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Development of “universal” gene-specific markers from Malus spp. cDNA sequences, their mapping and use in synteny studies within Rosaceae

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Abstract

The Rosaceae contains many economically valuable crop genera, including Malus (apple), Fragaria (strawberry), and Prunus (stone fruit). There has been increasing interest in the development of linkage maps for these species, with a view to marker-assisted selection to assist breeding programs and, recently, in the development of transferable markers to permit syntenic comparisons of maps of different rosaceous genera. In this investigation, a set of Malus cDNA sequences were downloaded from the European Molecular Biology Laboratory database. The sequences were aligned with homologous full-length Arabidopsis genomic DNA sequences to identify putative intron–exon junctions and conserved flanking exon sequences. Primer pairs were designed from the conserved exon sequences flanking predicted intron–exon junctions in the Malus cDNA sequences. These were used to amplify products by polymerase chain reaction from the parents of the Malus mapping progeny “Fiesta” × “Totem.” Eleven loci, representing ten genes (39%), were polymorphic in the “Fiesta” × “Totem” population and mapped to seven Malus linkage groups. Transferability to other rosaceous genera was high, with primer pairs representing 85% of genes, amplifying products from Fragaria and primer pairs representing 85% of genes, amplifying products from Prunus genomic DNA. These primers were screened in the Fragaria and Prunus mapping bin sets and 38% of the genes were successfully located on both maps. Analysis of the markers mapped in more than one rosaceous genus revealed patterns of synteny between genera, while a comparison with the physical positions of homologous genes on the Arabidopsis genome revealed high sequence conservation but only fragmentary patterns of macrosynteny.

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Acknowledgements

Rosaceous genomics at East Malling Research is funded by Defra through grant HH3724SSF (Comparative genomics of rosaceous fruit crops and HNS for sustainable production).

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Authors and Affiliations

  1. East Malling Research, New Road, East Malling, Kent, ME19 6BJ, UK

    Daniel J. Sargent, Annalisa Marchese, David W. Simpson, Felicidad Fernández-Fernández, Kate M. Evans & Kenneth R. Tobutt

  2. Dipartimento di Colture Arboree, Università di Palermo, Viale delle Scienze, 11 90128, Palermo, Italy

    Annalisa Marchese

  3. IRTA, Centre de Recerca en Agrigenòmica (CSIC-IRTA-UAB), Carretera de Cabrils Km2, 08348, Cabrils, Spain

    Werner Howad, Amparo Monfort & Pere Arús

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  1. Daniel J. Sargent
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  2. Annalisa Marchese
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  3. David W. Simpson
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  4. Werner Howad
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  5. Felicidad Fernández-Fernández
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  6. Amparo Monfort
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  7. Pere Arús
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  8. Kate M. Evans
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  9. Kenneth R. Tobutt
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Correspondence to Daniel J. Sargent.

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Communicated by A. Dandekar

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Sargent, D.J., Marchese, A., Simpson, D.W. et al. Development of “universal” gene-specific markers from Malus spp. cDNA sequences, their mapping and use in synteny studies within Rosaceae. Tree Genetics & Genomes 5, 133–145 (2009). https://doi.org/10.1007/s11295-008-0178-5

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  • DOI: https://doi.org/10.1007/s11295-008-0178-5

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