Open Access Highly Accessed Research article

Tomato breeding in the genomics era: insights from a SNP array

Marcela Víquez-Zamora124, Ben Vosman12, Henri van de Geest23, Arnaud Bovy12, Richard GF Visser12, Richard Finkers12 and Adriaan W van Heusden12*

Author Affiliations

1 Wageningen UR Plant Breeding, P.O. Box 16, AJ, Wageningen, 6700, The Netherlands

2 Centre for Biosystems Genomics, P.O. Box 98, AB, Wageningen, 6700, The Netherlands

3 Bioscience, Plant Research International, P.O. Box 619, AP Wageningen, 6700, The Netherlands

4 Graduate School Experimental Plant Sciences, Wageningen Campus, PB Wageningen, 6807, The Netherlands

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BMC Genomics 2013, 14:354  doi:10.1186/1471-2164-14-354

Published: 27 May 2013

Additional files

Additional file 1:

Example of genotyping graphs in GenomeStudio®. SNP marker within one population in which two different groups were clustered automatically by the program in one group (the heterozygous group) due to an outlier sample (NTC). The right grouping is in Figure 1B, this was confirmed by flanking markers in a segregating population. The red circle exemplifies an outlier sample.

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Additional file 2: Table S1:

Varieties from S. lycopersicum used for comparisons (also used by van Berloo, 2008). Table S2: Table with the accessions used in analysis. Table S3: Table with the introgressions known to be present in the initial breeding lines.

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Additional file 3:

All SNP scores in the varieties from S. lycopersicum used for comparisons (also used by van Berloo, 2008).

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Additional file 4:

Heat map representation of polymorphisms found in the TMV region of chromosome 9.Solanum lycopersicum allele - gray background), yellow heterozygous and homozygous wild relative allele – green background. (PPTX 536 kb)

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Additional file 5:

BioNJ tree with 1000 bootstrap analysis showing an implicit relation of the available species according the different tomato groups.

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Additional file 6:

Heat map of the genotype call of 188 markers distributed along Chromosome 12 of 100 RILs (horizontal) from a cross between S. lycopersicum cv Moneymaker (red) and S. pimpinellifolium G1.1554 (green). Heterozygous calls (yellow) and NCs (black) are also included. Certain loci marked for reference as: sequence name / position (Mbp). The positions were blasted towards the published tomato genome version 2.4 [16].

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