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

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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.

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The genotype data in this study are included as supplementary information.

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Acknowledgements

The authors thank scientists in the Corn Host Plant Resistance Research Unit, USDA-ARS at Mississippi State for their assistance in the field.

Funding

This work was supported through the USDA Agricultural Research Service (ARS) funded Specific Cooperative Agreements (No. 58-6406-1-600 and 58-6066-0-064) between the USDA-ARS and the Mississippi Agricultural & Forestry Experiment Station (MAFES) at Mississippi State University. The work was also supported by the National Corn Growers Association and the Aflatoxin Mitigation Center of Excellence Aflatoxin Research Programs.

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Authors and Affiliations

  1. Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS, USA

    Xueyan Shan

  2. Corn Host Plant Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, , Mississippi State, MS, USA

    W. Paul Williams

  3. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, USA

    Daniel G. Peterson

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  1. Xueyan Shan
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  2. W. Paul Williams
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  3. Daniel G. Peterson
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Contributions

XS, WPW, and DGP conceived and designed the experiments. XS, WPW, and DGP performed the experiments. XS analyzed the data and wrote the manuscript. WPW and DGP contributed to and edited the manuscript. All authors have reviewed and approved the final manuscript.

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Correspondence to Xueyan Shan.

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Supplementary Information

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10681_2023_3232_MOESM1_ESM.xlsx

A list of most polymorphic variants along with chromosome positions of known genes on maize QTL-4.06 region (AGP v3). (XLSX 208 kb)

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Shan, X., Williams, W.P. & Peterson, D.G. Genome resequencing facilitates high-resolution exploration of a maize quantitative trait locus for resistance to aflatoxin accumulation. Euphytica 219, 104 (2023). https://doi.org/10.1007/s10681-023-03232-y

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