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Confirmation and Fine Mapping of a Major QTL for Aflatoxin Resistance in Maize Using a Combination of Linkage and Association Mapping

View Article: PubMed Central - PubMed

ABSTRACT

Maize grain contamination with aflatoxin from Aspergillusflavus (A. flavus) is a serious health hazard to animals and humans. To map the quantitative trait loci (QTLs) associated with resistance to A. flavus, we employed a powerful approach that differs from previous methods in one important way: it combines the advantages of the genome-wide association analysis (GWAS) and traditional linkage mapping analysis. Linkage mapping was performed using 228 recombinant inbred lines (RILs), and a highly significant QTL that affected aflatoxin accumulation, qAA8, was mapped. This QTL spanned approximately 7 centi-Morgan (cM) on chromosome 8. The confidence interval was too large for positional cloning of the causal gene. To refine this QTL, GWAS was performed with 558,629 single nucleotide polymorphisms (SNPs) in an association population comprising 437 maize inbred lines. Twenty-five significantly associated SNPs were identified, most of which co-localised with qAA8 and explained 6.7% to 26.8% of the phenotypic variation observed. Based on the rapid linkage disequilibrium (LD) and the high density of SNPs in the association population, qAA8 was further localised to a smaller genomic region of approximately 1500 bp. A high-resolution map of the qAA8 region will be useful towards a marker-assisted selection (MAS) of A. flavus resistance and a characterisation of the causal gene.

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Related in: MedlinePlus

Genome-wide association mapping of the amount of aflatoxin (AA, μg/kg) and the score of resistance to A. flavus infection (RAI) based on SNPs. The dashed line indicates a significant association signal (−logP ≥ 5.74).
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toxins-08-00258-f004: Genome-wide association mapping of the amount of aflatoxin (AA, μg/kg) and the score of resistance to A. flavus infection (RAI) based on SNPs. The dashed line indicates a significant association signal (−logP ≥ 5.74).

Mentions: Three SNPs for the AA and 22 SNPs for the RAI score were identified as having significant marker-trait associations at the Bonferroni-adjusted significance threshold (−logP ≥ 5.74) (Table 5, Figure 4). The three significant SNPs associated with the AA were located on chromosomes 2 and 8 and explained 6.7%–10.4% of the phenotypic variation. Of the 22 significant marker-trait associations for the RAI score, 10 and 12 were detected in 2013 and 2014, respectively. The significant SNPs for the RAI score were located on chromosomes 5, 8, and 9 and explained 6.4%–26.6% of the phenotypic variation. The highly significant SNP cluster on chromosome 8 (which included four SNPs, p = 3.7 × 10−22) was repeatedly detected for the RAI score in 2013 and 2014. As with the RIL population, this SNP cluster was co-localised with the significant SNP markers for the AA in the association population. Importantly, this significant SNP cluster fell within the QTL region detected for the AA by linkage analysis (Table 3, Figure 2).


Confirmation and Fine Mapping of a Major QTL for Aflatoxin Resistance in Maize Using a Combination of Linkage and Association Mapping
Genome-wide association mapping of the amount of aflatoxin (AA, μg/kg) and the score of resistance to A. flavus infection (RAI) based on SNPs. The dashed line indicates a significant association signal (−logP ≥ 5.74).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5037484&req=5

toxins-08-00258-f004: Genome-wide association mapping of the amount of aflatoxin (AA, μg/kg) and the score of resistance to A. flavus infection (RAI) based on SNPs. The dashed line indicates a significant association signal (−logP ≥ 5.74).
Mentions: Three SNPs for the AA and 22 SNPs for the RAI score were identified as having significant marker-trait associations at the Bonferroni-adjusted significance threshold (−logP ≥ 5.74) (Table 5, Figure 4). The three significant SNPs associated with the AA were located on chromosomes 2 and 8 and explained 6.7%–10.4% of the phenotypic variation. Of the 22 significant marker-trait associations for the RAI score, 10 and 12 were detected in 2013 and 2014, respectively. The significant SNPs for the RAI score were located on chromosomes 5, 8, and 9 and explained 6.4%–26.6% of the phenotypic variation. The highly significant SNP cluster on chromosome 8 (which included four SNPs, p = 3.7 × 10−22) was repeatedly detected for the RAI score in 2013 and 2014. As with the RIL population, this SNP cluster was co-localised with the significant SNP markers for the AA in the association population. Importantly, this significant SNP cluster fell within the QTL region detected for the AA by linkage analysis (Table 3, Figure 2).

View Article: PubMed Central - PubMed

ABSTRACT

Maize grain contamination with aflatoxin from Aspergillusflavus (A. flavus) is a serious health hazard to animals and humans. To map the quantitative trait loci (QTLs) associated with resistance to A. flavus, we employed a powerful approach that differs from previous methods in one important way: it combines the advantages of the genome-wide association analysis (GWAS) and traditional linkage mapping analysis. Linkage mapping was performed using 228 recombinant inbred lines (RILs), and a highly significant QTL that affected aflatoxin accumulation, qAA8, was mapped. This QTL spanned approximately 7 centi-Morgan (cM) on chromosome 8. The confidence interval was too large for positional cloning of the causal gene. To refine this QTL, GWAS was performed with 558,629 single nucleotide polymorphisms (SNPs) in an association population comprising 437 maize inbred lines. Twenty-five significantly associated SNPs were identified, most of which co-localised with qAA8 and explained 6.7% to 26.8% of the phenotypic variation observed. Based on the rapid linkage disequilibrium (LD) and the high density of SNPs in the association population, qAA8 was further localised to a smaller genomic region of approximately 1500 bp. A high-resolution map of the qAA8 region will be useful towards a marker-assisted selection (MAS) of A. flavus resistance and a characterisation of the causal gene.

No MeSH data available.


Related in: MedlinePlus