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

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.