Molecular Breeding

, 38:139 | Cite as

QTL-seq and marker development for resistance to Fusarium oxysporum f. sp. niveum race 1 in cultivated watermelon

  • Sandra E. Branham
  • W. Patrick Wechter
  • Shaunese Lambel
  • Laura Massey
  • Michelle Ma
  • Julie Fauve
  • Mark W. Farnham
  • Amnon LeviEmail author


Fusarium wilt, caused by the fungus Fusarium oxysporum f. sp. niveum (Fon), is one of the predominant diseases of watermelon. Resistance to Fon race 1 is conferred by a single major quantitative trait locus (QTL), Fo-1.1, but resolution of this region has been poor due to low marker density. In this study, a combination of whole genome resequencing of bulked segregants (QTL-seq analysis) followed by QTL mapping with kompetitive allele specific PCR (KASP) markers developed across Fo-1.1 successfully increased the resolution from 2.03 to 1.56 Mb and 315 kb, respectively. The linkage of the KASP markers to Fon race 1 resistance across a wide range of watermelon germplasm was validated in a set of elite watermelon cultivars. The linked markers described here provide a breeder-friendly toolkit immediately available for high-throughput genotyping in large-scale breeding programs for fine mapping and incorporation of Fon race 1 resistance in watermelon.


Disease resistance QTL-seq Fusarium wilt Watermelon Resequencing KASP 


Funding information

This study was funded by the National Institute of Food and Agriculture, project no. 6080-21000-018-08.

Compliance with ethical standards

USDA is an equal opportunity provider and employer. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. The experiment conducted complies with the laws of the United States.

This research project was developed through a non-funded cooperative agreement (ARS Number: 58-6659-8-102) between USDA-ARS and HM.CLAUSE Seed Company.

This research was supported by a grant from USDA National Institute of Food and Agriculture Specialty Crop Research Initiative (2015-51181-24285).

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11032_2018_896_MOESM1_ESM.xlsx (21 kb)
Online resource 1 Sequence information for the Kompetitive Allele-Specific PCR markers, including: SNP ID, physical position of the SNP, primer sequences, SNP flanking sequence, and nucleotides of the resistant (R) and susceptible (S) alleles (XLSX 21 kb)
11032_2018_896_MOESM2_ESM.xlsx (5.5 mb)
Online resource 2 Results of the QTL-seq analysis of Fon race 1 resistance in a F2:3 watermelon population, including: SNP location (chromosome and position), quality information, read density, base calls, SNP index for each bulk, delta-SNP index and the lower (L) and upper (U) bounds of the 95% and 99% confidence intervals. All variant calls are relative to the susceptible parent reference genome. (XLSX 5646 kb)
11032_2018_896_MOESM3_ESM.png (933 kb)
Online resource 3 Scatterplots of the delta-SNP index values of association with Fon race 1 resistance. The red lines represent the results of a sliding window analysis with a 1 Mb interval and a window size of 10 kb. Regions lacking a red line had less than 10 SNPs per window and were excluded from analysis. Confidence intervals were calculated based on a null hypothesis of no QTL (p < 0.05 = green; p < 0.01 = orange) (PNG 933 kb)
11032_2018_896_MOESM4_ESM.xlsx (3.2 mb)
Online resource 4 Results of a sliding window analysis (1 Mb interval and a window size of 10 kb) of the delta-SNP index of association with Fon race 1 resistance. Each row corresponds to a window and includes the following information: chromosome, position (bp) of the center point of the window, width of the window, read depth and SNP index value for each bulk, the delta-SNP index, the upper and lower bounds of the 95% and 99% confidence intervals, and the number of SNPs in the window (XLSX 3291 kb)
11032_2018_896_MOESM5_ESM.png (855 kb)
Online resource 5 Scatterplots of the SNP-index for the Fon race 1 susceptible bulk. The red lines represent the results of a sliding window analysis with a 1 Mb interval and a window size of 10 kb (PNG 855 kb)
11032_2018_896_MOESM6_ESM.png (1012 kb)
Online resource 6 Scatterplots of the SNP-index for the Fon race 1 resistant bulk. The red lines represent the results of a sliding window analysis with a 1 Mb interval and a window size of 10 kb (PNG 1012 kb)
11032_2018_896_MOESM7_ESM.xlsx (20 kb)
Online resource 7 Genes located within the 1.5-LOD interval of QTLs significantly associated with Fon race 1 resistance in watermelon. Gene annotation information was obtained from the 97103 v1 genome (Guo et al. 2013), including: gene ID, chromosome (CS), start position (bp), stop position (bp), and functional description. The conserved domains and features were obtained from an NCBI conserved domain search (XLSX 20 kb)
11032_2018_896_MOESM8_ESM.xlsx (16 kb)
Online resource 8 List of cultivars included in the validation study of the Fon race 1 KASP markers. Seed company, seed lot, and date of receipt are reported for each cultivar, if known (XLSX 15 kb)


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Copyright information

© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2018

Authors and Affiliations

  • Sandra E. Branham
    • 1
  • W. Patrick Wechter
    • 1
  • Shaunese Lambel
    • 2
  • Laura Massey
    • 1
  • Michelle Ma
    • 2
  • Julie Fauve
    • 2
  • Mark W. Farnham
    • 1
  • Amnon Levi
    • 1
    Email author
  1. 1.USDA, ARS, U.S. Vegetable LaboratoryCharlestonUSA
  2. 2.HM.CLAUSEDavisUSA

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