Abstract
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.
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Claims 10
Claim · model-written summary
Nematode mortality in Clonostachys rosea culture filtrates was highly variable and continuously varied between strains
- Taxon
- wheat
Triticum aestivume0 - Outcome
- Nematode mortalitye1
- Qualifier
- indicating a polygenic inheritancee1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“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”
e0“against fusarium foot rot on wheat”
Claim · model-written summary
Twenty-one Clonostachys rosea strains produced culture filtrates with higher nematode mortality than the PDB control
- Taxon
- wheatTriticum aestivume0
- Treatment
- culture filtratese2
- Outcome
- nematode mortalitye2
- Direction
- highere2
- Comparator
- PDB control treatmente2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“Twenty-one strains produced culture filtrates with higher ( p ≤ .05) nematode mortality compared with the PDB control treatment”
e0“against fusarium foot rot on wheat”
Claim · model-written summary
Ten Clonostachys rosea strains lowered nematode mortality
- Taxon
- wheatTriticum aestivume0
- Treatment
- ten strainse3
- Outcome
- the mortalitye3
- Direction
- lowerede3
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e3“while ten strains lowered ( p ≤ .05) the mortality”
e0“against fusarium foot rot on wheat”
Claim · model-written summary
In vitro antagonism against Pratylenchus penetrans correlated with antagonism against Heterodera glycines
- Taxon
- wheatTriticum aestivume0
- Interactor
- P. penetrans
Pratylenchus penetranse4pest - Second interactor
- Heterodera glycines
Heterodera glycinese4pest - Outcome
- in vitro antagonism against P. penetranse4
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e4“The difference in in vitro antagonism against P. penetrans correlated with antagonism against the soybean cyst nematode Heterodera glycines”
e0“against fusarium foot rot on wheat”
Claim · model-written summary
An empirical Bayesian approach identified 279 SNP markers significantly associated with nematicidal antagonism in 53 Clonostachys rosea strains
- Taxon
- wheatTriticum aestivume0
- Material
- 53 previously genome re‐sequenced strainse6
- Outcome
- single nucleotide polymorphism markerse5
- Value
- 279e5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e5“identified 279 single nucleotide polymorphism markers significantly (local false sign rate < 10 –10 ) associated with the trait”
e6“in 53 previously genome re‐sequenced strains of the biocontrol fungus Clonostachys rosea”
e0“against fusarium foot rot on wheat”
Claim · model-written summary
Genes in the genomic regions associated with nematicidal activity include membrane transporters, a chitinase and secondary-metabolite biosynthesis genes
- Taxon
- wheatTriticum aestivume0
- Gene
- a chitinasee7
- Outcome
- Genes present in the genomic regions associated with nematicidal activitye7
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“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”
e0“against fusarium foot rot on wheat”
Claim · model-written summary
Gene deletion of nps4 and nps5 increased fungal growth and conidiation rates of Clonostachys rosea relative to the wild type
- Taxon
- wheatTriticum aestivume0
- Treatment
- Gene deletion strainse1
- Gene
- nps4 and nps5e1
- Outcome
- fungal growth and conidiation ratese1
- Direction
- increasede1
- Comparator
- wild typee1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“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”
e0“against fusarium foot rot on wheat”
Claim · model-written summary
Deletion strains of Clonostachys rosea showed reduced nematicidal activity
- Taxon
- wheatTriticum aestivume0
- Treatment
- Deletion strainse7
- Outcome
- nematicidal activitye7
- Direction
- reducede7
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“Deletion strains also exhibited reduced ( p < .001) nematicidal activity”
e0“against fusarium foot rot on wheat”
Claim · model-written summary
Deletion strains of Clonostachys rosea reduced biocontrol efficacy against nematode root disease
- Taxon
- wheatTriticum aestivume0
- Treatment
- Deletion strainse7
- Outcome
- biocontrol efficacye5
- Direction
- reducede5
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“Deletion strains also exhibited reduced ( p < .001) nematicidal activity”
e5“reduced ( p ≤ .05) biocontrol efficacy against nematode root disease”
e0“against fusarium foot rot on wheat”
Claim · model-written summary
Deletion strains of Clonostachys rosea reduced biocontrol efficacy against fusarium foot rot on wheat
- Taxon
- wheatTriticum aestivume0
- Treatment
- Deletion strainse7
- Outcome
- biocontrol efficacye6
- Direction
- reducede6
FusariumNot reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“Deletion strains also exhibited reduced ( p < .001) nematicidal activity”
e6“reduced ( p ≤ .05) biocontrol efficacy against nematode root disease and against fusarium foot rot on wheat”
e0“against fusarium foot rot on wheat”
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loss of function · pest · Triticum aestivum (wheat)Positive and negative results
1 in the opposite direction
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loss of function · control · Triticum aestivum (wheat)Positive and negative results
2 papers in the same direction as this paper · 1 in the opposite direction
- positive
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loss of function · Fusarium · Triticum aestivum (wheat)Positive and negative results
3 papers in the same direction as this paper · 3 in the opposite direction
- positive
- positive
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3 papers more in this group
See all 7 papers →Claims are grouped by organism, treatment and what was measured or targeted. A paper counts as positive when any of its claims in the group is positive.