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Bin mapping of genomic and EST-derived SSRs in melon (Cucumis melo L.)

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Abstract

We report the development of 158 primer pairs flanking SSR motifs in genomic (gSSR) and EST (EST-SSR) melon sequences, all yielding polymorphic bands in melon germplasm, except one that was polymorphic only in Cucurbita species. A similar polymorphism level was found among EST-SSRs and gSSRs, between dimeric and trimeric EST-SSRs, and between EST-SSRs placed in the open reading frame or any of the 5′- or 3′-untranslated regions. Correlation between SSR length and polymorphism was only found for dinucleotide EST-SSRs located within the untranslated regions, but not for trinucleotide EST-SSRs. Transferability of EST-SSRs to Cucurbita species was assayed and 12.7% of the primer pairs amplified at least in one species, although only 5.4% were polymorphic. A set of 14 double haploid lines from the cross between the cultivar “Piel de Sapo” and the accession PI161375 were selected for the bin mapping approach in melon. One hundred and twenty-one SSR markers were newly mapped. The position of 46 SSR loci was also verified by genotyping the complete population. A final bin-map was constructed including 80 RFLPs, 212 SSRs, 3 SNPs and the Nsv locus, distributed in 122 bins with an average bin length of 10.2 cM and a maximum bin length of 33 cM. Map density was 4.2 cM/marker or 5.9 cM/SSR.

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Acknowledgments

We thank Fuensanta García for technical support. This work was funded in part by grants AGL2006-12780-C02-01, GEN2003-20237-C06-02 [Spanish Ministry of Education and Science and Fondo Europeo de Desarrollo Regional (FEDER, European Union)] and RF2004-00003-00-00 [Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)]. IFS was supported by a fellowship from INIA.

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  1. Antonio José Monforte

    Present address: Instituto Celular y Molecular de Plantas (IBMCP) CSIC-UPV, Ciudad Politécnica de la Innovación Ed. 8E, Ingeniero Fausto Elio s/n, 46022, Valencia, Spain

Authors and Affiliations

  1. IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB (CRAG), Carretera de Cabrils, Km 2, 08348, Cabrils, Barcelona, Spain

    I. Fernandez-Silva, I. Eduardo, P. Arús, J. Garcia-Mas & Antonio José Monforte

  2. Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV), Camino de Vera, 8E, Escalera J, 46022, Valencia, Spain

    J. Blanca, C. Esteras, B. Picó & F. Nuez

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Communicated by I. Paran.

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122_2008_883_MOESM1_ESM.xls

ESM S1. Cucurbita accessions examined for assaying the transferability of melon SSRs with information about their origin and morphotype. Seed sources are: 1. COMAV (Institute for the Conservation and Improvement of the Agrodiversity, Spain); 2. NPGS (National Plant Germplasm System, USA); and 3. IPK (Institute of Plant Genetics and Crop Plant Research, Germany) (XLS 19 kb)

ESM S2. Genomic SSRs from Ritschel et al. (2004) assayed (XLS 10 kb)

122_2008_883_MOESM3_ESM.xls

ESM S3. EST-SSRs and gSSRs developed in the current work showing polymorphism in the sets of melon or Cucurbita accessions. MELOGEN EST name and accession number are shown. EST-SSR motif and allele size information were obtained directly from MELOGEN whereas for gSSRs they were obtained from the sequence of the clones obtained from PS enriched genomic libraries. Annealing temperature and [MgCl2] used for PCR amplification are also indicated. Polymorphism information content (PIC) was calculated using eight melon genotypes (Table 1). Bin map position for each marker is indicated as the number of the linkage group followed by the position in the reference map of the last marker of the bin. ECM60 mapped to three different loci indicated as a, b and c. The protein accession with higher homology with the EST found in the Uniref90 database, the significance of the sequence comparison and the organism from where the protein sequence was obtained are also shown. Comprehensive comparisons may be obtained from MELOGEN database (www.melogen.upv.es) Abbreviations: NM: not mapped, NA: not available, NS: not polymorphic between Piel de Sapo and Songwhan Charmi (XLS 91 kb)

122_2008_883_MOESM4_ESM.ppt

ESM S4. Bin mapping example. On the left. markers already mapped are indicated in relative order along the linkage group and grouped in bins. Bin definition is indicated by the number of the linkage group followed by the position of the last marker of the bin in the reference map. The genotype of the Double Haploid Lines (DHL) included in the bin-set is also shown. “A” means homozygous for SC allele and “B” homozygous for PS allele. The expected number of recombination points between adjacent bins are indicated in the last column. Two typical situations when mapping a new marker are shown: perfect match, the genotype of the bin-set is identical to one of the bins so the new marker can be placed in an existing bin, and putative bin, the genotype is compatible with a hypothetical bin located between two adjacent bins separated by two or more recombination points (PPT 144 kb)

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Fernandez-Silva, I., Eduardo, I., Blanca, J. et al. Bin mapping of genomic and EST-derived SSRs in melon (Cucumis melo L.). Theor Appl Genet 118, 139–150 (2008). https://doi.org/10.1007/s00122-008-0883-3

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