Open Access Highly Accessed Research article

A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.)

Aurora Diaz1, Mohamed Fergany172, Gelsomina Formisano3, Peio Ziarsolo4, José Blanca4, Zhanjun Fei5, Jack E Staub67, Juan E Zalapa6, Hugo E Cuevas68, Gayle Dace9, Marc Oliver10, Nathalie Boissot11, Catherine Dogimont11, Michel Pitrat11, René Hofstede12, Paul van Koert12, Rotem Harel-Beja13, Galil Tzuri13, Vitaly Portnoy13, Shahar Cohen14, Arthur Schaffer14, Nurit Katzir13, Yong Xu15, Haiying Zhang15, Nobuko Fukino16, Satoru Matsumoto16, Jordi Garcia-Mas2 and Antonio J Monforte12*

Author affiliations

1 Instituto de Biología Molecular y Celular de Plantas (IBMCP). Universidad Politécnica de Valencia (UPV)-Consejo Superior de Investigaciones Científicas (CSIC). Ciudad Politécnica de la Innovación (CPI), Ed. 8E. C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain

2 IRTA, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB), Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain

3 Department of Soil, Plant, Environmental and Animal Production Sciences, Federico II University of Naples, Via Università 100, 80055 Portici, Italy

4 COMAV-UPV, Institute for the Conservation and Breeding of Agricultural Biodiversity, Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain

5 Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA

6 USDA-ARS, Vegetable Crops Research Unit, Department of Horticulture, 1575 Linden Dr, University of Wisconsin, Madison, WI 53706, USA

7 Current address: USDA-ARS, Forage and Range Research Laboratory, Utah State University, Logan, UT 84322-6300, USA

8 Current address: USDA-ARS, Tropical Agricultural Research Station, 2200 Pedro Albizu Campus Ave, Mayaguez 00680-5470, Puerto Rico

9 Syngenta Biotechnology, Inc. Research Triangle Park, NC 27709, USA

10 Syngenta Seeds, 12 chemin de l'Hobit, F-31790 Saint-Sauveur, France

11 INRA, UR 1052, Unité de Génétique et d'Amélioration des Fruits et Légumes, Domaine St Maurice, BP 94, 84143 Montfavet Cedex, France

12 Keygene N.V. P.O. Box 216. 6700 AE Wageningen. The Netherlands

13 Institute of Plant Science, Agricultural Research Organization (ARO), Newe Ya'ar Research Center, Ramat Yishay 30095, Israel

14 Institute of Plant Science, Agricultural Research Organization, Volcani Research Center, Bet Dagan 50250, Israel

15 National Engineering Research Center for Vegetables (NERCV), Beijing Academy Agricultural and Forestry Science, Beijing 100097, China

16 National Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan

17 Agronomy Department Faculty of Agriculture, Ain Shams University, Cairo, Egypt

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Citation and License

BMC Plant Biology 2011, 11:111  doi:10.1186/1471-2229-11-111

Published: 28 July 2011



A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS).


Under the framework of the International Cucurbit Genomics Initiative (ICuGI, webcite), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in a broad array of melon germplasm.


Even though relatively unsaturated genetic maps in a diverse set of melon market types have been published, the integrated saturated map presented herein should be considered the initial reference map for melon. Most of the mapped markers contained in the reference map are polymorphic in diverse collection of germplasm, and thus are potentially transferrable to a broad array of genetic experimentation (e.g., integration of physical and genetic maps, colinearity analysis, map-based gene cloning, epistasis dissection, and marker-assisted selection).