Iqbal Mudassir, Broberg Martin, Haarith Deepak, Broberg Anders, Bushley Kathryn E, Brandström Durling Mikael, Viketoft Maria, Funck Jensen Dan, Dubey Mukesh, Karlsson Magnus
Department of Forest Mycology and Plant Pathology Uppsala BioCenter Swedish University of Agricultural Sciences Uppsala Sweden.
Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA.
Evol Appl. 2020 Jun 2;13(9):2264-2283. doi: 10.1111/eva.13001. eCollection 2020 Oct.
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.
生物防治是一种很有前景的方法，可减少由线虫引起的植物病害，以确保农业生产中的高产量。对用于生物防治的真菌物种的遗传变异进行大规模分析，可以产生有关相互作用机制的知识，从而提高生物防治应用的效果。在本研究中，我们对53株先前已进行全基因组重测序的生物防治真菌菌株进行了全基因组关联研究（GWAS），以检测其对根腐线虫的体外拮抗作用。在马铃薯葡萄糖肉汤（PDB）培养滤液中的线虫死亡率变化很大，并且在菌株之间呈现连续变异（P<0.001），表明这是一种多基因遗传。与PDB对照处理相比，21株菌株产生的培养滤液对线虫的死亡率更高（P≤0.05），而10株菌株降低了（P≤0.05）死亡率。对根腐线虫的体外拮抗作用差异与对大豆胞囊线虫的拮抗作用相关，表明该真菌缺乏宿主特异性。一种经验贝叶斯多重假设检验方法鉴定出279个与该性状显著相关（局部错误发现率<10）的单核苷酸多态性标记。与杀线虫活性相关的基因组区域中存在的基因包括几个膜转运蛋白、一个几丁质酶以及预测可生物合成次生代谢物的蛋白质编码基因。预测的非核糖体肽合成酶基因NPS4和NPS5的基因缺失菌株被构建出来，与野生型相比，它们显示出真菌生长和分生孢子形成率增加（P≤0.001）。缺失菌株还表现出杀线虫活性降低（P<0.001），以及对小麦线虫根病和镰刀菌足腐病的生物防治效果降低（P≤0.05）。总之，我们表明GWAS方法可用于鉴定该真菌中的生物防治因子，特别是推定的非核糖体肽合成酶NPS4和NPS5。
