Automated image processing framework for analysis of the density of fruiting bodies of Leptosphaeria maculans on oilseed rape stems

Abstract

Understanding the transmission of plant pathogen inoculum during the periods when the host plants are not present is crucial for predicting the initiation of epidemics and optimizing mitigation strategies. However, inoculum production at the end of the cropping season, survival during the intercrop period, and the emergence or release of inoculum can be highly variable, difficult to assess, and generally inferred indirectly from symptom data. As a result, a lack of large datasets hampers the study of these epidemiological processes. Here, inoculum production was studied in Leptosphaeria maculans, the cause of phoma stem canker of oilseed rape. The fungus survives on stubble left in the field, from which ascospores are released at the beginning of the next cropping season. An image processing framework was developed to estimate the density of fruiting bodies produced on stem pieces following incubation in field conditions, and a quality assessment of the processing chain was performed. A total of 2540 standardized RGB digital images of stems were then analysed, collected from 27 oilseed rape fields in Brittany over four cropping seasons. Manual post‐processing removed 16% of the pictures, e.g. when moisture‐induced darkening of the oilseed rape stems caused overestimation of the area covered with fruiting bodies. The potential level of inoculum increased with increasing phoma stem canker severity at harvest, and depended on the source field and the cropping season. This work shows how image‐based phenotyping generates high‐throughput disease data, opening up the prospect of substantially increased precision in epidemiological studies.

Besides stem canker severity, oilseed rape host genotype matters for the production ofLeptosphaeria maculansfruiting bodies

“…Further, by keeping track of individual stem severity and comparing a susceptible cultivar with one having quantitative resistance, Lô-Pelzer et al (2009) were able to see the effect of a genotype with quantitative resistance on the distributions of severities, though they observed no effect of the genotype at a given severity. Afterwards, it has been shown that the production of fruiting bodies on incubated stems can be significantly impacted by the field where they were collected (Bousset et al, 2019). However, this study did not allow distinguishing between the effects of genotype and cropping practices.…”

“…For instance, imaging and existing processing algorithms to segment and count regions, offers the prospect to circumvent the long and tedious manual counting (Stewart et al, 2016;Karisto et al, 2018;Yang & Hong, 2018). In the particular case of L. maculans, the automated quantification of fruiting bodies through image processing have already been tackled (Bousset et al, 2019), offering a means to overcome the experimental bottleneck and assessing the effect of host quantitative resistance on pathogen carry-over.…”

“…Following assessment of phoma stem canker severity pieces of stem comprising the crown and upper 10 cm were selected as described in Bousset et al (2019). This sampling was constrained by the availability of diseased stems.…”

“…A maximum of 30 stems in each of the 6 severity classes was randomly selected from each field while when fewer than 30 stem were available they were all kept. To keep track of phoma canker severity of stem pieces throughout the experiment, two 5 mm diameter holes were drilled, and stem pieces were grouped by 5 on two wooden BBQ sticks painted in blue and labelled with a barcode (Bousset et al 2019). Over summer, the selected stem pieces were incubated in field conditions at INRAE Le Rheu, on a 1:1:1 mix of sand, peat and compost, with moisture and temperature depending on the local climate and natural rain only.…”

“…To quantify fruiting bodies appeared on diseased stem pieces, we used the same imagebased phenotyping settings as in Bousset et al (2019). In short, a picture of each group of 5 dry stems was taken with the barcoded label, placed on a glass plate, 16 cm above a blue background (PVC sheet Lastolite Colormatt electric blue).…”