Microsatellite marker development in peony using next generation sequencing

Journal of the American Society for Horticultural Science

Volumn 138, Issue 1, 2013, Pages 64-74

  Gilmore, Barbara ^a   Bassil, Nahla ^b   Nyberg, April ^b   Knaus, Brian ^c   Smith, Don ^d   Barney, Danny L ^a   Hummer, Kim ^b  

^a U S DEPARTMENT OF AGRICULTURE   (United States)

^b USDA ARS National Clonal Germplasm Repository   (United States)

^c USDA FOREST SERVICE   (United States)

^d Yellow Peonies and More   (United States)

Author keywords

Illumina libraries; Intersectional; Paeonia suffruticosa; Paeonia lactiflora; Simple sequence repeat primers

Indexed keywords

EID: 84875096580     PISSN: 00031062     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (42)

1. Bay, L., E. Howells, and M. van Oppen. 2009. Isolation, characterisation and cross amplification of thirteen microsatellite loci for coral endo-symbiotic dinoflagellates (Symbiodinium clade C). Conservation Genet. Resources 1:199-203.
2. Boccacci, P., A. Akkak, N. Bassil, A. Mehlenbacher, and R. Botta. 2005. Characterization and evaluation of microsatellite loci in european hazelnut (Corylus avellana L) and their transferability to other Corylus species. Mol. Ecol. Notes 5:934-937.
3. Boches, P., L. Rowland, and N. Bassil. 2005. Microsatellite markers for Vaccinium from EST and genomic libraries. Mol. Ecol. Notes 5:657-660.
4. Brownstein, M., J. Carpten, and J. Smith. 1996. Modulation of nontemplated nucleotide addition by Taq DNA polymerase: Primer modifications that facilitate genotyping. Biotechniques 20:1004- 1006.
5. Burkhardt, C. 2012. Carsten Burkhardt's web project Paeonia. 20 July 2012. .
6. Castillo, N., N. Bassil, S. Wada, and B. Reed. 2010. Genetic stability of cryopreserved shoot tips of Rubus germplasm. In Vitro Cell. Dev. Biol. Plant 46:246-256.
7. Cronn, R., A. Liston, M. Parks, D. Gernandt, R. Shen, and T. Mockler. 2008. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res. 36:e122.
8. Gilmore, B., K. Hummer, and N. Bassil. 2011. DNA Extraction protocols from dormant buds of twelve woody plant genera. J. Amer. Pomol. Soc. 65:201-207.
9. Halda, J. and J. Waddick. 2004. The genus Paeonia. Timber Press, Portland, OR/Heartland Peony Soc., Gladstone, MO.
10. Harding, A. 1917. The book of the peony. Lippincott, Philadelphia, PA/London, UK.
11. Homolka, A., M. Berenyi, K. Burg, D. Kopecky, and S. Fluch. 2010. Microsatellite markers in the tree peony, Paeonia ·suffruticosa (Paeoniaceae). Amer. J. Bot. 97:e42-e44.
12. Hong, D. 2010. Peonies of the world, taxonomy and phytogeography. Kew Publishing, Richmond, UK.
13. Hsu, H., Y. Chen, S. Shen, S. Hsu, C. Chen, and H. Chang. 1986. Oriental material medica: A concise guide. Oriental Healing Arts. Inst., Keelung, Taiwan.
14. Jakubowski, R. (compiler). 2012. The Canadian Peony Society, peony parentage data. 1 June 2012. .
15. Jakubowski, R., D. Hollingsworth, J. Nordick, H. Buchite, and C. Schroer. 2007. Peonies 1997-2007. Amer. Peony Soc., Gladston, MO.
16. Jennings, T., B. Knaus, T. Mullins, S. Haig, and R. Cronn. 2011. Multiplexed microsatellite recovery using massively parallel sequencing. Mol. Ecol. Notes 11:1060-1067.
17. Knaus, B. 2011. Short read toolbox. 1 Oct. 2012. .
18. La Pivoinerie D#Aoust Peony Nursery. 2012. Learn about peonies. 1 May 2012. .
19. Li, L., F. Cheng, and Q. Zhang. 2011. Microsatellite markers for the chinese herbaceous peony Paeonia lactiflora (Paeoniaceae). Amer. J. Bot. 98:e16-e18.
20. Liu, K. and S. Muse. 2005. PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128-2129.
21. National Center for Biotechnology Information. 2012. Accession number: SRA054037. 29 June 2012. .
22. Niu, B., L. Fu, S. Sun, and W. Li. 2010. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics 11:187.
23. Powell, W., G. Machray, and J. Provan. 1996. Polymorphism revealed by simple sequence repeats. Trends Plant Sci. 1:215-222.
24. Rogers, A. 1995. Peonies. Timber Press, Portland, OR.
25. Rogers, A. 2004. Peonies. Timber Press, Portland, OR.
26. Rojas, G., M. Méndez, C. Munboz, G. Lemus, and P. Hinrichsen. 2008. Identification of a minimal microsatellite marker panel for the fingerprinting of peach and nectarine cultivars. Electron. J. Biotechnol. 11:1-12.
27. Sanger, F., S. Nicklen, and A. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463-5467.
28. Schuelke, M. 2000. An economic method for the fluorescent labeling of PCR fragments. Nat. Biotechnol. 18:233-234.
29. Smith, D. (ed.). 2000. Producing high quality intersectional hybrids. Paeonia 30:1-4.
30. Sook, J., M. Staton, T. Lee, A. Blenda, R. Svancara, A. Abbott, and D. Main. 2008. GDR (Genome Database for Rosaceae): Integrated webdatabase for Rosaceae genomics and genetics data. Nucleic Acids Res. 36:D1034-D1040.
31. Spellerberg, I. and P. Fedor. 2003. A tribute to Claude Shannon (1916- 2001) and a plea for more rigorous use of species richness, species diversity and the 'Shannon-Wiener' index. Glob. Ecol. Biogeogr. 12:177-179.
32. Sun, J., J. Yuan, B. Wang, J. Pan, and D. Zhang. 2011. Development and characterization of 10 microsatellite loci in Paeonia lactiflora Pall. (Paeoniaceae). Amer. J. Bot. 98:e242-e243.
33. U.S. Department of Agriculture. 2012. SSR summary report. 15 June 2012. .
34. Vakblad voor de Bloemisterji. 2012. De meest complete international vakbeurs voor de snijbloemen en bioeiende pot planten! 1 Feb. 2012. .
35. Wahdan, M., A. Abdelsalam, A. El-Naggar, and M. Hussein. 2011. Preliminary horticultural studies to describe and identify of two new egyptian mango strains using DNA fingerprint. J. Amer. Sci. 7:641- 650.
36. Wang, J., T. Xis, J. Zhang, and S. Zhou. 2009. Isolation and characterization of fourteen microsatellites from a tree peony (Paeonia ·suffruticosa). Conserv. Genet. 10:1029-1031.
37. Wu, W., R. Zhou, H. Huang, and X. Ge. 2010. Development of microsatellite for the invasive weed Wedelia trilobata (Asteraceae). Amer. J. Bot. 97:e114-e116.
38. Yan, Y., Y. Huang, X. Fang, L. Lu, R. Zhou, X. Ge, and S. Shi. 2011. Development and characterization EST-SSR markers in the invasive weed Mikania micrantha (Asteracea). Amer. J. Bot. 98:e1-e3.
39. You, F., N. Huo, Y. Gu, M. Luo, Y. Ma, D. Hane, G. Lazo, J. Dvorak, and O. Anderson. 2008. Batchprimer3: A high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9:253.
40. Yuan, J., F. Cheng, and S. Zhou. 2010. Hybrid origin of Paeonia yananensis revealed by microsatellite markers, chloroplast gene sequences, and morphological characteristics. Intl. J. Plant Sci. 171:409-420.
41. Zalapa, J., H. Cuevas, H. Zhu, S. Steffan, D. Senalik, E. Zeldin, B. McCown, R. Harbut, and P. Simon. 2012. Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Amer. J. Bot. 99:193-208.
42. Zhang, J., Q. Shu, Z. Lui, H. Ren, L. Wang, and E. De Keyser. 2012. Two EST-derived marker systems for cultivar identification in tree peony. Plant Cell Rptr. 31:299-310.