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

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Abstract

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.

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Acknowledgments

This project was supported by the USDA-NIFA (no. 2013-38821-21453), National Science Foundation under Grant No. NSF 09-570 - EPS-1003907, Gus R. Douglass Institute and NIH Grant P20RR016477 to the West Virginia IDeA Network for Biomedical Research Funding. The authors thank GRDI graduate assistantships for A. Bhandary and L. Abburi. The authors are grateful to R. Jarret, Plant Genetic Resources Conservation Unit, USDA-ARS (Griffin, GA) for providing the seeds of germplasm accessions.

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We declare that we have no conflict of interest.

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Author notes

  1. Pegadaraju Venkatramana

    Present address: Douglas Scientific LLC, 3600 Minnesota Street, Alexandria, MN, 56308, USA

Authors and Affiliations

  1. Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA

    Padma Nimmakayala, Venkata Lakshmi Abburi, Abhishek Bhandary, Lavanya Abburi, Venkata Gopinath Vajja, Rishi Reddy, Sridhar Malkaram, Yan R. Tomason & Umesh K. Reddy

  2. BioDiagnostics, Inc, 507 Highland Drive, River Falls, WI, 54022, USA

    Pegadaraju Venkatramana

  3. Molecular and Cellular Imagining Center, Ohio Agriculture Research and Development Center, Ohio State University, Wooster, OH, 44691, USA

    Asela Wijeratne

  4. U.S. Vegetable Laboratory, ARS, USDA, 2875 Savannah Highway, Charleston, SC, 29414, USA

    Amnon Levi

  5. Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695-7609, USA

    Todd C. Wehner

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  1. Padma Nimmakayala
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  2. Venkata Lakshmi Abburi
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  3. Abhishek Bhandary
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  5. Venkata Gopinath Vajja
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  7. Sridhar Malkaram
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  8. Pegadaraju Venkatramana
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  9. Asela Wijeratne
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  11. Amnon Levi
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  12. Todd C. Wehner
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  13. Umesh K. Reddy
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Correspondence to Umesh K. Reddy.

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Padma Nimmakayala and Umesh K. Reddy have contributed equally.

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Nimmakayala, P., Abburi, V.L., Bhandary, A. et al. Use of VeraCode 384-plex assays for watermelon diversity analysis and integrated genetic map of watermelon with single nucleotide polymorphisms and simple sequence repeats. Mol Breeding 34, 537–548 (2014). https://doi.org/10.1007/s11032-014-0056-9

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