Plant Research International develops and applies molecular marker technology for a range of purposes, including marker-assisted breeding, assessment of genetic biodiversity, and the study of population differentiation and ecological processes such as dispersal. Special attention is given to the application of molecular markers in polyploidy crop species, including potato and rose.

• Microsatellite markers
• DArT
• Motif-directed profiling(notably NBS profiling). 

[0] = The numbers refer to the publications below.

Microsatellite Markers
Microsatellites have been developed using an enrichment procedure in a range of plant and animal species, including: Dianthus caryophyllus (carnation)[9], Fagus sylvatica (beech)[8], Geum urbanum (wood avens)[10], Lactuca sativa (lettuce)[14], Lycopersicon esculentum (tomato), Mycelis muralis (wall lettuce)[11], Plantago coronopus (buck’s-horn plantain)[4], Populus nigra (black poplar)[2], Rosa hybrida (cut-rose)[7], Hypochaeris radicata (cat's ear)[16], Hyla arborea (tree frog) [1], Rana arvalis (heath frog), Liporrhopalum tentacularis (a fig wasp)[6], Brevicoryne brassicae (cabbage aphid), and Plutella xylostella (diamondback moth).
>> Contact: Dr. M.J.M. Smulders

NBS profiling
NBS profiling [13] is a newly developed method to probe functional diversity in and near disease resistance genes of the NBS-LRR type. NBS profiling can be used to produce markers tightly linked to R-genes and R-gene clusters for genomic mapping and positional cloning, and to mine for new alleles and new sources of disease resistance in available germplasm. NBS profiling has been carried out in various crop and ornamental species including potato, tomato, apple, lettuce, wheat and rose.
>> Contact: Dr. C.G. van der Linden

For the application of molecular markers, a number of studies have been performed and are being carried out:

• Use of microsatellites for variety identification [15] and establishment of databases [3,5] with genetic profiles
• Development of methods to detect the allelic composition of microsatellite and SNP markers in polyploids (notably rose [12] and potato)
• Analysis of associations using pedigree genotyping in diploids and tetraploids

>> Contact: Dr. B. Vosman

References

1. Arens P, W van ’t Westende, R Bugter, MJM Smulders, B Vosman (2000) Microsatellite markers for the European tree frog Hyla arborea. Molecular Ecology 9: 1944-1946
2. Smulders MJM, J van der Schoot, P Arens, B Vosman (2001) Trinucleotide repeat microsatellite markers for Black Poplar (Populus nigra L.). Molecular Ecology Notes 1: 188-190
3. Bredemeijer GMM, Cooke RJ, Ganal MW, Peeters R, Isaac P, Noordijk Y, Rendell S, Jackson J, Röder MS, Wendehake K, Dijcks M, Amelaine M, Wickaert V, Bertrand L, Vosman B (2002) Construction and testing of a microsatellite database containing more than 500 tomato varieties. Theor Appl Genet 105: 1019-1026
4. Koorevaar GN, S Ivanovic, JMM Van Damme, HP Koelewijn, WPC van 't Westende, MJM  Smulders, B Vosman (2002)  Dinucleotide repeat microsatellite markers for buck’s-horn plantain (Plantago coronopus). Molecular Ecology Notes 2, 524-526
5. Röder, M.S., Wendehake, K., Korzun, V., Bredemeijer, G., Laborie, D., Bertrand, L., Isaac, P., Rendell, S., Jackson, J., Cooke, R.J., Vosman, B., Ganal, M.W. (2002) Construction and analysis of a microsatellite-based database of European wheat varieties. Theor Appl Genet 106: 67-73
6. Zavodna M, P. Arens, B. Vosman, P. J. van Dijk, J.M.M. van Damme (2002) Development and characterisation of microsatellite markers for Liporrhopalum tentacularis Grandi, the pollinator fig wasp of Ficus montana Blume. Molecular Ecology Notes 2, 569-571
7. Esselink D, Smulders MJM, Vosman B (2003) Identification of cut-rose (Rosa hybrida) and rootstock varieties using robust Sequence Tagged Microsatellite markers. Theor Appl Genet 106: 277-286. DOI 10.1007/s00122-002-1122-y
8. Pastorelli R, MJM Smulders, WPC van ‘t Westende, B Vosman, R Giannini, C Vettori, GG Vendramin (2003) Characterisation of microsatellite markers in Fagus sylvatica L. and Fagus orientalis Lipsky. Molecular Ecology Notes 3: 76-78. DOI 10.1046/j.1471-8286.2003.00355.x
9. Smulders MJM, Y Noordijk, W Rus-Kortekaas, GMM Bredemeijer, B Vosman (2003) Microsatellite genotyping of carnation varieties. Theoretical and Applied Genetics 106: 1191-1195. DOI 10.1007/s00122-002-1166-z
10. Arens P, W Durka, JH Wernke-Lenting, MJM Smulders (2004) Isolation and characterisation of microsatellite loci in Geum urbanum (Rosaceae) and their transferability within the genus Geum. Mol Ecol Notes 4: 209-212
11. Chauvet S, M. van der Velde, E. Imbert, M. L. Guillemin, M. Mayol, M. Riba, M. J. M. Smulders, B. Vosman, L. Ericson, R. Bijlsma and B. E. Giles (2004) Past and current gene flow in the selfing, wind-dispersed species Mycelis muralis in western Europe. Mol Ecol. 13: 1391-1407 doi: 10.1111/j.1365-294X.2004.02166.x
12. Esselink GD, H Nybom, B Vosman (2004) Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting—peak ratios) method. Theoretical and Applied Genetics 109: 402-408. doi10.1007/s00122-004-1645-5
13. Linden CG van der, D.C.A.E. Wouters, Virag  Mihalka, Elena .Z. Kochieva, M. J. M. Smulders and B. Vosman (2004) Efficient targeting of plant disease resistance loci using NBS profiling. Theoretical and Applied Genetics 109: 384-393. doi 10.1007/s00122-004-1642-8
14. van de Wiel C, Arens P, Vosman B. (1999) Microsatellite retrieval in lettuce (Lactuca sativa L.). Genome 42:139-149
15. Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, van de Wiel C, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini P, Buiatti M, Maestri E, Malcevschi A, Marmiroli N, Aert R, Volckaert G, Rueda J, Linacero R, Vazquez A, Karp A (1997) Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol. Breeding 3: 381-390
16. Mix C, PFP Arens, NJ Ouborg, MJM Smulders (2004) Isolation and characterization of highly polymorphic microsatellite markers in Hypochaeris radicata (Asteraceae). Molecular Ecology Notes 4: 656–658 doi: 10.1111/j.1471-8286.2004.00773.x