Theoretical and Applied Genetics

, Volume 110, Issue 5, pp 802–811 | Cite as

Simple-sequence repeat markers used in merging linkage maps of melon (Cucumis melo L.)

  • M. J. Gonzalo
  • M. Oliver
  • J. Garcia-Mas
  • A. Monfort
  • R. Dolcet-Sanjuan
  • N. Katzir
  • P. Arús
  • A. J. MonforteEmail author
Original Paper


A set of 118 simple sequence repeat (SSR) markers has been developed in melon from two different sources: genomic libraries (gSSR) and expressed sequence-tag (EST) databases (EST-SSR). Forty-nine percent of the markers showed polymorphism between the ‘Piel de Sapo’ (PS) and PI161375 melon genotypes used as parents for the mapping populations. Similar polymorphism levels were found in gSSR (51.2%) and EST-SSR (45.5%). Two populations, F2 and a set of double haploid lines (DHLs), developed from the same parent genotypes were used for map construction. Twenty-three SSRs and 79 restriction fragment length polymorphisms (RFLPs), evenly distributed through the melon genome, were used to anchor the maps of both populations. Ten cucumber SSRs, 41 gSSRs, 16 EST-SSR, three single nucleotide polymorphism (SNP) markers, and the Nsv locus were added in the DHL population. The maps developed in the F2 and DHL populations were co-linear, with similar lengths, except in linkage groups G1, G9, and G10. There was segregation distortion in a higher proportion of markers in the DHL population compared with the F2, probably caused by selection during the construction of DHLs through in vitro culture. After map merging, a composite genetic map was obtained including 327 transferable markers: 226 RFLPs, 97 SSRs, three SNPs, and the Nsv locus. The map length is 1,021 cM, distributed in 12 linkage groups, and map density is 3.11 cM/marker. SSR markers alone cover nearly 80% of the map length. This map is proposed as a basis for a framework melon map to be merged with other maps and as an anchor point for map comparison between species of the Cucurbitaceae family.


Linkage Group Melon Simple Sequence Repeat Marker Segregation Distortion Double Haploid Line 
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.



The authors thank V. Alfaro and N. Galofré for technical assistance. This work was funded in part by grants for projects AGL2000-0360 and AGL2003-09175-C02-01 from The Spanish Ministry of Science and Technology and by the Semillas Fitó-Institut de Recerca i Tecnologia Agroalimentàries (IRTA) joint programme. A.J.M. was supported by a contract from Instituto Nacional de Investigaciones Agrarias (INIA). M.J.G. was supported by a fellowship from Institut de Recerca I Tecnologia Agroalimentàries (IRTA). The experiments presented here comply with current Spanish law.

Supplementary material

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Supplementary material, approximately 130 KB.


  1. Akashi Y, Fukunda N, Wako T, Masuda M, Kato K (2002) Genetic variation and phylogenetic relationships in East and South Asian melons, Cucumis melo L., based on the analysis of five isozymes. Euphytica 125:385–396CrossRefGoogle Scholar
  2. Aranzana MJ, Pineda A, Cosson P, Dirlewanger E, Ascasibar J, Cipriani G, Ryder CD, Testolin R, Abbott A, King GJ, Iezzoni AF, Arús P (2003) A set of simple-sequence repeat (SSR) markers covering the Prunus genome. Theor Appl Genet 106:819–825PubMedGoogle Scholar
  3. Areshchenkova T, Ganal MW (1999) Long tomato microsatellites are predominantly associated with centromeric regions. Genome 42:536–544PubMedCrossRefGoogle Scholar
  4. Baudracco-Arnas S, Pitrat M (1996) A genetic map of melon (Cucumis melo L.) with RFLP, RAPD, isozyme, disease resistance and morphological markers. Theor Appl Genet 93:57–64PubMedCrossRefGoogle Scholar
  5. Bryan GJ, Collins AJ, Stephenson P, Orry A, Smith JB, Gale MD (1997) Isolation and characterisation of microsatellites from hexaploid bread wheat. Theor Appl Genet 94:557–563CrossRefGoogle Scholar
  6. Chani E, Ashkenazi V, Hillel J, Veilleux E (2002) Microsatellite marker analysis of an anther-derived potato family: skewed segregation and gene-centromere mapping. Genome 45:236–242PubMedCrossRefGoogle Scholar
  7. Chiba N, Suwabe K, Nunome T, Hirai M (2003) Development of microsatellite markers in melon (Cucumis melo L.) and their application to major cucurbit crops. Breed Sci 53:21–27 CrossRefGoogle Scholar
  8. Chin ECL (1996) Maize simple repetitive DNA sequences: abundance and allele variation. Genome 39:866–873PubMedCrossRefGoogle Scholar
  9. Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Parl WD, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722CrossRefGoogle Scholar
  10. Danin-Poleg Y, Reis N, Baudracco-Arnas S, Pitrat M, Staub JE, Oliver M, Arús P, de Vicente CM, Katzir N (2000) Simple sequence repeats in Cucumis mapping and map merging. Genome 43:963–974PubMedGoogle Scholar
  11. Danin-Poleg Y, Reis N, Tzuri G, Katzir N (2001) Development and characterisation of microsatellite markers in Cucumis. Theor Appl Genet 102:61–72CrossRefGoogle Scholar
  12. Danin-Poleg Y, Tadmor Y, Tzuri G, Reis N, Hirschberg J, Katzir N (2002) Construction of a genetic map of melon with molecular markers and horticultural traits, and localization of genes associated with ZYMV resistance. Euphytica 125:373–384CrossRefGoogle Scholar
  13. Dolcet-Sanjuan R, Claveria E, Llauradó M, Ortigosa A, Arús P (2001) Carnation (Dianthus caryophyllus L.) dihaploid lines resistant to Fusarium oxysporum f. sp. Dianthi. Acta Hortic 560:141–144Google Scholar
  14. Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15Google Scholar
  15. Dufour P, Johnsson C, Antoine-Michard S, Cheng R, Murigneux A, Beckert M (2001) Segregation distortion at marker loci: variation during microspore embryogenesis in maize. Theor Appl Genet 102:993–1001CrossRefGoogle Scholar
  16. Eujayl I, Sorrells ME, Baum M, Wolters P, Powell W (2002) Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat Theor Appl Genet 104:399–407PubMedCrossRefGoogle Scholar
  17. Fazio G, Staub JE, Chung SM (2002) Development and characterization of PCR markers in cucumber (Cucumis sativus L.). J Am Soc Hortic Sci 127:545–557Google Scholar
  18. Garcia-Mas J, Monforte AJ, Arús P (2004) Phylogenetic relationships among Cucumis species based on the ribosomal internal transcribed spacer sequence and microsatellite markers. Plant Syst Evol 248:191–204CrossRefGoogle Scholar
  19. Gonzalo MJ (2003) Generación, caracterización molecular y evaluación morfológica de una población de líneas dihaploides en melón (Cucumis melo L.). PhD Dissertation, Universiad de LleidaGoogle Scholar
  20. Guzy-Wróbelska J, Szarejko I (2003) Molecular and agronomic evaluation of wheat doubled haploid lines obtained through maize pollination and anther culture methods. Plant Breed 122:305–313CrossRefGoogle Scholar
  21. Katzir N, Danin-Poleg Y, Tzuri G, Karchi A, Lavi U, Cregan PB (1996) Length polymorphisms and homologies of microsatellites in several Cucurbitaceae species. Theor Appl Genet 93:1282–1290PubMedCrossRefGoogle Scholar
  22. Kirkbride JH (1993) Biosystematic monograph of the genus Cucumis (Cucurbitaceae). Parkway, BooneGoogle Scholar
  23. Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175Google Scholar
  24. Lander ES, Green P, Abrahamson J, Barlow A, Daley M, Lincoln S, Newburg L (1987) MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181PubMedCrossRefGoogle Scholar
  25. Liebhard R, Koller B, Gianfranceschi L, Gessler C (2003) Creating a saturated reference map for the apple (Malus × domestica Borkh.) genome. Theor Appl Genet 106:1497–1508PubMedGoogle Scholar
  26. Liu L, Kakihara F, Kato M (2004) Characterization of six varieties of Cucumis melo L. based on morphological and physiological characters, including shelf-life of fruit. Euphytica 135:305–313CrossRefGoogle Scholar
  27. Manninen OM (2000). Associations between anther-culture response and molecular markers on chromosomes 2H, 3H and 4H of barley (Hordeum vulgare L.). Theor Appl Genet 100:57–62CrossRefGoogle Scholar
  28. Metzgar D, Bytof J, Wills C (2000) Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res 10:72–80PubMedGoogle Scholar
  29. Mliki A, Staub JE, Zhangyong S, Ghorbel A (2001) Genetic diversity in melon (Cucumis melo L.): an evaluation of African germplasm. Genet Res Crop Evol 48:587–597CrossRefGoogle Scholar
  30. Monforte AJ, Garcia-Mas J, Arús P (2003) Genetic variability in melon based on microsatellite variation. Plant Breed 122:153–157CrossRefGoogle Scholar
  31. Monforte AJ, Eduardo I, Abad S, Arús P (2004a) Inheritance mode of fruit traits in melon. Heterosis for fruit shape and its correlation with genetic distance. Euphytica (in press) Google Scholar
  32. Monforte AJ, Oliver M, Gonzalo MJ, Álvarez JM, Dolçet-Sanjuan R, Arús P (2004b) Identification of quantitative trait loci involved in fruit quality traits in melon. Theor Appl Genet 108:750–758CrossRefGoogle Scholar
  33. Morales M, Luís-Arteaga M, María Álvarez J, Dolcet-Sanjuan R, Monfort A, Arús P, Garcia-Mas J (2002) Marker saturation of the region flanking the gene NSV conferring resistance to the melon necrotic spot carmovirus (MNSV) in melon. J Am Soc Hortic Sci 127:540–544Google Scholar
  34. Morales M, Roig E, Monforte AJ, Arús P, Garcia-Mas J (2004) Single-nucleotide polymorphisms detected in expressed sequence tags of melon (Cucumis melo L.). Genome 47:352–360PubMedCrossRefGoogle Scholar
  35. Oliver M, Garcia-Mas J, Cardús M, Pueyo N, López-Sesé AI, Arroyo M, Gómez-Paniagua H, Arús P, De Vicente MC (2001) Construction of a reference linkage map for melon. Genome 44:836–845PubMedCrossRefGoogle Scholar
  36. Ooijen JW van, Voorrips RE (2001) JoinMap 3.0, software for the calculation of genetic linkage maps. Plant Research International, WageningenGoogle Scholar
  37. Paris HS, Yonash N, Portnoy V, Mozes-Daube N, Tzuri G, Katzir N (2003) Assessment of genetic relationships in Cucurbita pepo (Cucurbitaceae) using DNA markers. Theor Appl Genet 106:971–978PubMedGoogle Scholar
  38. Paterson AH, Lan TH, Reischmann KP, Chang C, Lin SC, Burow MD, Kowalski SP, Katsar CS, DelMonte TA, Feldmann KA, Schertz KF, Wendel JF (1996) Toward a unified genetic map of higher plants, transcending the monocot–dicot divergence. Nat Genet 14:380–382PubMedCrossRefGoogle Scholar
  39. Périn C, Hagen LS, de Conto V, Katzir N, Danin-Poleg Y, Portnoy V, Baudracco-Arnas S, Chadoeuf J, Dogimont C, Pitrat M (2002a) A reference map for Cucumis melo based on two recombinant inbred line populations. Theor Appl Genet 104:1017–1034CrossRefGoogle Scholar
  40. Périn C, Hagen LS, Giovinazzo N, Besombes, D, Dogimont C, Pitrat M (2002b) Genetic control of fruit shape acts prior to anthesis in melon (Cucumis melo L.). Mol Gen Genomics 266:933–941CrossRefGoogle Scholar
  41. Pitrat M (2002) 2002 melon gene list.
  42. Plomion C, O’Malley DM (1996) Recombination rate differences for pollen parents and seed parents in Pinus pinaster. Heredity 77:341–350CrossRefGoogle Scholar
  43. Ritschel PS, Lins TCL, Tristan RL, Buso GSC, Buso JA, Ferreira ME (2004) Development of microsatellite markers from an enriched genomic library for genetic analysis of melon (Cucumis melo L.). BMC Plant Biol 4:9PubMedCrossRefGoogle Scholar
  44. Rozen A, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana, Totowa, pp 365–386Google Scholar
  45. Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726CrossRefGoogle Scholar
  46. Silberstein L, Kovalski I, Brotman Y, Perin C, Dogimont C, Pitrat M, Klingler J, Thompson G, Portnoy V, Katzir N, Perl-Treves R (2003) Linkage map of Cucumis melo including phenotypic traits and sequence-characterized genes. Genome 46:761–773PubMedCrossRefGoogle Scholar
  47. Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3:739–744CrossRefGoogle Scholar
  48. Stepansky A, Kovalski I, Perl-Treves R (1999) Intraspecific classification of melons (Cucumis melo L.) in view of their phenotypic and molecular variation. Plant Syst Evol 217:313–332CrossRefGoogle Scholar
  49. Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712CrossRefGoogle Scholar
  50. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422PubMedGoogle Scholar
  51. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78PubMedCrossRefGoogle Scholar
  52. Wang G, Hyne V, Chao S, Henry Y, Buyser J, Gale MD, Snape JW (1995) A comparison of male and female recombination frequency in wheat using RFLP maps of homoeologous group 6 and 7 chromosomes. Theor Appl Genet 91:744–746PubMedCrossRefGoogle Scholar
  53. Wang YH, Thomas CE, Dean RA (1997) A genetic map of melon (Cucumis melo L.) based on amplified fragment length polymorphism (AFLP) markers. Theor Appl Genet 95:791–798CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • M. J. Gonzalo
    • 1
  • M. Oliver
    • 1
    • 3
  • J. Garcia-Mas
    • 1
  • A. Monfort
    • 1
  • R. Dolcet-Sanjuan
    • 1
  • N. Katzir
    • 2
  • P. Arús
    • 1
  • A. J. Monforte
    • 1
    Email author
  1. 1.Laboratori CSIC-IRTA Genètica Molecular VegetalCabrils (Barcelona)Spain
  2. 2.Department of Genetics and Vegetable Crops, Agricultural Research OrganizationNewe Ya’ar Research CenterRamat YishayIsrael
  3. 3.Syngenta Seeds S.A.SSaint SauveurFrance

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