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Identification and genomic characterization of major effect bacterial blight resistance locus (BB-13) in Upland cotton (Gossypium hirsutum L.)

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Identification and genomic characterization of major resistance locus against cotton bacterial blight (CBB) using GWAS and linkage mapping to enable genomics-based development of durable CBB resistance and gene discovery in cotton.

Abstract

Cotton bacterial leaf blight (CBB), caused by Xanthomonas citri subsp. malvacearum (Xcm), has periodically been a damaging disease in the USA. Identification and deployment of genetic resistance in cotton cultivars is the most economical and efficient means of reducing crop losses due to CBB. In the current study, genome-wide association study (GWAS) of CBB resistance using an elite diversity panel of 380 accessions, genotyped with the cotton single nucleotide polymorphism (SNP) 63 K array, and phenotyped with race-18 of CBB, localized the CBB resistance to a 2.01-Mb region in the long arm of chromosome D02. Molecular genetic mapping using an F6 recombinant inbred line (RIL) population showed the CBB resistance in cultivar Arkot 8102 was controlled by a single locus (BB-13). The BB-13 locus was mapped within the 0.95-cM interval near the telomeric region in the long arm of chromosome D02. Flanking SNP markers, i04890Gh and i04907Gh of the BB-13 locus, identified from the combined linkage analysis and GWAS, targeted it to a 371-Kb genomic region. Candidate gene analysis identified thirty putative gene sequences in the targeted genomic region. Nine of these putative genes and two NBS-LRR genes adjacent to the targeted region were putatively involved in plant disease resistance and are possible candidate genes for BB-13 locus. Genetic mapping and genomic targeting of the BB13 locus in the current study will help in cloning the CBB-resistant gene and establishing the molecular genetic architecture of the BB-13 locus towards developing durable resistance to CBB in cotton.

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Data availability

The plant material and datasets employed in this study are available from the corresponding author on reasonable request.

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Acknowledgements

The authors acknowledge the funding support provided by Cotton Incorporated (CI) and North Carolina Cotton Producers’ Association for the current research and an assistantship to Navin Shrestha. We also thank Kelli Kochan of Texas A&M University for her help with genotyping the lines using the Cotton 63K SNP array. Thanks to Marisa Yoder and Alex Weil at the Danforth Plant Science Center for their help with bacterial infiltrations and cotton planting. We appreciate Josh Udall, James Frelichowski and Janna Love of the Crop Germplasm Research, USDA-ARS, College Station, TX for providing the Upland cotton accessions used in this study.

Funding

Funding support for this research provided by Cotton Incorporated (projects: projects: 19-969 and 19-952) and North Carolina Cotton Producers’ Association (project 19-796NC) to Vasu Kuraparthy, National Science Foundation 2014192836 and 1928344 to Anne Phillips and Rebecca Bart, respectively. Taylor Harris is supported by a NIGMS-funded Initiative for Maximizing Student Development grant to Washington University.

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Author notes

  1. S. Anjan Gowda, Navin Shrestha, Taylor M. Harris and Vasu Kuraparthy contributed equally to research.

Authors and Affiliations

  1. Crop & Soil Sciences Department, North Carolina State University, Raleigh, NC, 27695, USA

    S. Anjan Gowda, Navin Shrestha, Hui Fang, Shilpa Sood, Kuang Zhang & Vasu Kuraparthy

  2. Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA

    Taylor M. Harris, Anne Z. Phillips & Rebecca Bart

  3. NE Research & Extension Center, Crop, Soil, and Environmental Sciences, University of Arkansas, Keiser, AR, 72351, USA

    Fred Bourland

  4. Division of Biology & Biomedical Sciences, Washington University in St. Louis, St Louis, MO, 63110, USA

    Taylor M. Harris

Authors
  1. S. Anjan Gowda
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  2. Navin Shrestha
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  3. Taylor M. Harris
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  4. Anne Z. Phillips
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  5. Hui Fang
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  6. Shilpa Sood
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  7. Kuang Zhang
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  8. Fred Bourland
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  9. Rebecca Bart
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  10. Vasu Kuraparthy
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Contributions

SAG performed data analysis on the GWAS and bi-parental mapping population. AZP screened the NAM parents for resistance to CBB. TH performed additional screening of NAM parents and the bi-parental mapping population and contributed to writing of the manuscript. NS, KZ and HF developed the RIL population. FB developed and contributed Arkot lines of cotton used in the research. VK and SS genotyped the RILs and DIV panel. RB oversaw the phytopathology experiments, provided general feedback on the mapping and interpretation of data and contributed to writing of the manuscript. VK conceived of the project and oversaw all aspects of the work. SAG and VK co-wrote the manuscript.

Corresponding author

Correspondence to Vasu Kuraparthy.

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Communicated by Tianzhen Zhang.

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Gowda, S.A., Shrestha, N., Harris, T.M. et al. Identification and genomic characterization of major effect bacterial blight resistance locus (BB-13) in Upland cotton (Gossypium hirsutum L.). Theor Appl Genet 135, 4421–4436 (2022). https://doi.org/10.1007/s00122-022-04229-2

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