Genome-wide analysis of Fusarium graminearum field populations reveals hotspots of recombination.

Firas Talas,Bruce A Mcdonald

doi:10.1186/s12864-015-2166-0

Abstract

BackgroundFusarium graminearum (Fg) is a ubiquitous pathogen of wheat, barley and maize causing Fusarium head blight. Large annual yield losses and contamination of foodstuffs with harmful mycotoxins make Fg one of the most-studied plant pathogens. Analyses of natural field populations can lead to a better understanding of the evolutionary processes affecting this pathogen. Restriction site associated DNA sequencing (RADseq) was used to conduct population genomics analyses including 213 pathogen isolates from 13 German field populations of Fg.ResultsHigh genetic diversity was found within Fg field populations and low differentiation (FST = 0.003) was found among populations. Linkage disequilibrium (LD) decayed rapidly over a distance of 1000 bp. The low multilocus LD indicates that significant sexual recombination occurs in all populations. Several recombination hotspots were detected on each chromosome, but different chromosomes showed different levels of recombination. There was some evidence for selection hotspots.ConclusionsThe population genomic structure of Fg is consistent with a high degree of sexual recombination that is not equally distributed across the chromosomes. The high gene flow found among these field populations should enable this pathogen to adapt rapidly to changes in its environment, including deployment of resistant cultivars, applications of fungicides and a warming climate.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2166-0) contains supplementary material, which is available to authorized users.

Highlights

Fusarium graminearum (Fg) is a ubiquitous pathogen of wheat, barley and maize causing Fusarium head blight
Population genomic studies that search for associations between markers and quantitative traits require a large number of genetic markers [1, 2], often using hybridization approaches based on dense panels of Single nucleotide polymorphism (SNP) markers that cover the genome
Analysis of molecular variance (AMOVA) revealed that 99.7 % of the total genetic variance was within field populations and only 0.3 % was among populations

Summary

Introduction

Fusarium graminearum (Fg) is a ubiquitous pathogen of wheat, barley and maize causing Fusarium head blight. Restriction site associated DNA sequencing (RADseq) was used to conduct population genomics analyses including 213 pathogen isolates from 13 German field populations of Fg. Population genomics analyses can provide insight into the evolutionary history of populations by providing rich, genome-wide measures of genetic variation and its related parameters including gene flow, population size and reproductive system [1, 2]. Population genomic studies that search for associations between markers and quantitative traits require a large number of genetic markers [1, 2], often using hybridization approaches based on dense panels of SNP markers that cover the genome. An alternative approach invented by Baird et al [3, 4], called restriction site associated DNA sequencing (RADseq), combines a high density of SNP markers, with a high genome coverage at a relatively low cost [5, 6]

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