Molecular Breeding

, Volume 34, Issue 2, pp 537–548 | Cite as

Use of VeraCode 384-plex assays for watermelon diversity analysis and integrated genetic map of watermelon with single nucleotide polymorphisms and simple sequence repeats

  • Padma Nimmakayala
  • Venkata Lakshmi Abburi
  • Abhishek Bhandary
  • Lavanya Abburi
  • Venkata Gopinath Vajja
  • Rishi Reddy
  • Sridhar Malkaram
  • Pegadaraju Venkatramana
  • Asela Wijeratne
  • Yan R. Tomason
  • Amnon Levi
  • Todd C. Wehner
  • Umesh K. Reddy


Watermelon (Citrullus lanatus var. lanatus) is one of the most important vegetable crops in the world. Molecular markers have become the tools of choice for resolving watermelon taxonomic relationships and evolution. Increased numbers of single nucleotide polymorphism (SNP) markers together with simple sequence repeat (SSR) markers would be useful for phylogenetic analyses of germplasm accessions and for linkage mapping for marker-assisted breeding with quantitative trait loci and single genes. We aimed to construct a genetic map based on SNPs (generated by Illumina Veracode multiplex assays for genotyping) and SSR markers and evaluate relationships inferred from SNP genotypes between 130 watermelon accessions collected throughout the world. We incorporated 282 markers (232 SNPs and 50 SSRs) into the linkage map. The genetic map consisted of 11 linkage groups spanning 924.72 cM with an average distance of 3.28 cM between markers. Because all of the SNP-containing sequences were assembled with the whole-genome sequence draft for watermelon, chromosome numbers could be readily assigned for all the linkage groups. We found that 134 SNPs were polymorphic in 130 watermelon accessions chosen for diversity studies. The current 384-plex SNP set is a powerful tool for characterizing genetic relatedness and for developing medium-resolution genetic maps.


SNPs High throughput genotyping SSRs Genetic mapping Watermelon Cultivar diversity 

Supplementary material

11032_2014_56_MOESM1_ESM.png (44 kb)
Supplementary material 1 GO annotation for biological processes (PNG 44 kb)
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Supplementary material 2 GO annotation for at molecular functions (PNG 38 kb)
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Supplementary material 3 GO annotation for cellular contents (PNG 46 kb)
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Supplementary material 4 Neighbor-joining phenogram depicting diversity of watermelon accessions (TIFF 10102 kb)
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Supplementary material 5 PCA of the first 2 components of African cultivated watermelon collections (TIFF 131 kb)
11032_2014_56_MOESM6_ESM.xlsx (14 kb)
Supplementary material 6 (XLSX 14 kb)
11032_2014_56_MOESM7_ESM.xlsx (61 kb)
Supplementary material 7 (XLSX 61 kb)
11032_2014_56_MOESM8_ESM.xlsx (21 kb)
Supplementary material 8 (XLSX 20 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Padma Nimmakayala
    • 1
  • Venkata Lakshmi Abburi
    • 1
  • Abhishek Bhandary
    • 1
  • Lavanya Abburi
    • 1
  • Venkata Gopinath Vajja
    • 1
  • Rishi Reddy
    • 1
  • Sridhar Malkaram
    • 1
  • Pegadaraju Venkatramana
    • 2
    • 3
  • Asela Wijeratne
    • 4
  • Yan R. Tomason
    • 1
  • Amnon Levi
    • 5
  • Todd C. Wehner
    • 6
  • Umesh K. Reddy
    • 1
  1. 1.Department of Biology, Gus R. Douglass InstituteWest Virginia State UniversityInstituteUSA
  2. 2.BioDiagnostics, IncRiver FallsUSA
  3. 3.Douglas Scientific LLCAlexandriaUSA
  4. 4.Molecular and Cellular Imagining Center, Ohio Agriculture Research and Development CenterOhio State UniversityWoosterUSA
  5. 5.U.S. Vegetable Laboratory, ARSUSDACharlestonUSA
  6. 6.Department of Horticultural ScienceNorth Carolina State UniversityRaleighUSA

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