Theoretical and Applied Genetics

, Volume 130, Issue 2, pp 319–330 | Cite as

A GBS-SNP-based linkage map and quantitative trait loci (QTL) associated with resistance to Fusarium oxysporum f. sp. niveum race 2 identified in Citrullus lanatus var. citroides

  • Sandra E. Branham
  • Amnon Levi
  • Mark W. Farnham
  • W. Patrick WechterEmail author
Original Article


Key message

A major QTL for resistance to Fusarium oxysporum f. sp. niveum race 2 was mapped to a narrow 1.2 Mb interval using a high-density GBS-SNP linkage map, the first map of Citrullus lanatus var. citroides.


Fusarium wilt, a fungal disease caused by Fusarium oxysporum f. sp. niveum (Fon), devastates watermelon crop production worldwide. Several races, which are differentiated by host range, of the pathogen exist. Resistance to Fon race 2, a particularly virulent strain prevalent in the United States, does not exist in edible cultivars of the sweet cultivated watermelon Citrullus lanatus var. lanatus (Cll) and has been well described in a few plant introductions of the wild subspecies of watermelon, C. lanatus var. citroides (Clc). Clc provides a vital source of genetic diversity, as well as resistance to numerous diseases. Unfortunately, both genetic diversity and disease resistance are lacking in Cll due to the narrow genetic base. Despite the importance of Clc to continued watermelon improvement, intra-variety genetic studies are lacking. Here, we present the first Clc genetic linkage map, generated with 2495 single nucleotide polymorphisms developed through genotyping-by-sequencing, and use it to identify quantitative trait loci associated with Fon race 2 resistance. Multiple QTL mapping in a Clc F2:3 population (N = 173) identified one major and four minor QTL. The major QTL explained 43% of the variation in Fon race 2 resistance and was delimited to a 1.2-Mb interval on chromosome 9, a region spanning 44 genes.


Quantitative Trait Locus Fusarium Wilt Plant Introduction Resistance Allele Major Quantitative Trait Locus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This study was funded by the United States Department of Agriculture, project no. 6080-22000-025-00 and the National Institute of Food and Agriculture, project no. 6080-21000-018-08. We would like to acknowledge and thank Dr. Yong Xu and Honghe Sun of National Engineering Research Center for Vegetables, China and Dr. Zhangjun Fei of USDA-ARS, Boyce Thompson Institute, Cornell University, USA for providing the genome information for Citrullus lanatus var citroides PI 296341.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The experiment conducted complies with the laws of the United States.

Supplementary material

122_2016_2813_MOESM1_ESM.xlsx (15 kb)
Online Resource 1 Percentage of surviving (surv) F3 individuals for each F2:3 family (line) and the parents in two blocks (XLSX 15 kb)
122_2016_2813_MOESM2_ESM.sam (456.6 mb)
Online Resource 2 Tag sequence and position information in SAM format (SAM 4,67,592 kb)
122_2016_2813_MOESM3_ESM.xlsx (1.5 mb)
Online Resource 3 Imputed genotypes for 173 F2 individuals at 2,495 SNPs in “csvr” format for import into Rqtl. The first row is the F2:3 family ID (line). The second row has the best linear unbiased predictor value (blup) of Fusarium oxysporum f. sp. niveum race 2 resistance for each F2:3 family. The first column contains the SNP ID is in the format of “S”+chromosome number+”_” + physical position (bp). The second and third columns list the linkage group and genetic position (cM), respectively. The remaining information is the imputed genotypes with “A” indicating homozygous for the resistant parent alleles, “B” homozygous for the susceptible parent alleles, and “H” heterozygous (XLSX 1488 kb)
122_2016_2813_MOESM4_ESM.xlsx (60 kb)
Online Resource 4 Chromosome, start and stop positions, and functional information for the 832 genes that collocated with Fusarium oxysporum f.sp. niveum race 2 resistance QTL (XLSX 60 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg (outside the USA) 2016

Authors and Affiliations

  • Sandra E. Branham
    • 1
  • Amnon Levi
    • 1
  • Mark W. Farnham
    • 1
  • W. Patrick Wechter
    • 1
    Email author
  1. 1.USDA, ARS, US Vegetable LaboratoryCharlestonUSA

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