Natural variation of root lesion nematode antagonism in the biocontrol fungus and identification of biocontrol factors through genome-wide association mapping.

Biological control is a promising approach to reduce plant diseases caused by nematodes to ensure high productivity in agricultural production. Large-scale analyses of genetic variation in fungal species used for biocontrol can generate knowledge regarding interaction mechanisms that can improve efficacy of biocontrol applications. In this study, we performed a genome-wide association study (GWAS) for in vitro antagonism against the root lesion nematode in 53 previously genome re-sequenced strains of the biocontrol fungus . Nematode mortality in potato dextrose broth (PDB) culture filtrates was highly variable and showed continuous variation ( < .001) between strains, indicating a polygenic inheritance. Twenty-one strains produced culture filtrates with higher ( ≤ .05) nematode mortality compared with the PDB control treatment, while ten strains lowered ( ≤ .05) the mortality. The difference in in vitro antagonism against correlated with antagonism against the soybean cyst nematode , indicating lack of host specificity in . An empirical Bayesian multiple hypothesis testing approach identified 279 single nucleotide polymorphism markers significantly (local false sign rate < 10) associated with the trait. Genes present in the genomic regions associated with nematicidal activity included several membrane transporters, a chitinase and genes encoding proteins predicted to biosynthesize secondary metabolites. Gene deletion strains of the predicted nonribosomal peptide synthetase genes and were generated and showed increased ( ≤ .001) fungal growth and conidiation rates compared to the wild type. Deletion strains also exhibited reduced ( < .001) nematicidal activity and reduced ( ≤ .05) biocontrol efficacy against nematode root disease and against fusarium foot rot on wheat. In summary, we show that the GWAS approach can be used to identify biocontrol factors in , specifically the putative nonribosomal peptide synthetases NPS4 and NPS5.