Molecular quantification of the pea footrot disease pathogen (Nectria haematococca) in agricultural soils

Abstract

Footrot disease due to Nectria haematococca (anamorph Fusarium solani f. sp. pisi) is an economically important disease of peas globally. However, our ability to predict accurately the likelihood of footrot infections is limited because there is no method to determine inoculum density prior to planting. In this research, a PCR-based assay was developed to quantify the pea pathogenicity gene (PEP3), exclusive to highly pathogenic forms of N. haematococca, from DNA extracted from agricultural field soils. The applicability of using quantitative PCR (qPCR) to measure this gene in soil was validated, and the relationship between PEP3 gene numbers and footrot disease was also studied. Results showed that the quantitative assay is both efficient and specific; amplification efficiency of the Q-PCR assay for the PEP3 gene was 92. Gene copy numbers were shown to vary significantly (P= 0.01) between fields, and were positively correlated to the number of spores of pathogenic N. haematococca, and to footrot disease. PEP3 numbers of up to 100 g -1 soil constituted a threshold number for infection-potentially capable of causing economically significant pea footrot disease. The density of virulent N. haematococca in soil fields capable of causing footrot disease could be determined with a high degree of accuracy, with this assay. It offers the opportunity for prediction of pea footrot infections in agricultural soils prior to cultivation. © 2010 Springer Science+Business Media B.V

A Review of Indicators of Healthy Agricultural Soils with Pea Footrot Disease Suppression Potentials

“…Recent works aimed at studying various factors responsible for pea footrot disease also corroborate these earlier findings (Etebu & Osborn, 2010, 2011c. Whilst organic carbon was observed to be positively correlated to total ammonium-nitrogen (NH 4 -N) (P≤0.05), it showed a significant (P≤0.05) inverse correlation to pea footrot disease (Etebu & Osborn, 2011c).…”

“…The inoculum load within or near fields of host plants is critical in plant disease epidemics (Cullen et al, 2001(Cullen et al, , 2002Goud & Termorshuizen, 2003). Generally, increasing the amount of inoculum load enhances disease severity and reduces the time required for maximal disease development (Bhatti & Kraft, 1992;Etebu & Osborn, 2010, 2011bNavas-Cortés et al, 2000;Rush & Kraft 1986;Sugha et al, 1994). Whilst the inoculum potential of a soil, defined as the pathogenic energy present to cause infection (Bouhot, 1979), is dependent on many factors, it is common practice to allow fallow periods between susceptible crops, to avoid build-up of high inoculum load in fields, and in so doing, also avoid disease outbreaks in such fields.…”

“…Comm., 2005;Oyarzun et al, 1994) has been unsuitable (Oyarzun et al, 1997), essentially because the medium is not exclusively selective for N. haematococca, neither does it discriminate between pathogenic and non-pathogenic forms (Etebu & Osborn, 2009, 2010, 2011aKistler www.ccsenet.org/sar Sustainable Agriculture Research Vol. 1, No.…”

“…Following the discovery of these genes, several PCR-based molecular assays have been developed to selectively detect and quantify pea pathogenic forms of N. haematococca in agricultural soils without recourse to culture (Etebu & Osborn, 2009, 2010, 2011b. These assays showed that gene copy numbers of each of three genes (PDA, PEP3 and PEP5) quantified from soil-DNA were comparable to the number of pea pathogenic forms of N. haematococca in soil.…”

“…Some soil chemical factors that contribute to pea plant health and productivity include soil organic matter (SOM), Salinity, pH, Potassium, Phosphorus etc. Physical factors, on the other hand, would include temperature, water holding capacity (Etebu, 2008;Etebu & Osborn, 2011c).…”