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Monitoring important soil-borne plant pathogens in Swedish crop production using real-time PCR

Almquist, Charlotta (2016). Monitoring important soil-borne plant pathogens in Swedish crop production using real-time PCR. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis Agriculturae Sueciae, 1652-6880 ; 2016:26
ISBN 978-91-576-8554-4
eISBN 978-91-576-8555-1
[Doctoral thesis]

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The global demand for food will increase considerably in the nearest future and among the major constraints to agricultural productivity are biotic stresses caused by microorganisms. In this thesis, the causal agents of four of the most important soil-borne diseases threatening the Swedish production of oilseed rape, sugar beets and red clover were selected as targets for developing diagnostic assays using real-time PCR.

The disease risk assessment of clubroot in oilseed rape was improved by developing a real-time PCR assay for quantification of the causal pathogen Plasmodiophora brassicae directly in soil samples. Broad disease risk categories including a threshold level for growing resistant cultivars were established. A real-time PCR assay for quantification of Aphanomyces cochlioides, the oomycete causing root rot in sugar beets, was also developed in the present study. The potential use of this assay as a tool in disease risk assessment was demonstrated for fields with high risk of infection.

Real-time PCR was used to monitor the plant- and airborne inoculum of Sclerotinia sclerotiorum, the causal fungus of Sclerotinia stem rot, in spring oilseed rape. We found that determining the presence of S. sclerotiorum on petals was not useful for stem rot risk assessment since (i) the inoculum incidence on petals varied during flowering, (ii) there was no clear relationship between petal infection and stem rot incidence and (iii) spore release and flowering were not synchronized at one of the field experimental sites. Real-time PCR detection of the incidence of S. sclerotiorum DNA on leaves revealing the field-borne inoculum and quantification of the airborne inoculum are likely more reliable tools for predicting the potential risk of disease.

The pathogen complex causing red clover root rot was monitored over three years in two field experiments. Fusarium avenaceum, Phoma spp. and Cylindrocarpon destructans were detected in red clover roots early in the seeding year using real-time PCR and the levels of pathogen DNA generally increased during the following years. Significant linear relationships were found between the amount of pathogen DNA and disease severity index.

Authors/Creators:Almquist, Charlotta
Title:Monitoring important soil-borne plant pathogens in Swedish crop production using real-time PCR
Series Name/Journal:Acta Universitatis Agriculturae Sueciae
Year of publishing :March 2016
Depositing date:18 March 2016
Number of Pages:78
IWallenhammar, A-C., Almquist, C., Söderström, M. & Jonsson A. (2012). In-field distribution of Plasmodiophora brassicae measured using quantitative real-time PCR. Plant Pathology 61, 16-28.
IIAlmquist, C., Persson, L., Olsson, Å., Sundström, J. & Jonsson, A. (2016). Disease risk assessment of sugar beet root rot using quantitative real-time PCR analysis of Aphanomyces cochlioides in naturally infested soil samples. European Journal of Plant Pathology, doi 10.1007/s10658-016- 0862-5.
IIIAlmquist, C. & Wallenhammar, A-C. (2015). Monitoring of plant and airborne inoculum of Sclerotinia sclerotiorum in spring oilseed rape using real-time PCR. Plant Pathology 64, 109-118.
IVAlmquist, C., Wallenhammar, A-C., Stoltz, E. & Sundström, J. (2016). Monitoring disease development caused by soil-borne plant pathogens associated with root rot in red clover (Trifolium pratense) crop stands using quantitative real-time PCR (manuscript).
Place of Publication:Uppsala
Publisher:Department of Plant Biology, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-576-8554-4
ISBN for electronic version:978-91-576-8555-1
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:H Protection of plants and stored products > H20 Plant diseases
P Natural resources > P31 Soil surveys and mapping
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Biochemistry and Molecular Biology
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
Agrovoc terms:plasmodiophora brassicae, aphanomyces cochlioides, sclerotinia sclerotiorum, gibberella avenacea, fusarium culmorum, phoma, nectria radicicola, soilborne organisms, pathogens, plant diseases, brassica napus, oil crops, beta vulgaris, sugar crops, trifolium pratense, pcr, soil testing, disease control, sweden
Keywords:Plasmodiophora brassicae, Aphanomyces cochlioides, Phoma spp., Sclerotinia sclerotiorum, Fusarium culmorum, Fusarium avenaceum, Cylindrocarpon destructans, real-time PCR, diagnostics, disease risk assessment
Permanent URL:
ID Code:13060
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Department of Plant Biology (from 140101)
Deposited By: Charlotta Almquist
Deposited On:18 Mar 2016 08:34
Metadata Last Modified:10 Sep 2020 13:41

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