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A genome-wide association study uncovers consistent quantitative trait loci for resistance to Verticillium wilt and Fusarium wilt race 4 in the US Upland cotton

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Key message

A high-resolution GWAS detected consistent QTL for resistance to Verticillium wilt and Fusarium wilt race 4 in 376 U.S. Upland cotton accessions based on six independent replicated greenhouse tests.

Abstract

Verticillium wilt (VW, caused by Verticillium dahliae Kleb.) and Fusarium wilt (FOV, caused by Fusarium oxysporum f.sp. vasinfectum Atk. Sny & Hans) are the most important soil-borne fungal diseases in cotton. To augment and refine resistance quantitative trait loci (QTL), we conducted a genome-wide association study (GWAS) using high-density genotyping with the CottonSNP63K array. Resistance of 376 US Upland cotton accessions to a defoliating VW and virulent FOV4 was evaluated in four and two independent replicated greenhouse tests, respectively. A total of 15 and 13 QTL for VW and FOV4 resistances were anchored by 30 (on five chromosomes) and 56 (on six chromosomes) significant single nucleotide polymorphic (SNPs) markers, respectively. QTL on c8, c10, c16, and c21 were consistent in two or more tests for VW resistance, while two QTL on c8 and c14 were consistent for FOV4 resistance in two tests. Two QTL clusters on c16 and c19 were observed for both VW and FOV4 resistance, suggesting that these genomic regions may harbor genes in response to both diseases. Using BLAST search against the sequenced TM-1 genome, 30 and 35 candidate genes were identified on four QTL for VW resistance and on three QTL for FOV4 resistance, respectively. These genomic regions were rich in NBS-LRR genes presented in clusters. The results create opportunities for further studies to determine the correlations of field resistance with these QTL, molecular examinations of VW and FOV4 resistances, marker-assisted selection (MAS) and eventual cloning of QTL for disease resistance in cotton.

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Authors and Affiliations

  1. Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA

    Abdelraheem Abdelraheem, Hanan Elassbli, Yi Zhu & Jinfa Zhang

  2. Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695-7620, USA

    Vasu Kuraparthy

  3. Crop Germplasm Research, USDA-ARS, College Station, TX, 77845, USA

    Lori Hinze

  4. Department of Soil and Crop Sciences, Texas A & M University, College Station, TX, 77843, USA

    David Stelly

  5. Cotton Incorporated, Cary, NC, USA

    Tom Wedegaertner

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  1. Abdelraheem Abdelraheem
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  3. Yi Zhu
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Contributions

JZ and TW conceived the study. AA, HE, and YZ performed the study. VK created the diversity panel and provided the seeds for the study. LH and DS performed CottonSNP63K array for part of the diversity panel. AA analyzed the results and drafted the manuscript. All authors read, edited, and approved the manuscript.

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Correspondence to Jinfa Zhang.

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Abdelraheem, A., Elassbli, H., Zhu, Y. et al. A genome-wide association study uncovers consistent quantitative trait loci for resistance to Verticillium wilt and Fusarium wilt race 4 in the US Upland cotton. Theor Appl Genet 133, 563–577 (2020). https://doi.org/10.1007/s00122-019-03487-x

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