The diploid origins of allopolyploid rose species studied using single nucleotide polymorphism haplotypes flanking a microsatellite repeat

Journal of Horticultural Science and Biotechnology

Volumn 88, Issue 1, 2013, Pages 85-92

  Zhang, J ^a,b   Esselink, G D ^b   Che, D ^a   Fougere Danezan M ^c   Arens, P ^b   Smulders, M J M ^b  

^a NORTHEAST AGRICULTURAL UNIVERSITY   (China)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c CHENGDU INSTITUTE OF BIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84872742571     PISSN: 14620316     EISSN: None     Source Type: Journal    
DOI: 10.1080/14620316.2013.11512940     Document Type: Article

References (33)

1. Alvarez, A. E., Van De Wiel, C. C. M., Smulders, M. J. M. and Vosman, B. (2001). Use of microsatellites to evaluate genetic diversity and species relationships in the genus Lycopersicon. Theoretical and Applied Genetics, 103, 1283-1292.
2. Babaei, A., Tabaei-Aghdaei, S. R., Khosh-Khui, M., Omidbaigi, R., Naghavi, M. R., Esselink, G. D. and Smulders, M. J. M. (2007). Microsatellite analysis of Damask rose (Rosa damascena Mill.) accessions from various regions in Iran reveals multiple genotypes. BMC Plant Biology, 10, 12.
3. Brassac, J., Jakob, S. S. and Blattner, F. R. (2012). Progenitorderivative relationships of Hordeum polyploids (Poaceae, Triticeae) inferred from sequences of TOPO6, a nuclear lowcopy gene region. PLoS ONE, 7, e33808.
4. Bruneau, A., Starr, J. R. and Joly, S. (2007). Phylogenetic relationships in the genus Rosa: New evidence from chloroplast DNA sequences and an appraisal of current knowledge. Systematic Botany, 32, 366-378.
5. Burland, T. G. (2000). DNASTAR's Lasergene sequence analysis software. Methods in Molecular Biology, 132, 71-91.
6. Chatrou, L. W., Escribano, M. P., Viruel, M. A., Maas, J.W., Richardson, J. E. and Hormaza, J. I. (2009). Flanking regions of monomorphic microsatellite loci provide a new source of data for plant species-level phylogenetics. Molecular Phylogenetics and Evolution, 53, 726-733.
7. De Cock, K., Van Der Mijnsbrugge, K., Breyne, P., Van Bockstaele, E. and Van Slycken, J. (2008). Morphological and AFLP-based differentiation within the taxonomical complex section Caninae (subgenus Rosa). Annals of Botany, 102, 685-697.
8. Esselink, G. D., Smulders, M. J. M. and Vosman, B. (2003). Identification of cut rose (Rosa hybrida) and rootstock varieties using robust sequence tagged microsatellite site markers. Theoretical and Applied Genetics, 106, 277-286.
9. Griffin, P. A., Robin, C. and Hoffmann, A. A. (2011). A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. BMC Biology, 9, 19.
10. Joly, S., Starr, J. R., Lewis, W. H. and Bruneau, A. (2006). Polyploid and hybrid evolution in roses east of the Rocky Mountains. American Journal of Botany, 93, 412-425.
11. Koning-Boucoiran, C. F. S., Gitonga, V. W., Yan, Z., Dolstra, O., Van Der Linden, C. G., Van Der Schoot, J., Uenk, G. E., Verlinden, K., Smulders, M. J. M., Krens, F. A. and Maliepaard, C. (2012). The mode of inheritance in tetraploid cut roses. Theoretical and Applied Genetics, 125, 591-607.
12. Koopman, W. J. M., Wissemann, V., De Cock, K., Van Huylenbroeck, J., De Riek, J., Sabatino, G. J. H., Visser, D., Vosman, B., Ritz, C.M., Maes, B., Werlemark, G., Nybom, H., Debener, T., Linde, M. and Smulders, M. J. M. (2008). AFLP markers as a tool to reconstruct complex relationships: A case study in Rosa (Rosaceae). American Journal of Botany, 95, 353-366.
13. Leus, L., Jeanneteau, F., Van Huylenbroeck, J., Van Bockstaele, E. and De Riek, J. (2004). Molecular evaluation of a collection of rose species and cultivars by AFLP, ITS, rbcL and matK. Acta Horticulturae, 651, 141-147.
14. Matsumoto, S., Kouchi, M., Yabuki, J., Kusunoki, M., Ueda, Y. and Fukui, H. (1998). Phylogenetic analyses of the genus Rosa using the matK sequence: Molecular evidence for the narrow genetic background of modern roses. Scientia Horticulturae, 77, 73-82.
15. Matsumoto, S., Nishio, H., Ueda, Y. and Fukui, H. (2001). Phylogenetic analyses of the genus Rosa: Polyphyly of the Section Pimpinellifoliae and the origin of Rosa × fortuniana Lindl. Acta Horticulturae, 547, 357-363.
16. Mountain, J. L., Knight, A., Jobin, M., Gignoux, C., Miller, A., Lin, A. A. and Underhill, P. A. (2002). SNPSTRs: Empirically derived, rapidly typed, autosomal haplotypes for inference of population history and mutational processes. Genome Research, 12, 1766-1772.
17. Payseur, B. A. and Cutter, A. D. (2006). Integrating patterns of polymorphism at SNPs and STRs. Trends in Genetics, 22, 424-429.
18. Ramakrishnan, U. and Mountain, J. L. (2004). Precision and accuracy of divergence time estimates from STR and SNPSTR variation. Molecular Biology and Evolution, 21, 1960-1971.
19. Rehder, A. (1940). Manual of Cultivated Trees and Shrubs. 2nd Edition. McMillan Co., New York, NY, USA. 996 pp.
20. Samiei, L., Naderi, R., Khalighi, A., Bushehri, A. A., Mozaffarian, V., Esselink, D. and Smulders, M. J. M. (2009). In search of genetic diversity in Rosa foetida Herrmann in Iran. Acta Horticulturae, 836, 25-30.
21. Samiei, L., Naderi, R., Khalighi, A., Shahnejat-Bushehri, A.A., Mozaffarian, V., Esselink, G.D., Kazempour Osaloo, S. and Smulders, M. J. M. (2010). Genetic diversity and genetic similarities between Iranian rose species. Journal of Horticultural Science & Biotechnology, 85, 231-237.
22. Scariot, V., AKkak, A. and Botta, R. (2006). Characterization and genetic relationships of wild species and old garden roses based on microsatellite analysis. Journal of the American Society for Horticultural Science, 131, 66-73.
23. Smulders, M. J.M., Bredemeijer, G., Rus-Kortekaas, W., Arens, P. and Vosman, B. (1997). Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species. Theoretical and Applied Genetics, 94, 264-272.
24. Smulders, M. J. M., Esselink, D., Voorrips, R. E. and Vosman, B. (2009). Analysis of a database of DNA profiles of 734 hybrid tea rose varieties. Acta Horticulturae, 836, 169-174.
25. Smulders, M. J. M., Arens, P., Koning-Boucoiran, C., Gitonga, V., Krens, F., Atanassov, A., Atanassov, I., Rusanov, K., Bendahmane, M., Dubois, A., Raymond, O., Caissard, J. C., Baudino, S., Crespel, L., Gudin, S., Ricci, S. C., Kovatcheva, N., Van Huylenbroeck, J., Leus, L., Wissemann, V., Zimmermann, H., Hensen, I., Werlemark, G. and Nybom, H. (2011). Rosa. In:Wild Crop Relatives: Genomic and Breeding Resources Plantation and Ornamental Crops. (Kole, C., Ed.). Springer-Verlag, Berlin, Heidelberg, Germany. 243-275.
26. Sorenson, M. D. and DaCosta, J. M. (2011). Genotyping HapSTR loci: phase determination from direct sequencing of PCR products. Molecular Ecology Resources, 11, 1068-1075.
27. Spiller, M., Linde, M., Hibrand-Saint Oyant, L., Tsai, C.-J., Byrne, D. H., Smulders, M. J. M., Foucher, F. and Debener, T. (2011). Towards a unified genetic map of diploid rose. Theoretical and Applied Genetics, 122, 489-500.
28. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731-2739.
29. Van Der Mijnsbrugge, K., De Cock, K., Cox, K. and Breyne, P. (2010). Conservation measures for Rosa arvensis Huds. in Flanders (Belgium) based on congruent genetic and phenotypic population differentiation. Conservation Genetics, 11, 2243-2253.
30. Wissemann, V. (2003). Conventional taxonomy of wild roses. In: Encyclopedia of Rose Science. (Roberts, A., Debener, T. and Gudin, S., Eds.). Elsevier, London, UK. 111-117.
31. Wissemann, V. and Ritz, C. M. (2005). The genus Rosa (Rosoideae, Rosaceae) revisited: molecular analysis of nrITS-1 and atpBrbcL intergenic spacer (IGS) versus conventional taxonomy. Botanical Journal of the Linnean Society, 147, 275-290.
32. Wu, S., Ueda, Y., He, H., Nishihara, S. and Matsumoto, S. (2000). Phylogenetic analysis of Japanese Rosa species using matK sequences. Breeding Science, 50, 275-281.
33. Wu, S., Ueda, Y., Nishihara, S. and Matsumoto, S. (2001). Phylogenetic analysis of Japanese Rosa species using DNA sequences of nuclear ribosomal internal transcribed spacers (ITS). Journal of Horticultural Science & Biotechnology, 76, 127-132.