Open Access Highly Accessed Research article

High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping

Cristina Esteras1, Pedro Gómez2, Antonio J Monforte3, José Blanca1, Nelly Vicente-Dólera2, Cristina Roig1, Fernando Nuez1 and Belén Picó1*

Author Affiliations

1 Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain

2 Instituto de Investigación y Formación Agraria y Pesquera (IFAPA). Área de Mejora y Biotecnología de cultivos. Camino San Nicolás 1, 04745, La Mojonera, Almería, Spain

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

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BMC Genomics 2012, 13:80  doi:10.1186/1471-2164-13-80

Published: 22 February 2012

Additional files

Additional file 1:

Sequence and primers for genotyping the 384 SNP included in the GoldenGate platform. The sequences of each of the 384 SNP included in the GoldenGate platform are indicated, including the polymorphic nucleotide and a 60 bp flanking sequence, along with the locus-specific and two allele-specific primers designed for detecting each locus with the GoldenGate assay, the three universal primers and the Illumicode.

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Additional file 2:

Primers for genotyping the SSR included in the map. The primers for genotyping the 25 SSR selected from the previous C. pepo map [44] are listed, along with the genotyping results and map position for each locus.

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Additional file 3:

Annotation data and map position of the 384 loci included in the GoldenGate platform. Annotation data of the 384 unigenes included in the GoldenGate platform are described. Previous annotation data provided by Blanca et al. [20], after in silico detection of the unigenes, consist of unigene length, position of the SNP, in ORF or UTR, number of reads in each parental, GO terms, gene description after sequential BLAST of Swissprot, Arabidopsis org and Uniref90 [51-53], orthologs detected with Arabidopsis and C. melo by reciprocal BLAST of Arabidopsis_pep and ICUGI databases [52,17] and putative SNP-CAPS. Data generated in this paper are final CRG/CEGEN scores for GoldenGate genotyping reactions, GoldenGate genotyping results, distribution of the unigenes in the C. sativus genome (scaffolds or chromosomes) after BLAST against cucumber genome available at ICUGI [17], linkage group according to the Zucchini × Scallop map obtained, variability of SNP in the germplasm panel of C. pepo subsp. pepo and subsp. ovifera accessions and amplification in C. moschata.

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Additional file 4:

Number of unigenes in each functional category. Number of unigenes, of the 384 included in the GoldenGate platform, assigned to each GO Slim in the Biological Process category (A) and the Molecular Function category (B).

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Additional file 5:

Quantitative and qualitative traits. A. Scored quantitative traits are described. Mean values, ranges and standard deviation for parental, F2 and backcross populations are indicated. B. Pearson correlations between pairs of quantitative traits. C. Visually scored qualitative traits are described. Relative frequency of each phenotype is shown for both parental, F2 and backcross population.

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Additional file 6:

QTL analysis for quantitative and qualitative traits 1. QTL whose effects have not been validated in the backcross populations are included. A. Linkage group positions and flanking markers of 31 QTL, along with their associated logarithms of odds (LOD) for 20 vine, flowering and fruit quantitative traits analyzed in the F2 population derived from the Zucchini × Scallop cross. Major QTL (R2> 25%) are indicated in bold. B. Linkage group positions and flanking markers of 3 QTL, along with their associated logarithms of odds (LOD) and contingency χ2 results for fruit qualitative traits analyzed in the F2 population derived from the cross Zucchini × Scallop. Major QTL (R2> 25%) are indicated in bold.

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Additional file 7:

QTL analysis for quantitative and qualitative traits 2. QTL whose effects have been validated in the backcross populations are included. A. Linkage group positions and flanking markers of 17 QTL, along with their associated logarithms of odds (LOD) for 16 flowering and fruit quantitative traits analyzed in the F2 population derived from the Zucchini × Scallop cross. Major QTL (R2> 25%) are indicated in bold. Heritabilities have been calculatedfor these traits B. Linkage group positions and flanking markers of 8 QTL, along with their associated logarithms of odds (LOD) and contingency χ2 results for vine and fruit qualitative traits analyzed in the F2 population derived from the cross Zucchini × Scallop. Major QTL (R2> 25%) are indicated in bold.

Format: XLSX Size: 20KB Download file

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