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. https://doi.org/10.1007/s10681-023-03232-y.
DOI: https://doi.org/10.1007/s10681-023-03232-y

Interpretive Summary: 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 the 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.

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 the 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.