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Fusarium head blight monitored in the field by imaging

Breeding resistant varieties is one of the agronomic levers available to reduce the risk of fusarium in cereal crops.  To facilitate the work of breeders, INRA and its partners (Veodis 3D, Limagrain, Secobra Recherches, Agri-Obtentions) have developed a field phenotyping system that can efficiently and rapidly judge the behaviour of different varieties.

FHB symptoms in a field of wheat. © ARVALIS, Arvalis - Institut du végétal
Updated on 11/03/2016
Published on 08/23/2016

Fusarium head blight: a fungal disease that harms both yield and health quality

Fusarium head blight is a fungal disease caused by a complex of species belonging to the Fusarium and Microdochium genera.  Its presence is indicated by “scorched” spikelets that are reddish-orange in colour. F. graminearum is currently the principal species found in the field, which as well as its direct impact on yield linked to symptoms of the disease, also poses a health problem due to the production in planta of mycotoxins, the most common being deoxynivalenol.  This contamination affects the health quality of grain, disqualifying it from use in human foods and livestock feeds. One method that can control the spread of this disease is the use of genetically-resistant varieties.

Phenotyping to determine the susceptibility of wheat ears to fusarium

The method currently used by breeders involves phenotyping in the field based on a visual examination.  This evaluation, subject to interpretation and requiring repeated visits from experts, is incompatible with high-throughput phenotyping. In order to improve these health assessments of  plots, without damaging the plants, the scientists have developed a field imaging method involving the use of optical sensors that will operate whatever the weather conditions, supplemented by image processing and analysis software to quantify head blight damage at the plot scale. 

A multi-site experimental system tested on several varieties and pathosystems

The reliability of the protocol was tested during multi-site experiments – in Clermont-Ferrand (63), Estrées-Mons (80), Maule (78) and Rosenthal (Germany) – between 2013 and 2015, on more than 400 cereal genotypes (cone wheat, winter wheat, triticale, barley, winter barley) and various pathosystems. Elite soft wheat cultivars, developed by some fifteen breeders between 1974 and 2012, already formed part of the test panel for the Investments for the Future (PIA) programme, BreadWheat.  The different varieties of barley (20 cultivars) and triticale (10 cultivars), representing the morphological diversity of these two species, were supplied by Secobra and Agri-Obtentions. On wheat, artificial contamination was performed at the mid-anthesis stage by spraying with an inoculum of the aggressive and mycotoxigenic strain, F. graminearum Fg1.

Development of a platform for image acquisition and analytical tools

The field phenotyping system was automated by designing an image acquisition platform made up of a digital reflex camera and flash lighting. The scientists then specifically developed two complementary algorithms.  The first, SegEpis, was based on texture analysis enabling the isolation of pixels only concerning wheat ears, while the second, SegFusa, only takes account of differences in colour and can thus calculate the surface area of ears affected by the symptoms.

FusatechProcessing V1©: a software program for breeders

SegEpis and SegFusa now form part of  FusatechProcessing V1©, a software that can target images specific to cereal ears, count them and measure the severity of an attack. This decision-support tool is available to breeders and enables the precision phenotyping of cereals in the field. It has been developed with the support of the Céréales Vallée competitiveness cluster and has received financial support from the Auvergne-Rhone-Alpes Regional Council and the European Regional Development Fund (FEDER).

Contact(s)
Scientific contact(s):

  • Thierry Langin (04 73 62 44 47) Experimental Unit for the Field Phenotyping of Cereals (UE1375 PHACC) INRA Site de Crouël -5 chemin de Beaulieu -63039 CLERMONT-FERRAND CEDEX
  • Denis Tourvieille (04 73 62 44 45)
Associated Division(s):
Plant Biology and Breeding, Plant Health and Environment
Associated Centre(s):
Auvergne-Rhône-Alpes

Find out more

Veodis 3D (http://www.veodis-3d.com/)
A consultancy in environmental engineering, metrology and river geomorphology, Veodis 3D is a spin-off from the CNRS Geolab laboratory. The company offers a range of tools associated with specialised software: GPS for topography and mapping, bathymetry, airborne and terrestrial photogrammetry, geographical information systems, 3D laser scanner, and the development of algorithms for image and video processing.

On the subject of

The Céréales Vallée Competitiveness Cluster contributes through innovation to the sustainable cultivation of cereals and thus constitutes a response to the food, non-food and and environmental challenges faced by our society. Born in 2005, Céréales Vallée is the only competitiveness cluster focused on the cereals sector, from seed to finished products.  Based in Auvergne, it already enjoys an international reputation, combining unique skills that enable innovation in cereals, and federating more than 900 public and private sector actors involved in research, industry and training in the cereals sector. In a context of strong global competition, the Cluster facilitates the development and coordination of innovative collaborative projects in four main thematic areas: cereal production and sustainable agriculture, cereals for livestock feeds, cereals for human nutrition and cereals for agricultural materials.

The wheat varieties which served to obtain the research results described above were those which had been retained in the context of the BreadWheat project. This aims to drive competitiveness in the French wheat breeding sector by responding to demands from society for sustainable and high quality products.

  • Project leader: Joint Research Unit for the Genetics, Diversity and Ecophysiology of Cereals (UMR INRA-UBP 1095, GDEC), Auvergne-Rhône-Alpes Research Centre
  • Duration: 2011 – 2020 (9 years)
  • Budget: €34 million (including €9 million from the Investments for the Future programme).
  • 26 partners: 13 public research laboratories based in different INRA Research Centres and universities throughout France, ten seed companies and cooperatives specialised in biotechnologies, two technical institutes and the Céréales Vallée Competitiveness Cluster.

BreadWheat is an unprecedented effort that combines new genotyping and high-throughput phenotyping technologies to identify the genetic factors involved in traits of agronomic interest such as yield, quality or the tolerance of biotic and abiotic stresses.  It is enabling the development of new breeding methodologies and is using hitherto unexploited genetic resources to identify and combine alleles of interest to obtain new varieties that will be more efficient under cultivation conditions that are environmentally friendly and adapted to climate change.