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Genetics and next-generation sequencing in identifying marker for aflatoxin resistance in maize.
M. L. WARBURTON (1), W. P. Williams (1), G. Windham (1), S. Murray (2), W. Xu (2), A. Perkins (3), J. Tang (1), L. Hawkins (1). (1) USDA ARS CHPRRU, Mississippi State, MS, U.S.A.; (2) Dept. Soil and Crop Sciences TAMU, College Station, TX, U.S.A.; (3) Computer Science and Engineering Mississippi State University, Mississippi State, MS, U.S.A.

Resistance to aflatoxin accumulation and ear rot caused by <i>Aspergillus flavus</i> has been studied using various genetic mapping strategies. Quantitative Trait Loci mapping has identified several QTL for resistance from various sources, but little is known about underlying genes and mechanisms. An association panel of 300 maize inbred lines was genotyped by sequencing and phenotyped as testcrosses for aflatoxin levels following inoculation by <i>A. flavus</i> in replicated trials in 8 environments. Over 400K Single Nucleotide Polymorphisms were identified. After filtering for minor allele frequency >5%, 261,184 SNPs were used for genome wide association study, in which we identified 117 SNPs associated with aflatoxin levels in grain (<i>P</i> ≤ 9.78 x 10-6 | 1/N). Ten SNP/trait associations exceeded the 10% false discovery rate level (p< 3.83 x 10-7). These 10 significant associations fall within linkage disequilibrium distance of 5 genes. The work of characterizing the correct candidate genes will now begin. Multiple associations (between one or multiple linked SNPs and aflatoxin levels in one or more environments) increase confidence of certain regions; 21 of these regions with multiple associations were identified. Thirteen of 10 associated SNPs or 21 regions fell within a previously identified QTL. The associated SNPs and their gene effects are being analyzed with annotated maize pathways to help identify genetic resistance mechanisms.

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