Saint-Georges-de-Luzençon, France
Saint-Georges-de-Luzençon, France
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Pierre J.,Agrocampus Ouest | Teulat B.,Agrocampus Ouest | Juchaux M.,University of Angers | Mabilleau G.,University of Angers | And 2 more authors.
Plant Science | Year: 2014

Hypocotyl growth is a key characteristic for plant emergence, influenced by environmental conditions, particularly temperature, and varying among genotypes. Cellular changes in Medicago truncatula hypocotyl were characterized to study the impact of the environment on heterotrophic growth and analyze differences between genotypes. The number and length of epidermal cells, ploidy levels, and sugar contents were measured in hypocotyls grown in the dark at 20. °C and 10. °C using two genotypes with contrasting maximum hypocotyl length. Hypocotyl elongation in the dark was due to cell elongation and not to an increase in cell number. A marked increase in cell ploidy level was observed just after germination and until mid elongation of the hypocotyl under all treatments. Larger ploidy levels were also observed in the genotype with the shorter hypocotyl and in cold conditions, but they were associated with larger cells. The increase in ploidy level and in cell volume was concomitant with a marked increase in glucose and fructose contents in the hypocotyl. Finally, differences in hypocotyl length were mainly due to different number of epidermal cells in the seed embryo, shown as a key characteristic of genotypic differences, whereas temperature during hypocotyl growth affected cell volume. © 2013 Elsevier Ireland Ltd.

Tribouillois H.,French National Institute for Agricultural Research | Durr C.,French National Institute for Agricultural Research | Demilly D.,GEVES | Wagner M.-H.,GEVES | Justes E.,French National Institute for Agricultural Research
PLoS ONE | Year: 2016

A wide range of species can be sown as cover crops during fallow periods to provide various ecosystem services. Plant establishment is a key stage, especially when sowing occurs in summer with high soil temperatures and low water availability. The aim of this study was to determine the response of germination to temperature and water potential for diverse cover crop species. Based on these characteristics, we developed contrasting functional groups that group species with the same germination ability, which may be useful to adapt species choice to climatic sowing conditions. Germination of 36 different species from six botanical families was measured in the laboratory at eight temperatures ranging from 4.5-43°C and at four water potentials. Final germination percentages, germination rate, cardinal temperatures, base temperature and base water potential were calculated for each species. Optimal temperatures varied from 21.3-37.2°C, maximum temperatures at which the species could germinate varied from 27.7-43.0°C and base water potentials varied from -0.1 to -2.6 MPa. Most cover crops were adapted to summer sowing with a relatively high mean optimal temperature for germination, but some Fabaceae species were more sensitive to high temperatures. Species mainly from Poaceae and Brassicaceae were the most resistant to water deficit and germinated under a low base water potential. Species were classified, independent of family, according to their ability to germinate under a range of temperatures and according to their base water potential in order to group species by functional germination groups. These groups may help in choosing the most adapted cover crop species to sow based on climatic conditions in order to favor plant establishment and the services provided by cover crops during fallow periods. Our data can also be useful as germination parameters in crop models to simulate the emergence of cover crops under different pedoclimatic conditions and crop management practices. © 2016 Tribouillois et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Belin E.,French National Institute for Agricultural Research | Belin E.,University of Notre Dame | Rousseau D.,University of Notre Dame | Lechappe J.,GEVES | And 2 more authors.
Computers and Electronics in Agriculture | Year: 2011

In the context of high-throughput plant phenotyping, measurements are carried out on large populations of plants and produce large amounts of data to be analyzed and stored. The need for automated phenotyping in plant biology opens new fields of application for image acquisition and compression algorithms. In this report, we focus on X-ray imaging for high-throughput analysis of seeds. A practical tradeoff between the tolerated distortion on images and image acquisition rates is demonstrated for measurement, visual inspection or pattern recognition. In these contexts, using the same methodology, we quantify the highest acquisition and compression rates achievable while preserving all the useful biological information with standard lossy compression formats. Using a study case, we quantitatively demonstrate the interest of considering the final biological task as a priori knowledge to optimize the design of phenotyping systems. © 2011 Elsevier B.V.

Belin E.,French National Institute for Agricultural Research | Belin E.,University of Notre Dame | Rousseau D.,INSA Lyon | Rojas-Varela J.,University of Notre Dame | And 4 more authors.
Computers and Electronics in Agriculture | Year: 2011

We demonstrate the value of thermal imaging for monitoring growth of seedling organs. An automated procedure is introduced to perform the segmentation of the organs of the seedlings from the thermal contrasts in the images. Results of the automated procedure were assessed visually by expert operators in a separate procedure. This constitutes a new application of thermal imaging as a non invasive imaging providing functional information on the physiology of the seedlings. © 2011 Elsevier B.V.

Villemot J.,GEVES | Rolland M.,GEVES
Journal of Virological Methods | Year: 2016

Winter barley is subjected to severe yield losses due to the yellow mosaic virus disease. Two soil borne bymoviruses, BaYMV (Barley yellow mosaic virus) and BaMMV (Barley mild mosaic virus) are responsible for this disease in Europe. As breeding resistant cultivars is the only control method against the disease, barley varieties carrying the recessive resistance rym4 were introduced. However, a new pathotype BaYMV-2 overcoming rym4 resistance appeared in the late 1980s. In France, little is known about BaYMV-2 and the common BaYMV (BaYMV-1) distribution, but the increase of the disease occurrence is becoming a concern. There is currently no valid molecular tool for BaYMV-1 and BaYMV-2 differentiation; thus the development of a dCAPS (derived Cleaved Amplified Polymorphic Sequences) tool was investigated. BaYMV-1 and BaYMV-2 diversity was first estimated by Sanger sequencing. The Single Nucleotide Polymorphism (SNP) previously described as providing the ability to overcome rym4-mediated resistance was targeted. A dCAPS tool was developed to digest specifically BaYMV-1. This assay was successfully tested with seventy naturally infected samples. This new tool will be useful to investigate BaYMV-1 and 2 distributions. © 2016 Elsevier B.V.

Benoit L.,University of Notre Dame | Belin T.,University of Notre Dame | Durr C.,CNRS Research Institute on Horticulture and Seeds | Chapeau-Blondeau F.,University of Notre Dame | And 3 more authors.
Computers and Electronics in Agriculture | Year: 2015

This article proposes a computer-vision based protocol, useful to contribute to high-throughput automated phenotyping of seedlings during elongation, the stage following germination. Radicle and hypocotyl are two essential organs which start to develop at this stage, with the hypocotyl growing towards the soil surface and the radicle exploring deeper layers for nutrient absorption. Early identification and measurement of these two organs are important to the characterization of the plant emergence and to the prognosis of the adult plant. In normal conditions, this growth process of radicle and hypocotyl takes place in the soil, in the dark. Identification and measurement of these two organs are therefore challenging, because they need to be achieved with no light that could alter normal growth conditions. We propose here an original protocol exploiting an inactinic green light, produced by a controlled LED source, coupled to a standard low-cost gray-level camera. On the resulting digital images, we devise a simple criterion based on gravitropism and amenable to direct computer implementation. The automated criterion, through comparison with the performance of human experts, is demonstrated to be efficient for the detection and separation of radicle and hypocotyl, and generic for various species of seedlings. Our protocol especially brings improvement in terms of cost reduction over the current method found in the recent literature which resorts to higher-cost passive thermal imaging to perform the same task in the dark, and that we also consider here for comparison. Our protocol connected to automation of image acquisition, can serve to improve high-throughput phenotyping equipments for analysis of seed quality and genetic variability. © 2014 Elsevier B.V.

Benoit L.,University of Notre Dame | Rousseau D.,CNRS Research Center for Image Acquisition and Processing for Health | Belin T.,University of Notre Dame | Demilly D.,GEVES | Chapeau-Blondeau F.,University of Notre Dame
Computers and Electronics in Agriculture | Year: 2014

This article proposes a methodology for the numerical validation of image processing algorithms dedicated to the segmentation of roots of plants with machine vision. A simulator of plant growth is coupled to a simulator of the image acquisition to generate images of simulated plants associated with a known synthetic ground truth. The simulator incorporates parameters of the plant and parameters of the experimental imaging system acquiring the images. This opens the possibility to assess the impact of these parameters on the performance of any segmentation algorithm on unlimited populations of virtual plants. Illustrations of this approach are given for the segmentation in 2D of seedlings with several classical algorithms and also with an algorithm of recent introduction. The presented results can be easily extended to 3D and are therefore also appropriate for other segmentation algorithms of roots with imaging modalities adapted for 3D root tracking like X-ray or MRI. © 2014 Elsevier B.V.

PubMed | University of Angers, University of Notre Dame, GEVES and INSA Lyon
Type: | Journal: Plant methods | Year: 2015

We review a set of recent multiscale imaging techniques, producing high-resolution images of interest for plant sciences. These techniques are promising because they match the multiscale structure of plants. However, the use of such high-resolution images is challenging in the perspective of their application to high-throughput phenotyping on large populations of plants, because of the memory cost for their data storage and the computational cost for their processing to extract information. We discuss how this renews the interest for multiscale image processing tools such as wavelets, fractals and recent variants to analyse such high-resolution images.

Matthews S.,University of Aberdeen | Noli E.,University of Bologna | Demir I.,Ankara University | Khajeh-Hosseini M.,Ferdowsi University of Mashhad | Wagner M.-H.,GEVES
Seed Science Research | Year: 2012

Seed quality standards enable seed users to achieve their objectives in the establishment of uniform seedlings to a high and reliable level for a range of agricultural and horticultural crops, growing systems and market outlets. Quality standards of commercial seed lots are determined by their positions on the seed survival curves and the shape of their germination progress curves. Although comparative descriptions of germination curves can be achieved by the calculation of the mean germination time (MGT; delay to radicle emergence), single early counts of radicle emergence provide a convenient means of predicting MGT and differences between seed lots. Evidence is presented for an ageing and metabolic repair hypothesis as the overall physiological basis to explain the principles behind the standard germination and vigour tests (ageing, electrolyte leakage, cold test, germination rate and seedling size). The work of the International Seed Testing Association (ISTA) in developing convenient, inexpensive and internationally repeatable tests is illustrated. © 2012 Cambridge University Press.

PubMed | University of Nantes and GEVES
Type: | Journal: Frontiers in plant science | Year: 2016

Broomrapes are holoparasitic plants spreading through seeds. Each plant produces hundreds of thousands of seeds which remain viable in the soils for decades. To limit their spread, drastic measures are being taken and the contamination of a commercial seed lot by a single broomrape seed can lead to its rejection. Considering that broomrapes species identification from a single seed is extremely difficult even for trained botanists and that among all the described species, only a few are really noxious for the crops, numerous seed lots are rejected because of the contamination by seeds of non-noxious broomrape species. The aim of this study was to develop and evaluate a High Resolution Melting assay identifying the eight most noxious and common broomrape species (

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