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Association of single nucleotide polymorphic sites in candidate genes with aggressiveness and deoxynivalenol production in Fusarium graminearum causing wheat head blight.

Talas F, Würschum T, Reif JC, Parzies HK, Miedaner T - BMC Genet. (2012)

Bottom Line: Two neighboring SNPs in MetAP1 and one SNP in Erf2 were significantly (P < 0.05) associated with aggressiveness explaining proportions of genotypic variance (pG) of 25.6%, 0.5%, and 13.1%, respectively.One SNP in TRI1 was significantly associated with DON production (pG = 4.4).Our findings underline the potential of candidate gene association mapping approaches to identify functional SNPs underlying aggressiveness and DON production for F. graminearum s.s populations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Universitaet Hohenheim, State Plant Breeding Institute, Stuttgart, Germany.

ABSTRACT

Background: Fusarium graminearum sensu stricto (s.s.) is an ubiquitous pathogen of cereals. The economic impact of Fusarium head blight (FHB) is characterized by crop losses and mycotoxin contamination. Our objective was to associate SNP diversity within candidate genes with phenotypic traits. A total of 77 F. graminearum s.s. isolates was tested for severity of fungal infection (= aggressiveness) and deoxynivalenol (DON) production in an inoculated field experiment at two locations in each of two years. For seven genes known to control fungal growth (MetAP1, Erf2) or DON production (TRI1, TRI5, TRI6 TRI10 and TRI14) single nucleotides polymorphic sites (SNPs) were determined and evaluated for the extent of linkage disequilibrium (LD). Associations of SNPs with both phenotypic traits were tested using linear mixed models.

Results: Decay of LD was in most instances fast. Two neighboring SNPs in MetAP1 and one SNP in Erf2 were significantly (P < 0.05) associated with aggressiveness explaining proportions of genotypic variance (pG) of 25.6%, 0.5%, and 13.1%, respectively. One SNP in TRI1 was significantly associated with DON production (pG = 4.4).

Conclusions: We argue that using the published sequence information of Fusarium graminearum as a template to amplify comparative sequence parts of candidate genes is an effective method to detect quantitative trait loci. Our findings underline the potential of candidate gene association mapping approaches to identify functional SNPs underlying aggressiveness and DON production for F. graminearum s.s populations.

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Linkage disequilibrium (LD) decay. Robust locally fitted regression of linkage disequilibrium over base-pair distance within the two candidate genes, MetAP1 (25 SNPs) and Erf2 (11 SNPs).
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Figure 3: Linkage disequilibrium (LD) decay. Robust locally fitted regression of linkage disequilibrium over base-pair distance within the two candidate genes, MetAP1 (25 SNPs) and Erf2 (11 SNPs).

Mentions: Percentage of polymorphic sites per total sequenced region of each gene (without singletons) varied from 0.9% (5/513) on TRI10b to 8.8% (65/734) on MetAP1 indicating a high nucleotide diversity in most tested genes (Table 1). LD of SNPs within the gene MetAP1 decayed rapidly within 200 bp of physical distance, i.e., the robust locally fitted regression of r2 values has a trend to decay from r2 = 0.35 to r2 < 0.1, whereas LD within the gene Erf2 had r2 values ranging from 0.8 to 0.2 and the regression of r2 trends to decay already after 150 bp (Figure 3). LD with r2 values higher than 0.1 were detected between all allele combinations within the tested genes followed by a rapid decay negatively correlated with the physical distance in base pair (Figure 4). In line with the rapid decay, LD between genes located on the same chromosome (i.e., TRI1 and MetAP1) is low (r2 < 0.1). Interestingly, 48%, 19%, and 45% of the SNP pairs between the genes TRI10/MetAP1, MetAP1/TRI5 and MetAP1/Erf2, respectively, have higher values of r2 than 0.1, although they are located on different chromosomes. Low r2 values (< 0.1) were observed for SNPs of gene pairs TRI10/Erf2 and TRI5/Erf2, whereas r2 values of 0.2 were detected between SNP pairs of TRI10b and TRI5, followed by a rapid decay of LD.


Association of single nucleotide polymorphic sites in candidate genes with aggressiveness and deoxynivalenol production in Fusarium graminearum causing wheat head blight.

Talas F, Würschum T, Reif JC, Parzies HK, Miedaner T - BMC Genet. (2012)

Linkage disequilibrium (LD) decay. Robust locally fitted regression of linkage disequilibrium over base-pair distance within the two candidate genes, MetAP1 (25 SNPs) and Erf2 (11 SNPs).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3361471&req=5

Figure 3: Linkage disequilibrium (LD) decay. Robust locally fitted regression of linkage disequilibrium over base-pair distance within the two candidate genes, MetAP1 (25 SNPs) and Erf2 (11 SNPs).
Mentions: Percentage of polymorphic sites per total sequenced region of each gene (without singletons) varied from 0.9% (5/513) on TRI10b to 8.8% (65/734) on MetAP1 indicating a high nucleotide diversity in most tested genes (Table 1). LD of SNPs within the gene MetAP1 decayed rapidly within 200 bp of physical distance, i.e., the robust locally fitted regression of r2 values has a trend to decay from r2 = 0.35 to r2 < 0.1, whereas LD within the gene Erf2 had r2 values ranging from 0.8 to 0.2 and the regression of r2 trends to decay already after 150 bp (Figure 3). LD with r2 values higher than 0.1 were detected between all allele combinations within the tested genes followed by a rapid decay negatively correlated with the physical distance in base pair (Figure 4). In line with the rapid decay, LD between genes located on the same chromosome (i.e., TRI1 and MetAP1) is low (r2 < 0.1). Interestingly, 48%, 19%, and 45% of the SNP pairs between the genes TRI10/MetAP1, MetAP1/TRI5 and MetAP1/Erf2, respectively, have higher values of r2 than 0.1, although they are located on different chromosomes. Low r2 values (< 0.1) were observed for SNPs of gene pairs TRI10/Erf2 and TRI5/Erf2, whereas r2 values of 0.2 were detected between SNP pairs of TRI10b and TRI5, followed by a rapid decay of LD.

Bottom Line: Two neighboring SNPs in MetAP1 and one SNP in Erf2 were significantly (P < 0.05) associated with aggressiveness explaining proportions of genotypic variance (pG) of 25.6%, 0.5%, and 13.1%, respectively.One SNP in TRI1 was significantly associated with DON production (pG = 4.4).Our findings underline the potential of candidate gene association mapping approaches to identify functional SNPs underlying aggressiveness and DON production for F. graminearum s.s populations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Universitaet Hohenheim, State Plant Breeding Institute, Stuttgart, Germany.

ABSTRACT

Background: Fusarium graminearum sensu stricto (s.s.) is an ubiquitous pathogen of cereals. The economic impact of Fusarium head blight (FHB) is characterized by crop losses and mycotoxin contamination. Our objective was to associate SNP diversity within candidate genes with phenotypic traits. A total of 77 F. graminearum s.s. isolates was tested for severity of fungal infection (= aggressiveness) and deoxynivalenol (DON) production in an inoculated field experiment at two locations in each of two years. For seven genes known to control fungal growth (MetAP1, Erf2) or DON production (TRI1, TRI5, TRI6 TRI10 and TRI14) single nucleotides polymorphic sites (SNPs) were determined and evaluated for the extent of linkage disequilibrium (LD). Associations of SNPs with both phenotypic traits were tested using linear mixed models.

Results: Decay of LD was in most instances fast. Two neighboring SNPs in MetAP1 and one SNP in Erf2 were significantly (P < 0.05) associated with aggressiveness explaining proportions of genotypic variance (pG) of 25.6%, 0.5%, and 13.1%, respectively. One SNP in TRI1 was significantly associated with DON production (pG = 4.4).

Conclusions: We argue that using the published sequence information of Fusarium graminearum as a template to amplify comparative sequence parts of candidate genes is an effective method to detect quantitative trait loci. Our findings underline the potential of candidate gene association mapping approaches to identify functional SNPs underlying aggressiveness and DON production for F. graminearum s.s populations.

Show MeSH
Related in: MedlinePlus