Genome-wide association studies can identify novel genomic regions and genes that affect quantitative traits. Fusarium head blight is a destructive disease caused by Fusarium graminearum that exhibits several quantitative traits, including aggressiveness, mycotoxin production, and fungicide resistance. Restriction site-associated DNA sequencing was performed for 220 isolates of F. graminearum. A total of 119 isolates were phenotyped for aggressiveness and deoxynivalenol (DON) production under natural field conditions across four environments. The effective concentration of propiconazole that inhibits isolate growth in vitro by 50% was calculated for 220 strains. Approximately 29,000 single nucleotide polymorphism markers were associated to each trait, resulting in 50, 29, and 74 quantitative trait nucleotides (QTNs) that were significantly associated to aggressiveness, DON production, and propiconazole sensitivity, respectively. Approximately 41% of these QTNs caused nonsynonymous substitutions in predicted exons, while the remainder were synonymous substitutions or located in intergenic regions. Three QTNs associated with propiconazole sensitivity were significant after Bonferroni correction. These QTNs were located in genes not previously associated with azole sensitivity. The majority of the detected QTNs were located in genes with predicted regulatory functions, suggesting that nucleotide variation in regulatory genes plays a major role in the corresponding quantitative trait variation.

Fusarium head blight (FHB) is one of the most destructive diseases of wheat. Twelve small commercial wheat fields (size 1-3 hectares) were sampled in Germany for Fusarium populations at three spots per field with 10 heads each. PCR assays using generic primers confirmed 338 isolates as F. graminearum sensu stricto (s.s.) (64.9%) out of 521 Fusarium spp. that were further analyzed. Populations of F. graminearum s.s. in Germany contain three types of trichothecenes with a dominancy of 15-acetyldeoxynivalenol chemotype (92%) followed by 3-acetyldeoxynivalenol chemotype (6.8%) and a few isolates of nivalenol chemotype (1.2%). All these isolates were genotyped using 19 microsatellite loci. The 12 populations showed a high genetic diversity within the small scale sampling areas resulting in 300 different haplotypes. Genetic diversity within populations (71.2%) was considerably higher than among populations (28.8%) as shown by analysis of molecular variance. Gene flow (Nm) between populations ranged from 0.76-3.16. Composition of haplotypes of one population followed over 2 years changed considerably. No correlation between genetic and geographical distance was found. In conclusion, populations of F. graminearum s.s. in Germany display a tremendous genetic variation on a local scale with a restricted diversity among populations.

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.

Fusarium head blight (FHB) is a destructive disease of wheat all over the world. FHB causes high economic losses for durum wheat because of the lack of resistance sources. Initially, sixty-eight Syrian landraces were tested in field conditions after inoculation to discriminate the most resistant and environmentally stable landraces. Further tests across a total of four environments revealed four landraces with a low mean FHB rating (19-25%) compared to common German durum varieties (56-60%) and an environmentally stable resistance. They are considered as promising resistance sources to FHB for introgression in the adapted durum wheat gene pool.Fusarium head blight (FHB) caused by Fusarium graminearum Schwabe (perfect stage: Gibberella zeae (Schw.) Petch) and other Fusarium species is a common disease in all cereals including maize. Common wheat (Triticum aestivum L.) is already more susceptible and provides higher contents of the mycotoxin deoxynivalenol than triticale and rye (Miedaner and Reinbrecht 2001), but durum wheat (Triticum turgidum L. var. durum) is even more sensitive (McMullen et al. 1997, Stack et al. 2003. Deployment of FHB-resistant cultivars is considered the most effective and cost-efficient strategy to combat this disease (Miedaner 1997). Sources of effective FHB resistance have not been found in adapted durum wheat (Chen et al. 2007). No resistant durum varieties are currently available (Buerstmayr et al. 2009). Attempts to transfer the highly effective resistance loci on chromosomes 5A and 3BS from the hexaploid Chinese landrace ÔSumaiÕ 3 to durum wheat had limited success only (Kumar et al. 2007; F. Lacoudre and L. Gervais, personal communications). Resistance to FHB in tetraploid wheat has been extensively evaluated in wild emmer wheat T. turgidum L. var. dicoccoides (AABB, 2n = 4· = 28). Buerstmayr et al. (2003) tested 151 accessions from different geographical areas in Israel and Turkey and identified eight accessions with moderate FHB resistance. Similarly, Oliver et al. (2008) tested 376 accessions of five subspecies of T. turgidum and found that 16 T. turgidum subsp. carthlicum and four T. turgidum subsp. dicoccum consistently exhibited resistance or moderate resistance to FHB that was much better than observed in actual durum varieties. Four major QTL for FHB in tetraploid wheat were identified so far on chromosomes 3A (Qfhs.ndsu-3AS, Otto et al. 2002), 7A (Qfhs.fcu-7AL; Kumar et al. 2007), 6BS and 2BL (Somers et al. 2006) with the three former QTL derived from wild relatives of durum wheat or emmer. Results of Somers et al. (2006) showed that FHB resistance QTL from wild relatives can be successfully transferred to adapted durum wheat. However, breeding would be much more effective if sources of FHB resistance were found in germplasm of cultivated durum wheat. It might be promising to search such sources in regions where cultivated wheat evolutionary developed, i.e. in the Fertile Crescent. Our objective aimed (i) to analyse Syrian landraces of durum wheat for their FHB resistance b...