, Etienne Paux, Stéphane Lafarge, Jacques Le Gouis, Gilles Charmet - Field Crops Research, 2018
Abstract: Plant breeding has always sought to develop crops able to withstand environmental stresses, but this is all the more urgent now as climate change is affecting the agricultural regions of the world. It is currently difficult to screen genetic material to determine how well a crop will tolerate various stresses. Multi-environment trials (MET) which include a particular stress condition could be used to train a genomic selection model thanks to molecular marker information that is now readily available. Our study focuses on understanding how and predicting whether a plant is adapted to a particular environmental stress. We propose a way to use genomic random regression, an extension of factorial regression, to model the reaction norms of a genotype to an environmental stress: the factorial regression genomic best linear unbiased predictor (FR-gBLUP). Twenty-eight wheat trials in France (3 years, 12 locations, nitrogen or water stress treatments) were split into two METs where different stresses limited grain number and yield. In MET1, drought at flowering was responsible for 46.7% of the genotype-by-environment (G ×E) interactions for yield while in MET2, heat stress during booting was identified as the main factor responsible for G× E interactions, but that explained less of the interaction variance (33.6%). Since drought at flowering explained a fairly large variance in G ×E in MET1, the FR-gBLUP model was more accurate than the additive gBLUP across all types of cross validation. Accuracy gains varied from 2.4% to 12.9% for the genomic regression to drought. In MET2 accuracy gains were modest, varying from −5.7% to 2.4%. When a major stress influencing G ×E is identified, the FR-gBLUP strategy makes it possible to predict the level of adaptation of genotyped individuals to varying stress intensities, and thus to select them in silico. Our study demonstrates how genome-wide selection can facilitate breeding for adaptation. Keywords: Genotype-by-environment interaction, Factorial regression, Genomic prediction, Reaction norm, Drought adaptation. DOI 10.1016/j.fcr.2017.08.020
Optimization of multi‑environment trials for genomic selection based on crop models
Renaud Rincent, E. Kuhn, H. Monod, F.‑X. Oury, M. Rousset, V. Allard, J. Le Gouis - Theoretical and Applied Genetics, 2017
Summary: Key message We propose a statistical criterion to optimize multi-environment trials to predict genotype × environment interactions more efficiently, by combining crop growth models and genomic selection models. Abstract Genotype × environment interactions (GEI) are common in plant multi-environment trials (METs). In this context, models developed for genomic selection (GS) that refers to the use of genome-wide information for predicting breeding values of selection candidates need to be adapted. One promising way to increase prediction accuracy in various environments is to combine ecophysiological and genetic modelling thanks to crop growth models (CGM) incorporating genetic parameters. The efficiency of this approach relies on the quality of the parameter estimates, which depends on the environments composing this MET used for calibration. The objective of this study was to determine a method to optimize the set of environments composing the MET for estimating genetic parameters in this context. A criterion called OptiMET was defined to this aim, and was evaluated on simulated and real data, with the example of wheat phenology. The MET defined with OptiMET allowed estimating the genetic parameters with lower error, leading to higher QTL detection power and higher prediction accuracies. MET defined with OptiMET was on average more efficient than random MET composed of twice as many environments, in terms of quality of the parameter estimates. OptiMET is thus a valuable tool to determine optimal experimental conditions to best exploit MET and the phenotyping tools that are currently developed. DOI 10.1007/s00122-017-2922-4
Grain subproteome responses to nitrogen and sulfur supply in diploid wheat Triticum monococcum ssp monococcum
Titouan Bonnot, Emmanuelle Bancel, David Alvarez, Marlène Davanture, Julie Boudet, Marie Pailloux, Michel Zivy, Catherine Ravel, Pierre Martre - The Plant Journal, 2017
Summary: Wheat grain storage proteins (GSPs) make up most of the protein content of grain and determine flour enduse value. The synthesis and accumulation of GSPs depend highly on nitrogen (N) and sulfur (S) availability and it is important to understand the underlying control mechanisms. Here we studied how the einkorn (Triticum monococcum ssp. monococcum) grain proteome responds to different amounts of N and S supply during grain development. GSP composition at grain maturity was clearly impacted by nutrition treatments, due to early changes in the rate of GSP accumulation during grain filling. Large-scale analysis of the nuclear and albumin-globulin subproteomes during this key developmental phase revealed that the abundance of 203 proteins was significantly modified by the nutrition treatments. Our results showed that the grain proteome was highly affected by perturbation in the N:S balance. S supply strongly increased the rate of accumulation of S-rich a/b-gliadin and c-gliadin, and the abundance of several other proteins involved in glutathione metabolism. Post-anthesis N supply resulted in the activation of amino acid metabolism at the expense of carbohydrate metabolism and the activation of transport processes including nucleocytoplasmic transit. Protein accumulation networks were analyzed. Several central actors in the response were identified whose variation in abundance was related to variation in the amounts of many other proteins and are thus potentially important for GSP accumulation. This detailed analysis of grain subproteomes provides information on how wheat GSP composition can possibly be controlled in low-level fertilization condition. Keywords: Triticum monococcum, grain, nitrogen, sulfur, storage proteins, nuclear proteins, albumin-globulin, network. DOI: 10.1111/tpj.13615
Modeling the spatial distribution of plants on the row for wheat crops: Consequences on the green fraction at the canopy level
Shouyang Liu, Frédéric Baret, Bruno Andrieu, Mariem Abichou, Denis Allard, Benoit de Solan, Philippe Burger - Computers and Electronics in Agriculture, 2017
Abstract: This work investigates the spatial distribution of wheat plants and its consequences on the canopy structure. A set of RGB images were taken from nadir on a total 14 plots showing a range of sowing densities, cultivars and environmental conditions. The coordinates of the plants were extracted from RGB images. Results show that the distance between-plants along the row follows a gamma distribution law, with no dependency between the distances. Conversely, the positions of the plants across rows follow a Gaussian distribution, with strongly interdependent. A statistical model was thus proposed to simulate the possible plant distribution pattern. Through coupling the statistical model with 3D Adel-Wheat model, the impact of the plant distribution pattern on canopy structure was evaluated using emerging properties such as the green fraction (GF) that drives the light interception efficiency. Simulations showed that the effects varied over different development stages but were generally small. For the intermediate development stages, large zenithal angles and directions parallel to the row, the deviations across the row of plant position increased the GF by more than 0.1. These results were obtained with a wheat functionalstructural model that does not account for the capacity of plants to adapt to their local environment. Nevertheless, our work will extend the potential of functional-structural plant models to estimate the optimal distribution pattern for given conditions and subsequently guide the field management practices. Keywords: Plant distribution pattern, Green fraction, FSPMs, Wheat. DOI: 10.1016/j.compag.2017.02.022
Estimation of Wheat Plant Density at Early Stages Using High Resolution Imagery
Shouyang Liu, Fred Baret, Bruno Andrieu, Philippe Burger and Matthieu Hemmerlé - Frontiers in Plant Science, 2017
Abstract: Crop density is a key agronomical trait used to manage wheat crops and estimate yield. Visual counting of plants in the field is currently the most common method used. However, it is tedious and time consuming. The main objective of this work is to develop a machine vision based method to automate the density survey of wheat at early stages. RGB images taken with a high resolution RGB camera are classified to identify the green pixels corresponding to the plants. Crop rows are extracted and the connected components (objects) are identified. A neural network is then trained to estimate the number of plants in the objects using the object features. The method was evaluated over three experiments showing contrasted conditions with sowing densities ranging from 100 to 600 seeds.m-2. Results demonstrate that the density is accurately estimated with an average relative error of 12%. The pipeline developed here provides an efficient and accurate estimate of wheat plant density at early stages. Keywords: plant density, RGB imagery, neural network, wheat, recursive feature elimination, Hough transform. DOI: 10.3389/fpls.2017.00739
A method to estimate plant density and plant spacing heterogeneity: application to wheat crops
Shouyang Liu, Fred Baret, Denis Allard, Xiuliang Jin, Bruno Andrieu, Philippe Burger, Matthieu Hemmerlé and Alexis Comar - Plant Methods, 2017
Abstract: Background: Plant density and its non-uniformity drive the competition among plants as well as with weeds. They need thus to be estimated with small uncertainties accuracy. An optimal sampling method is proposed to estimate the plant density in wheat crops from plant counting and reach a given precision. Results: Three experiments were conducted in 2014 resulting in 14 plots across varied sowing density, cultivars and environmental conditions. The coordinates of the plants along the row were measured over RGB high resolution images taken from the ground level. Results show that the spacing between consecutive plants along the row direction are independent and follow a gamma distribution under the varied conditions experienced. A gamma count model was then derived to define the optimal sample size required to estimate plant density for a given precision. Results suggest that measuring the length of segments containing 90 plants will achieve a precision better than 10%, independently from the plant density. This approach appears more efficient than the usual method based on fixed length segments where the number of plants are counted: the optimal length for a given precision on the density estimation will depend on the actual plant density. The gamma count model parameters may also be used to quantify the heterogeneity of plant spacing along the row by exploiting the variability between replicated samples. Results show that to achieve a 10% precision on the estimates of the 2 parameters of the gamma model, 200 elementary samples corresponding to the spacing between 2 consecutive plants should be measured. Conclusions: This method provides an optimal sampling strategy to estimate the plant density and quantify the plant spacing heterogeneity along the row. Keywords: Wheat, Gamma-count model, Density, RGB imagery, Sampling strategy, Plant spacing heterogeneity. DOI 10.1186/s13007-017-0187-1
Bridging the gap between ideotype and genotype: Challenges and prospects for modelling as exemplified by the case of adapting wheat (Triticum aestivum L.) phenology to climate change in France
David Gouache, Matthieu Bogard, Marie Pegard, Stéphanie Thepot,Cécile Garcia, Delphine Hourcade, Etienne Paux, Francois-Xavier Oury, Michel Rousset, Jean-Charles Deswarte, Xavier Le Bris - Field Crops Research, 2017
Abstract: Simulations using crop models can assist designing ideotypes for current and future agricultural conditions. This approach consists in running simulations for different “in silico genotypes” obtained by varying the most sensitive genotypic parameters of these models, and analyzing results obtained for different environments, so as to identify the best genotypes for a target population of environments. However, this approach has rarely been used to guide commercial breeding programs so far. In this paper, we attempt to address some of the gaps yet to be filled before this kind of approach can be implemented,and identify some remaining issues that should be addressed in future research. Our focus is on optimizing wheat phenology, integrating simulations from a modified version of the ARCWHEAT model of wheat growth stages with available knowledge on the genetic control of wheat phenology obtained via molecular markers. Based on simulations, stem extension could be advanced by 10 days in 2025–2049 without increasing frost risks, thus opening up opportunities for lengthening the rapid growth period.Analysis of the current genetic variability for major phenology genes in French elite varieties, showed that the insensitive PpdD1—spring Vrn3 allele combination appears undesirable and current genotypes with early stem extensions are unstable (i.e. show a strong response to temperature and can start the stem extension very early in case of mild winter temperatures). We finally use a case study on gene-based modelling of wheat phenology in France to illustrate how it can be used to dissect the genetic basis of the quantitative nature of the three components of earliness, beyond the effects of major genes. We identify the need to link the variability for optimized model parameters and the allelic variations at the gene level as a critical step of this type of approach. Keywords: Wheat, Earliness, Stem extension, Marker-based model, Plasticity, Photoperiod sensitivity. DOI: 10.1016/j.fcr.2015.12.012
Fortune telling: metabolic markers of plant performance
Olivier Fernandez, Maria Urrutia, Stéphane Bernillon, Catherine Giauffret, François Tardieu, Jacques Le Gouis, Nicolas Langlade, Alain Charcosset, Annick Moing, Yves Gibon - Metabolomics, 2016
Background: In the last decade, metabolomics has emerged as a powerful diagnostic and predictive tool in many branches of science. Researchers in microbes, animal, food, medical and plant science have generated a large number of targeted or non-targeted metabolic profiles by using a vast array of analytical methods (GC–MS, LC–MS, 1H-NMR….). Comprehensive analysis of such profiles using adapted statistical methods and modeling has opened up the possibility of using single or combinations of metabolites as markers. Metabolic markers have been proposed as proxy, diagnostic or predictors of key traits in a range of model species and accurate predictions of disease outbreak frequency, developmental stages, food sensory<br /> evaluation and crop yield have been obtained. Aim of review (i) To provide a definition of plant performance and metabolic markers, (ii) to highlight recent key applications involving metabolic markers as tools for monitoring or predicting plant performance, and (iii) to propose a workable and cost-efficient pipeline to generate and use metabolic markers with a special focus on plant breeding. Key message Using examples in other models and domains, the review proposes that metabolic markers are tending to complement and possibly replace traditional molecular markers in plant science as efficient estimators of performance. Keywords Breeding: Metabolic marker, Metabolomics, Plant performance, Prediction. DOI: 10.1007/s11306-016-1099-1
transPLANT Resources for Triticeae Genomic Data
Manuel Spannagl, Michael Alaux, Matthias Lange, Daniel M. Bolser, Kai C. Bader, Thomas Letellier, Erik Kimmel, Raphael Flores, Cyril Pommier, Arnaud Kerhornou, Brandon Walts, Thomas Nussbaumer, Christoph Grabmuller, Jinbo Chen, Christian Colmsee, Sebastian Beier, Martin Mascher, Thomas Schmutzer, Daniel Arend, Anil Thanki, Ricardo Ramirez-Gonzalez, Martin Ayling, Sarah Ayling, Mario Caccamo, Klaus F.X. Mayer, Uwe Scholz, Delphine Steinbach, Hadi Quesneville, and Paul J. Kersey - The Plant Genome 9, 2016
Abstract: The genome sequences of many important Triticeae species, including bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analyses strategies, several of these have recently been deciphered. These efforts have generated new insights into Triticeae biology and genome organization and have important implications for downstream usage by breeders, experimental biologists, and comparative genomicists. transPLANT (http://www.transplantdb.eu) is an EU-funded project aimed at constructing hardware, software, and data infrastructure for genome-scale research in the life sciences. Since the Triticeae data are intrinsically complex, heterogenous, and distributed, the transPLANT consortium has undertaken efforts to develop common data formats and tools that enable the exchange and integration of data from distributed resources. Here we present an overview of the individual Triticeae genome resources hosted by transPLANT partners, introduce the objectives of transPLANT, and outline common developments and interfaces supporting integrated data access. DOI: 10.3835/plantgenome2015.06.0038
CN-Wheat, a functional-structural model of carbon and nitrogen metabolism in wheat culms after anthesis. I. Model description
Romain Barillot, Camille Chambon and Bruno Andrieu - Annals of Botany, 2016
Abstract: Background and Aims Improving crops requires better linking of traits and metabolic processes to whole plant performance. In this paper, we present CN-Wheat, a comprehensive and mechanistic model of carbon (C) and nitrogen (N) metabolism within wheat culms after anthesis. Methods The culm is described by modules that represent the roots, photosynthetic organs and grains. Each of them includes structural, storage and mobile materials. Fluxes of C and N among modules occur through a common pool and through transpiration flow. Metabolite variations are represented by differential equations that depend on the physiological processes occurring in each module. A challenging aspect of CN-Wheat lies in the regulation of these processes by metabolite concentrations and the environment perceived by organs. Key Results CN-Wheat simulates the distribution of C and N into wheat culms in relation to photosynthesis, N-uptake, metabolite turnover, root exudation and tissue death. Regulation of physiological activities by local concentrations of metabolites appears to be a valuable feature for understanding how the behaviour of the whole plant can emerge from local rules. Conclusions The originality of CN-Wheat is that it proposes an integrated view of plant functioning based on a mechanistic approach. The formalization of each process can be further refined in the future as knowledge progresses. This approach is expected to strengthen our capacity to understand plant responses to their environment and investigate plant traits adapted to changes in agronomical practices or environmental conditions. A companion paper will evaluate the model. Key words: Amino acids, carbon, cytokinins, fructans, process-based functional–structural plant model, nitrogen, proteins, plant metabolism and physiology, sink–source relations, sucrose, Triticum aestivum, wheat. DOI: https://doi.org/10.1093/aob/mcw143
CN-Wheat, a functional–structural model of carbon and nitrogen metabolism in wheat culms after anthesis. II. Model evaluation
Romain Barillot, Camille Chambon and Bruno Andrieu - Annals of Botany, 2016
Abstract: Background and Aims Simulating resource allocation in crops requires an integrated view of plant functioning and the formalization of interactions between carbon (C) and nitrogen (N) metabolisms. This study evaluates the functional–structural model CN-Wheat developed for winter wheat after anthesis. Methods In CN-Wheat the acquisition and allocation of resources between photosynthetic organs, roots and grains are emergent properties of sink and source activities and transfers of mobile metabolites. CN-Wheat was calibrated for field plants under three N fertilizations at anthesis. Model parameters were taken from the literature or calibrated on the experimental data. Key Results The model was able to predict the temporal variations and the distribution of resources in the culm. Thus, CN-Wheat accurately predicted the post-anthesis kinetics of dry masses and N content of photosynthetic organs and grains in response to N fertilization. In our simulations, when soil nitrates were non-limiting, N in grains was ultimately determined by availability of C for root activity. Dry matter accumulation in grains was mostly affected by photosynthetic organ lifespan, which was regulated by protein turnover and C-regulated root activity.<br /> Conclusions The present study illustrates that the hypotheses implemented in the model were able to predict realistic dynamics and spatial patterns of C and N. CN-Wheat provided insights into the interplay of C and N metabolism and how the depletion of mobile metabolites due to grain filling ultimately results in the cessation of resource capture. This enabled us to identify processes that limit grain mass and protein content and are potential targets for plant breeding. Key words: Amino acids, carbon, cytokinins, fructans, process-based functional–structural plant model, nitrogen, proteins, plant metabolism and physiology, sink-source relations, sucrose, Triticum aestivum, wheat. DOI: https://doi.org/10.1093/aob/mcw144
Proteomic Approach to Identify Nuclear Proteins in Wheat Grain
Emmanuelle Bancel, Titouan Bonnot, Marlène Davanture, Gérard Branlard, Michel Zivy, and Pierre Martre - Journal of Proteome Research, 2015
Abstract: The nuclear proteome of the grain of the two cultivated wheat species Triticum aestivum (hexaploid wheat; genomes A, B, and D) and T. monococcum (diploid wheat; genome A) was analyzed in two early stages of development using shotgun-based proteomics. A procedure was optimized to purify nuclei, and an improved protein sample preparation was developed to efficiently remove nonprotein substances (starch and nucleic acids). A total of 797 proteins corresponding to 528 unique proteins were identified, 36% of which were classified in functional groups related to DNA and RNA metabolism. A large number (107 proteins) of unknown functions and hypothetical proteins were also found. Some identified proteins may be multifunctional and may present multiple localizations. On the basis of the MS/MS analysis, 368 proteins were present in the two species, and in two stages of development, some qualitative differences between species and stages of development were also found. All of these data illustrate the dynamic function of the grain nucleus in the early stages of development. Keywords: cereal, grain development, bread wheat (Triticum aestivum), einkorn wheat (Triticum monococcum), LC−MS/MS, nuclear proteome. DOI: 10.1021/acs.jproteome.5b00446
Changes in the nuclear proteome of developing wheat (Triticum aestivumL.) grain
Titouan Bonnot, Emmanuelle Bancel, Christophe Chambon, Julie Boudet, Gérard Branlard, and Pierre Martre - Frontiers in Plant Science, 2015
Abstract: Wheat grain end-use value is determined by complex molecular interactions that occur during grain development, including those in the cell nucleus. However, our knowledge of how the nuclear proteome changes during grain development is limited. Here, we analyzed nuclear proteins of developing wheat grains collected during the cellularization, effective grain-filling, and maturation phases of development, respectively. Nuclear proteins were extracted and separated by two-dimensional gel electrophoresis. Image analysis revealed 371 and 299 reproducible spots in gels with first dimension separation along pH 4–7 and pH6–11 isoelectric gradients, respectively. The relative abundance of 464 (67%) protein spots changed during grain development. Abundance profiles of these proteins clustered in six groups associated with the major phases and phase transitions of grain development. Using nano liquid chromatography-tandem mass spectrometry to analyse 387 variant and non-variant protein spots, 114 different proteins were identified that were classified into 16 functional classes. We noted that some proteins involved in the regulation of transcription, like HMG1/2-like protein and histone deacetylase HDAC2, were most abundant before the phase transition from cellularization to grain-filling, suggesting that major transcriptional changes occur during this key developmental phase. The maturation period was characterized by high relative abundance of proteins involved in ribosome biogenesis. Data are available via ProteomeXchange with identifier PXD002999. Keywords: wheat, developing grain, nuclear proteins, 2D gel electrophoresis, LC-MS/MS. DOI: 10.3389/fpls.2015.00905
RulNet: A Web-Oriented Platform for Regulatory Network Inference, Application to Wheat –Omics Data
Jonathan Vincent, Pierre Martre, Benjamin Gouriou, Catherine Ravel, Zhanwu Dai, Jean-Marc Petit, Marie Pailloux - PLOS one, 2015
With the increasing amount of –omics data available, a particular effort has to be made to provide suitable analysis tools. A major challenge is that of unraveling the molecular regulatory networks from massive and heterogeneous datasets. Here we describe RulNet, a weboriented platform dedicated to the inference and analysis of regulatory networks from qualitative and quantitative –omics data by means of rule discovery. Queries for rule discovery can be written in an extended form of the RQL query language, which has a syntax similar to SQL. RulNet also offers users interactive features that progressively adjust and refine the inferred networks. In this paper, we present a functional characterization of RulNet and compare inferred networks with correlation-based approaches. The performance of RulNet has been evaluated using the three benchmark datasets used for the transcriptional network inference challenge DREAM5. Overall, RulNet performed as well as the best methods that participated in this challenge and it was shown to behave more consistently when compared across the three datasets. Finally, we assessed the suitability of RulNet to analyze experimental –omics data and to infer regulatory networks involved in the response to nitrogen and sulfur supply in wheat (Triticum aestivum L.) grains. The results highlight putative actors governing the response to nitrogen and sulfur supply in wheat grains. We evaluate the main characteristics and features of RulNet as an all-in-one solution for RN inference, visualization and editing. Using simple yet powerful RulNet queries allowed RNs involved in the adaptation of wheat grain to N and S supply to be discovered.We demonstrate the effectiveness and suitability of RulNet as a platform for the analysis of RNs involving different types of –omics data. The results are promising since they are consistent with what was previously established by the scientific community. DOI: 10.1371/journal.pone.0127127
Evolution de l'organisation de la recherche et du secteur des semences
Aline Fugeray-Scarbel & Stéphane Lemarie - Le selectionneur français, 2013
Depuis son émergence à la fin du XIXème siècle, le secteur des semences a connu des évolutions importantes conduisant à une réorganisation générale de la recherche en amélioration des plantes. Le premier fait marquant de cette évolution concerne le positionnement relatif de la recherche publique et de la recherche privée. L'effort privé en recherche a augmenté suite aux évolutions réglementaires (DHS, VAT), à la mise en place de droits de propriété (COV) et, dans certains cas, au développement des semences hybrides. La recherche publique s'est alors repositionnée sur les domaines pour lesquels il existait des défaillances du marché (recherche amont, recherche méthodologique, segments orphelins). Le deuxième fait marquant de cette évolution concerne la structure interne du secteur des semences. Bien qu'il soit encore globalement peu concentré, ce secteur a vu progressivement émerger des acteurs majeurs ayant des positions fortes à la fois sur les semences et dans le domaine des biotechnologies, ces positions étant renforcées par le développement de brevets sur le vivant. Cette concentration croissante s'explique également par les coûts (fixes) croissants liés à la recherche, la réglementation, et la gestion de la propriété intellectuelle. Key words: amélioration des plantes, biotechnologie, structure industrielle, recherche publique