Detection and Quantification of Rhizoctonia solani and Rhizoctonia solani AG1-IB Causing the Bottom Rot of Lettuce in Tissues and Soils by Multiplex qPCR

Abstract

In the muck soil region of southwestern Quebec, vegetable growers are threatened by several soilborne diseases, particularly the bottom rot of lettuce caused by the fungus Rhizoctonia solani. The particularly warm temperature of the few last seasons was marked by an increase in disease severity, and the associated yield losses were significant for Quebec lettuce growers. In the absence of registered fungicides and resistant cultivars, the management of Rhizoctonia solani-induced diseases in lettuce is based on good agricultural practices, which require detailed knowledge of the pathogen. In this study, Rhizoctonia solani fungal strains were isolated from infected field-grown lettuce plants presenting bottom rot symptoms to determine the anastomotic groups (AGs) of these isolates by internal transcribed spacer region (ITS) sequencing. Rhizoctonia solani AG 1-IB was identified as the main anastomotic group causing bottom rot lettuce in field-grown lettuce in organic soils in the Montérégie region. Two specific and sensitive quantitative PCR assays were then developed for R. solani AG1-IB and R. solani. The AG 1-IB qPCR assay amplified all strains of R. solani AG 1-IB tested, and no PCR product was obtained for any non-target strains. The R. solani qPCR assay amplified all strains of R. solani and did not amplify non-target strains, except for two strains of binucleate Rhizoctonia AG-E. In artificially inoculated soils, the sensitivity of both qPCR assays was set to 1 μg of sclerotia g−1 of dry soil. In the growth chamber experiment, a minimum concentration between 14 and 42 μg sclerotia g−1 of dry soil was required to induce the development of symptoms on the lettuce. Indeed, the AG 1-IB qPCR assay was sensitive enough to detect the lowest soil concentration of AG1-IB capable of inducing symptoms in head lettuce. In addition, the qPCR assays successfully detected R. solani and R. solani AG 1-IB from infected plant tissue samples and soil samples from lettuce fields. The qPCR assays developed in this study will be useful tools in lettuce bottom rot management.

Molecular identification and pathogenicity of Rhizoctonia solani and Pythium spp. associated with damping‐off disease on baby leafy vegetables in Greece

“…The levels of variability in ITS1 and ITS2 for the examined R . solani isolates were similar to those found in previous studies (Claerbout et al, 2019; Kuramae et al, 2003; Wallon et al, 2021). The results from the ITS sequencing showed a limited variability in AG of R .…”

“…R . solani has been associated with bottom rot of field‐grown lettuce in the USA, Canada, Germany and Brazil (Grosch et al, 2004; Herr, 1992; Kuramae et al, 2003; Wallon et al, 2021). To date, the anastomosis groups (AGs) of R .…”

“…To date, the anastomosis groups (AGs) of R . solani identified from greenhouse‐ or field‐grown lettuce include AG1, AG1‐IB, AG1‐IC, AG2, AG2‐1, AG2‐1Nt, AG2‐2, AG3, AG4, AG4‐HGI, AG5, AG10 and AG‐BI, as well as some unidentified AGs (Claerbout et al, 2019; Grosch et al, 2004; Herr, 1992; Kuramae et al, 2003; Van Beneden et al, 2009; Wallon et al, 2021). AG1‐IB, AG4‐HGI, AG10, AG2–1, AG2–1Nt and AG3, with AG1‐IB and AG4‐HGI being the most frequently observed, were associated with basal rot of lettuce cultivated in greenhouses in Belgium (Van Beneden et al, 2009).…”

“…solani has been associated with bottom rot of field-grown lettuce in the USA, Canada, Germany and Brazil (Grosch et al, 2004;Herr, 1992;Kuramae et al, 2003;Wallon et al, 2021). To date, the anastomosis groups (AGs) of R. solani identified from greenhouseor field-grown lettuce include AG1, AG1-IB, AG1-IC, AG2, AG2-1, AG2-1Nt, AG2-2, AG3, AG4, AG4-HGI, AG5, AG10 and AG-BI, as well as some unidentified AGs (Claerbout et al, 2019;Grosch et al, 2004;Herr, 1992;Kuramae et al, 2003;Van Beneden et al, 2009;Wallon et al, 2021). AG1-IB, AG4-HGI, AG10, AG2-1, AG2-1Nt and AG3, with AG1-IB and AG4-HGI being the most frequently observed, were associated with basal rot of lettuce cultivated in greenhouses in Belgium (Van Beneden et al, 2009).…”

Improving Soil Quality and Potato Productivity with Manure and High-Residue Cover Crops in Eastern Canada

“…Vegetative compatibility group 4 is virulent on potato and related Solanaceous species in North America [ 75 ]. A variety of DNA assays by qPCR has been developed and used to determine the population densities of soil-borne pathogens [ 76 , 77 , 78 ]. It was reported that DNA of fungi and nematodes became mostly undetectable within a week after the organisms had died, meaning that results of the assays closely approximated the DNA density in soil for living organisms [ 76 ].…”