Molecular Breeding

, Volume 31, Issue 4, pp 829–841

Map-based molecular diversity, linkage disequilibrium and association mapping of fruit traits in melon


  • Yan Tomason
    • Department of Biology, Gus R. Douglass InstituteWest Virginia State University
    • Dnipropetrovsk State Agrarian University
  • Padma Nimmakayala
    • Department of Biology, Gus R. Douglass InstituteWest Virginia State University
  • Amnon Levi
    • U.S. Vegetable LaboratoryUSDA, ARS
    • Department of Biology, Gus R. Douglass InstituteWest Virginia State University

DOI: 10.1007/s11032-013-9837-9

Cite this article as:
Tomason, Y., Nimmakayala, P., Levi, A. et al. Mol Breeding (2013) 31: 829. doi:10.1007/s11032-013-9837-9


Melon has tremendous fruit diversity, the product of complex interactions of consumer preferences in different countries and a wide range of agro-climatic zones. Understanding footprints of divergence underlying formation of various morphotypes is important for developing sustainable and high-quality melons. Basic understanding of population structure and linkage disequilibrium (LD) is limited in melon and has lagged behind other crops. Characterization of population structure and LD are essential for carrying out association mapping of quantitative trait loci (QTL) underlying various complex traits. Mapped single-locus microsatellite markers are known to be very valuable for resolving the population structure and 268 such markers were used in the current study to resolve population structure and LD pattern using 87 accessions of melons belonging to Eastern European, Euro-North American and Asian types. A mixed linear model was implemented to detect QTL for various fruit traits. Various levels of QTL with high to moderate stringency were detected for fruit shape, fruit weight, soluble solids, and rind pressure and a majority of them was found to be in agreement with the previously published data, indicating that association mapping can be very useful for melon molecular breeding. Minor discrepancies in the position, strength and the variation explained by the QTL present between the methods of association and recombinant mapping approaches can be bridged if more melon groups and larger sets of accessions are involved in future studies, combined with high-throughput marker panels.


Linkage disequilibriumFruit traitsMicrosatellitesMelonPopulation structure

Supplementary material

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Supplementary Fig. 1 Heterozygosity (Nei) levels at various SSR loci (TIFF 1,281 kb)
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Supplementary Fig. 2 PIC values for various markers among the melon collections in study (TIFF 1,641 kb)
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Supplementary Fig. 3 Distribution of DeltaK across various predicted clusters (K) (TIFF 438 kb)
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Supplementary Fig. 4 (JPG 1170 kb)
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Supplementary Fig. 5 LD decay estimated based on single locus microsatellite marker associations (TIFF 583 kb)
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Supplementary Fig. 6 LD pattern in Euro-North American group of melons (TIFF 9,595 kb)
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Supplementary Fig. 7 LD pattern in Asian melons (TIFF 5,938 kb)
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Supplementary material 8 (DOC 41 kb)
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Supplementary material 9 (DOC 30 kb)
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Supplementary material 10 (DOC 60 kb)
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Supplementary material 11 (DOC 63 kb)

Copyright information

© Springer Science+Business Media Dordrecht 2013