Abstract
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 Pratylenchus penetrans in 53 previously genome re‐sequenced strains of the biocontrol fungus Clonostachys rosea. Nematode mortality in C. rosea potato dextrose broth (PDB) culture filtrates was highly variable and showed continuous variation (p < .001) between strains, indicating a polygenic inheritance. Twenty‐one strains produced culture filtrates with higher (p ≤ .05) nematode mortality compared with the PDB control treatment, while ten strains lowered (p ≤ .05) the mortality. The difference in in vitro antagonism against P. penetrans correlated with antagonism against the soybean cyst nematode Heterodera glycines, indicating lack of host specificity in C. rosea. An empirical Bayesian multiple hypothesis testing approach identified 279 single nucleotide polymorphism markers significantly (local false sign rate < 10–10) 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 nps4 and nps5 were generated and showed increased (p ≤ .001) fungal growth and conidiation rates compared to the wild type. Deletion strains also exhibited reduced (p < .001) nematicidal activity and reduced (p ≤ .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 C. rosea, specifically the putative nonribosomal peptide synthetases NPS4 and NPS5.
Highlights
Nematodes belong to the phylum Nematoda and comprise > 25,000 known species that display a wide range of feeding habits, including animal-parasitic, plant-parasitic, bacterivorous, fungivorous, omnivorous and predatory (Blaxter, 2003)
By generating C. rosea deletion strains of the nps4 and nps5 Nonribosomal peptide synthetases (NRPSs) genes, we show that NPS4 and NPS5 play a role in growth, conidiation and biocontrol of fusarium foot rot and nematode root disease of wheat
We explored the natural variation in nematode in vitro antagonism among 53 strains of C. rosea to identify potential factors that influence the outcome of biocontrol interactions in C. rosea
Summary
Nematodes belong to the phylum Nematoda (kingdom Animalia) and comprise > 25,000 known species that display a wide range of feeding habits, including animal-parasitic, plant-parasitic, bacterivorous, fungivorous, omnivorous and predatory (Blaxter, 2003). Chemical-based nematicides have been used for controlling plant-parasitic nematodes This option is limited due to environmental protection concerns, development of resistance in nematodes (Abad et al, 2008; Viglierchio & Wu, 1989), high costs, toxicity to plants, livestock and biodiversity (Beketov, Kefford, Schäfer, & Liess, 2013). This emphasizes the need for developing effective and environment-friendly alternatives to chemical nematicides such as biological control. By generating C. rosea deletion strains of the nps and nps NRPS genes, we show that NPS4 and NPS5 play a role in growth, conidiation and biocontrol of fusarium foot rot and nematode root disease of wheat
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