Molecular prediction of pea footrot disease

PCR based assays were developed in this study to quantitatively predict pea footrot infections in agricultural soils prior to cultivation. Pea footrot disease due to Nectria haematococca (anamorph Fusarium solani f.sp. pisi) is linked to the presence of six pea pathogenicity (PEP) genes (PDA1, PEP1, PEP2, PEP3, PEP4 and PEP5). Whilst molecular assays have been used recently to selectively detect these genes in soil DNA,quantitative molecular assay has been extended to only the PEP3 gene whose role in pea pathogenicity is yet unknown. In this research, PCR-based quantification assays were developed to quantify the two pea pathogenicity genes (PDA and PEP5) with identified roles in pea pathogenicity from soil-DNA obtained from fields with pea footrot histories. Results showed that the quantitative molecular assays developed herein were both efficient. Amplification efficiency of the Q-PCR assay for the PDA and PEP5 gene were 97 and 89%, respectively. PDA and PEP5 gene copy numbers were shown to vary significantly (p = 0.01) between fields. However, the PDA gene copy numbers were relatively higher than those of the PEP5 gene in agricultural fields. The genes, especially PEP5 gene, were comparable to and positively correlated to the number of spores of pathogenic N. haematococca, and footrot disease. The PDA gene alone in soil could not cause footrot disease in peas after 8 weeks of planting; assays directed at it alone may therefore be insufficient to predict pea footrot disease. However, the molecular assay targeting the PDA alongside the PEP5 gene offers the opportunity for quantitative prediction of pea footrot infections in agricultural soils prior to cultivation.