Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Record number 439661
Title Tomato breeding in the genomics era: insights from a SNP array
Author(s) Víquez-Zamora, M.; Vosman, B.; Geest, H. van; Bovy, A.G.; Visser, R.G.F.; Finkers, H.J.; Heusden, A.W. van
Source BMC Genomics 14 (2013). - ISSN 1471-2164 - 28 p.
DOI https://doi.org/10.1186/1471-2164-14-354
Department(s) Plant Breeding
BIOS Applied Metabolic Systems
Plant Breeding
EPS
Publication type Refereed Article in a scientific journal
Publication year 2013
Keyword(s) backcross qtl analysis - phylogenetic-relationships - lycopersicon-hirsutum - evolutionary history - essential derivation - genus lycopersicon - l-pimpinellifolium - dna - construction - technologies
Abstract Background - The major bottle neck in genetic and linkage studies in tomato has been the lack of a sufficient number of molecular markers. This has radically changed with the application of next generation sequencing and high throughput genotyping. A set of 6000 SNPs was identified and 5528 of them were used to evaluate tomato germplasm at the level of species, varieties and segregating populations. Results - From the 5528 SNPs, 1980 originated from 454-sequencing, 3495 from Illumina Solexa sequencing and 53 were additional known markers. Genotyping different tomato samples allowed the evaluation of the level of heterozygosity and introgressions among commercial varieties. Cherry tomatoes were especially different from round/beefs in chromosomes 4, 5 and 12. We were able to identify a set of 750 unique markers distinguishing S. lycopersicum 'Moneymaker' from all its distantly related wild relatives. Clustering and neighbour joining analysis among varieties and species showed expected grouping patterns, with S. pimpinellifolium as the most closely related to commercial tomatoesearlier results. Conclusions - Our results show that a SNP search in only a few breeding lines already provides generally applicable markers in tomato and its wild relatives. It also shows that the Illumina bead array generated data are highly reproducible. Our SNPs can roughly be divided in two categories: SNPs of which both forms are present in the wild relatives and in domesticated tomatoes (originating from common ancestors) and SNPs unique for the domesticated tomato (originating from after the domestication event). The SNPs can be used for genotyping, identification of varieties, comparison of genetic and physical linkage maps and to confirm (phylogenetic) relations. In the SNPs used for the array there is hardly any overlap with the SolCAP array and it is strongly recommended to combine both SNP sets and to select a core collection of robust SNPs completely covering the entire tomato genome
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