Development and characterization of a new set of 164 polymorphic EST-SSR markers for diversity and breeding studies in rubber tree (Hevea brasiliensis Müll. Arg.)

Plant Breeding

Volumn 133, Issue 3, 2014, Pages 419-426

  Cubry, Philippe ^a,b   Pujade Renaud, Valérie ^a,c   Garcia, Dominique ^a   Espeout, Sandra ^a   Le Guen, Vincent ^a   Granet, Françoise ^b   Seguin, Marc ^a  

^a UMR AGAP   (France)

^b Michelin   (France)

^c UNIVERSITÉ CLERMONT AUVERGNE   (France)

Author keywords

EST SSR; Hevea spp.; Microcyclus ulei; Microsatellites; Rubber tree

Indexed keywords

HEVEA; HEVEA BRASILIENSIS; MICROCYCLUS ULEI;

EID: 84901851970     PISSN: 01799541     EISSN: 14390523     Source Type: Journal    
DOI: 10.1111/pbr.12158     Document Type: Article

References (31)

1. Argout, X., O. Fouet, P. Wincker, K. Gramacho, T. Legavre, X. Sabau, A. Risterucci, C. Da Silva, J. Cascardo, M. Allegre, D. Kuhn, J. Verica, B. Courtois, G. Loor, R. Babin, O. Sounigo, M. Ducamp, M. Guiltinan, M. Ruiz, L. Alemanno, R. Machado, W. Phillips, R. Schnell, M. Gilmour, E. Rosenquist, D. Butler, S. Maximova, and C. Lanaud, 2008: Towards the understanding of the cocoa transcriptome: production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions. BMC Genomics 9, 512.
2. Besse, P., M. Seguin, P. Lebrun, M. H. Chevallier, D. Nicolas, and C. Lanaud, 1994: Genetic diversity among wild and cultivated populations of Hevea brasiliensis assessed by nuclear RFLP analysis. Theor. Appl. Genet. 88, 199-207.
3. Conesa, A., S. Gotz, J. M. Garcia-Gomez, J. Terol, M. Talon, and M. Robles, 2005: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674-3676.
4. Cubry, P., F. De Bellis, K. Avia, S. Bouchet, D. Pot, M. Dufour, H. Legnate, and T. Leroy, 2013: An initial assessment of linkage disequilibrium (LD) in coffee trees: LD patterns in groups of Coffea canephora Pierre using microsatellite analysis. BMC Genomics 14, 10.
5. Ellis, J. R., and J. M. Burke, 2007: EST-SSR as a resource for population genetic analyses. Heredity 99, 125-132.
6. Feng, S. P., W. G. Li, H. S. Huang, J. Y. Wang, and Y. T. Wu, 2009: Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis). Mol. Breed. 23, 85-97.
7. Garcia, D., N. Carels, D. M. Koop, L. A. de Sousa, S. J. de Andrade Junior, V. Pujade-Renaud, C. R. Reis Mattos, and J. C. de Mattos Cascardo, 2011: EST profiling of resistant and susceptible Hevea infected by Microcyclus ulei. Physiol. Mol. Plant Pathol. 76, 126-136.
8. Gupta, P. K., S. Rustgi, and P. L. Kulwal, 2005: Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol. Biol. 57, 461-485.
9. Gupta, S., K. Kumari, M. Muthamilara, A. Subramanian, and M. Prasad, 2013: Development and utilization of novel SSRs in foxtail millet [Setaria italica (L.) P. Beauv.]. Plant Breeding 132, 367-374.
10. Kumar Yadav, H., A. Ranjan, M. H. Asif, S. Mantri, S. V. Sawant, and R. Tuli, 2010: EST-derived SSR markers in Jatropha curcas L.: development, characterization, polymorphism, and transferability across the species/genera. Tree Genet. Genomes 7, 207-219.
11. Le Guen, V., 2008: Exploration de la diversité des résistances génétiques à la maladie sud-américaine des feuilles de l'hévéa (Microcyclus ulei) par cartographie et génétique d'association au sein de populations naturelles. Université Montpellier II, Montpellier, France.
12. Le Guen, V., F. Doaré, C. Weber, and M. Seguin, 2009: Genetic structure of Amazonian populations of Hevea brasiliensis is shaped by hydrographical network and isolation by distance. Tree Genet. Genomes 5, 673-683.
13. Le Guen, V., C. Gay, T. C. Xiong, L. M. Souza, M. Rodier-Goud, and M. Seguin, 2011: Development and characterization of 296 new polymorphic microsatellite markers for rubber tree (Hevea brasiliensis). Plant Breeding 130, 294-296.
14. Lespinasse, D., M. Rodier-Goud, L. Grivet, A. Leconte, H. Legnate, and M. Seguin, 2000: A saturated genetic linkage map of rubber tree (Hevea spp.) based on RFLP, AFLP, microsatellite, and isozyme markers. Theor. Appl. Genet. 100, 127-138.
15. Li, D., Z. Deng, B. Qin, X. Liu, and Z. Men, 2012: De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics 13, 192.
16. Liu, K., and S. V. Muse, 2005: PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21, 2128-2129.
17. Ohyama, A., E. Asamizu, S. Negoro, K. Miyatake, H. Yamaguchi, S. Tabata, and H. Fukuoka, 2009: Characterization of tomato SSR markers developed using BAC-end and cDNA sequences from genome databases. Mol. Breed. 23, 685-691.
18. Perovic, D., J. Förster, P. Devaux, D. Hariri, M. Guilleroux, K. Kanyuka, R. Lyons, J. Weyen, D. Feuerhelm, U. Kastirr, M. Röder, and F. Ordon, 2009: Mapping and diagnostic marker development for Soil-borne cereal mosaic virus resistance in bread wheat. Mol. Breed. 23, 641-653.
19. Perrier, X., and J. P. Jacquemoud-Collet, 2006: DARwin software: http://darwin.cirad.fr/darwin. 5 edn. Cirad, Montpellier, France.
20. Perrier, X., A. Flori, and F. Bonnot, 2003: Methods of data analysis. In: P. Hamon, M. Seguin, X. Perrier, and J. C. Glaszmann (eds), Genetic Diversity of Tropical Crops, 31-64. CIRAD & Science Publ. Inc., Montpellier, France & Enfield (NH), USA.
21. Pootakham, W., J. Chanprasert, N. Jomchai, D. Sangsrakru, T. Yoocha, S. Tragoonrung, and S. Tangphatsornruang, 2012: Development of genomic-derived simple sequence repeat markers in Hevea brasiliensis from 454 genome shotgun sequences. Plant Breeding 131, 555-562.
22. Rafalski, J. A., 2010: Association genetics in crop improvement. Curr. Opin. Plant Biol. 13, 174-180.
23. Rozen, S., and H. J. Skaletsky, 2000: Primer3 on the WWW for general users and for biologist programmers. In: S. Krawetz, and S. Misener (eds), Bioinformatics Methods and Protocols: Methods in Molecular Biology, 365-386. Humana Press, Totowa, NJ.
24. Saitou, N., and M. Nei, 1987: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
25. Seguin, M., A. Flori, H. Legnate, and A. Clément-Demange, 2003: Rubber tree. In: P. Hamon, M. Seguin, X. Perrier, and J. C. Glaszmann (eds) Genetic Diversity of Tropical Crops, 277-305. CIRAD & Science Publ. Inc., Montpellier, France & Enfield (NH), USA.
26. Souza, L. M., C. C. Mantello, M. O. Santos, P. Souza Gonçalves, and A. P. Souza, 2009: Microsatellites from rubber tree (Hevea brasiliensis) for genetic diversity analysis and cross-amplification in six Hevea wild species. Conserv. Genet. Res. 1, 75-79.
27. Triwitayakorn, K., P. Chatkulkawin, S. Kanjanawattanawong, S. Sraphet, T. Yoocha, D. Sangsrakru, J. Chanprasert, C. Ngamphiw, N. Jomchai, K. Therawattanasuk, and S. Tangphatsornruang, 2011: Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map. DNA Res. 18, 471-482.
28. Tyrka, M., D. Perovic, A. Wardyńska, and F. Ordon, 2008: A new diagnostic SSR marker for selection of theRym4/Rym5 locus in barley breeding. J. Appl. Genet. 49, 127-134.
29. Varshney, R. K., A. Graner, and M. E. Sorrells, 2005: Genic microsatellite markers in plants: features and applications. Trends Biotech. 23, 48-55.
30. Vigouroux, Y., S. Mitchell, Y. Matsuoka, M. Hamblin, S. Kresovich, J. S. C. Smith, J. Jaqueth, O. S. Smith, and J. Doebley, 2005: An analysis of genetic diversity across the maize genome using microsatellites. Genetics 169, 1617-1630.
31. Wen, M., H. Wang, Z. Xia, M. Zou, C. Lu, and W. Wang, 2010: Development of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha Curcas L. BMC Res. Notes 3, 42.