Out in the Cold: Identification of Genomic Regions Associated With Cold Tolerance in the Biocontrol Fungus Clonostachys rosea Through Genome-Wide Association Mapping.

Martin Broberg,Mukesh Dubey,Mikael Brandström Durling,Dan Funck Jensen,Hans-Josef Schroers,Magnus Karlsson,Shi-Dong Li,Katarina Ihrmark,Man-Hong Sun

doi:10.3389/fmicb.2018.02844

Abstract

There is an increasing importance for using biocontrol agents in combating plant diseases sustainably and in the long term. As large scale genomic sequencing becomes economically viable, the impact of single nucleotide polymorphisms (SNPs) on biocontrol-associated phenotypes can be easily studied across entire genomes of fungal populations. Here, we improved a previously reported genome assembly of the biocontrol fungus Clonostachys rosea strain IK726 using the PacBio sequencing platform, which resulted in a total genome size of 70.7 Mbp and 21,246 predicted genes. We further performed whole-genome re-sequencing of 52 additional C. rosea strains isolated globally using Illumina sequencing technology, in order to perform genome-wide association studies in conditions relevant for biocontrol activity. One such condition is the ability to grow at lower temperatures commonly encountered in cryic or frigid soils in temperate regions, as these will be prevalent for protecting growing crops in temperate climates. Growth rates at 10°C on potato dextrose agar of the 53 sequenced strains of C. rosea were measured and ranged between 0.066 and 0.413 mm/day. Performing a genome wide association study, a total of 1,478 SNP markers were significantly associated with the trait and located in 227 scaffolds, within or close to (< 1000 bp distance) 265 different genes. The predicted gene products included several chaperone proteins, membrane transporters, lipases, and proteins involved in chitin metabolism with possible roles in cold tolerance. The data reported in this study provides a foundation for future investigations into the genetic basis for cold tolerance in fungi, with important implications for biocontrol.

Highlights

As the human global population grows and plant pathogens and pests increase and spread, sustainable agricultural production, and disease control increases in importance to ensure future food security (Syed Ab Rahman et al, 2018)
The analysis identified 1,478 single nucleotide polymorphisms (SNPs) markers associated with the trait and certain genes located in the vicinity were predicted to encode several chaperone proteins, membrane transporters, lipases, and proteins involved in chitin metabolism with possible roles in cold tolerance
The growth rate at 10◦C for each strain was normalized by the growth rate at 25◦C (Table 1) for the genome-wide association studies (GWAS) analysis, to enable identification of SNPs and genomic regions contributing to higher growth rate at colder temperature

Summary

Introduction

As the human global population grows and plant pathogens and pests increase and spread, sustainable agricultural production, and disease control increases in importance to ensure future food security (Syed Ab Rahman et al, 2018). Biological control agents (BCAs) demonstrate an environmentally sustainable and potent alternative to current industrial pesticide practices in agriculture, due to the risk chemicals may pose to human and animal health (Syed Ab Rahman et al, 2018). (Schroers et al, 1999) is a widely studied BCA, effective against several economically important fungal plant pathogens such as Botrytis cinerea, Bipolaris sorokiniana, Fusarium spp., and Sclerotinia sclerotiorum (Knudsen et al, 1995; Sutton et al, 1997; Teperi et al, 1998; Xue et al, 2009; Rodríguez et al, 2011). The biocontrol effect of C. rosea can be derived from its ability to directly parasitize plant pathogenic fungi, and from exploitation competition for space and nutrients and from interference competition via antibiosis (Li et al, 2002; Rodríguez et al, 2011; Jensen et al, 2017)

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Results

Conclusion