Genome resequencing facilitates high-resolution exploration of a maize quantitative trait locus for resistance to aflatoxin accumulation

Authors: SHAN, XUEYAN - Mississippi State University; Williams, William; PETERSON, DANIEL - Mississippi State University

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/16/2023
Publication Date: 9/13/2023
Citation: Shan, X., Williams, W.P., Peterson, D.G. 2023. Genome resequencing facilitates high-resolution exploration of a maize quantitative trait locus for resistance to aflatoxin accumulation. Euphytica. 219(104:1-11. https://doi.org/10.1007/s10681-023-03232-y.
DOI: https://doi.org/10.1007/s10681-023-03232-y

Interpretive Summary: Contamination of the grain with aflatoxin is a major food and feed safety concern in corn production in the southeastern United States. Screening for sources of genetic resistance in corn to aflatoxin accumulation has led to the discovery of quantitative trait loci (QTL) associated with resistance to aflatoxin accumulation in several maize inbred lines developed by USDA-ARS scientists at Mississippi State, MS. In this study, we used next generation sequencing to investigate the genomic architecture and DNA polymorphisms on a region of Chromosome 4 of four inbred lines of corn, two lines resistant to aflatoxin accumulation and two lines susceptible to aflatoxin accumulation. We demonstrated a strategy for genome sequencing analysis through assembling and aligning genome sequencing reads only to the target region of interest of the reference genome. We assembled genome-sequencing reads from individual maize inbred lines to the targeted chromosomal region of the B73 reference genome. We identified a long list of single nucleotide polymorphisms (SNPs) by variant calling methods from the comparative analysis of the targeted QTL region among four inbred lines. Our study provided a thorough list of SNPs in the chromosomal region associated with resistance to aflatoxin accumulation. We demonstrated that next generation sequencing can be used to generate sufficient molecular markers for breeding for resistance to aflatoxin accumulation in corn as well as other important agronomical traits.

Technical Abstract: Aflatoxin contamination is a major threat to maize production in the Southeastern United States. Screening for genetic resistance to aflatoxin has led to the identification of aflatoxin-resistance quantitative trait loci (QTL) in maize inbred lines. However, these QTLs typically span large DNA regions making identification of actual resistance-associated sequences difficult. In this study, we took the portion of the maize B73 genome at chromosome bin 4.06 (APG v3) containing a 22 Mbp QTL (QTL-4.06) associated with aflatoxin resistance and used it as a reference to identify single-nucleotide polymorphisms (SNPs) and insertion/deletion variants (INDELs) that differ between resistant (Mp313E and Mp715) and susceptible (B73 and Va35) maize inbred lines. Our study provides a rich list of SNPs and INDELs that can be used as markers in fine-mapping of candidate regions in QTL-4.06 and demonstrates the great potential of resequencing in generating higher density molecular maps that can be leveraged in molecular breeding-based crop improvement.