Exploiting the Transcriptome of Euphrates Poplar, Populus euphratica (Salicaceae) to Develop and Characterize New EST-SSR Markers and Construct an EST-SSR Database

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Du, Fang K ^a   Xu, Fang ^a   Qu, Hong ^b   Feng, Sisi ^a   Tang, Jijun ^c   Wu, Rongling ^a  

^a BEIJING FORESTRY UNIVERSITY   (China)

^b PEKING UNIVERSITY   (China)

^c University of South Carolina   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEXANUCLEOTIDE; NUCLEOTIDE; TRANSCRIPTOME; TRINUCLEOTIDE; UNCLASSIFIED DRUG;

ARTICLE; CHINA; COMPUTER MODEL; EXPRESSED SEQUENCE TAG; GENE MAPPING; GENETIC DATABASE; GENETIC VARIABILITY; MICROSATELLITE MARKER; NONHUMAN; NUCLEOTIDE MOTIF; PLANT GENOME; POLYMORPHIC LOCUS; POPULUS; POPULUS EUPHRATICA; POPULUS NIGRA; POPULUS PRUINOSA; POPULUS PSEUDOGLAUCA; POPULUS THEVESTINA; POPULUS TOMENTOSA; POPULUS TRICHOCARPA; POPULUS USSURIENSIS; POPULUS WILSONII; SALICACEAE; SEQUENCE ANALYSIS; SIMPLE SEQUENCE REPEAT; SPECIES DIFFERENCE; WEB BROWSER;

CHINA; CHROMOSOME MAPPING; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; GENETIC MARKERS; GENETIC VARIATION; INTERNET; MICROSATELLITE REPEATS; POPULUS; TRANSCRIPTOME;

POPULUS; POPULUS EUPHRATICA; POPULUS TRICHOCARPA; SALICACEAE;

EID: 84876121206     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0061337     Document Type: Article

References (61)

1. Sharma A, Dwivedi BN, Singh B, Kumar K, (1999) Introduction of Populus euphratica in Indian semi-arid trans-Gangetic Plains. Ann For Sci 7: 1-8.
2. Hou H (1985) Floodplain meadows, gallery forests, and oases. In: Goodin JR & Northington DK (eds) Plant Resource of Arid and Semi Arid Lands- A global perspective Academic Press, Orlando. pp. 246-249.
3. Bruelheide H, Jandt U, Gries D, Thomas FM, Foetzki A, et al. (2003) Vegetation changes in a river oasis on the southern rim of the Taklamakan Desert in China between 1956 and 2000. Phytocoenologia 33: 801-818.
4. Gu R, Fonseca S, Puskás LG, Hackler L, Zvara Á, et al. (2004) Transcript identification and profiling during salt stress and recovery of Populus euphratica. Tree Physiol 24: 265-276.
5. Kang JM, Kojima K, Ide Y, Sasaki S, (1996) Growth response to the stress of low osmotic potential, salinity and high pH in cultured shoot of Chinese poplars. J For Res 1: 27-29.
6. Watanabe S, Kojima K, Ide Y, Sasaki S, (2000) Effects of saline and osmotic stress on proline and sugar accumulation in Populus euphratica in vitro. Plant Cell Tissue Organ Cult 63: 199-206.
7. Zeng F, Yan H, Arndt SK, (2009) Leaf and whole tree adaptations to mild salinity in field grown Populus euphratica. Tree Physiol 29: 1237-1246.
8. Fay MF, Lledó MD, Kornblum MM, Crespo MB, (1999) From the waters of Babylon? Populus euphratica in Spain is clonal and probably introduced. Biodivers Conserv 8: 769-778.
9. Vonlanthen B, Zhang X, Bruelheide H, (2010) Clonal structure and genetic diversity of three desert phreatophytes. Am J Bot 97: 234-242.
10. Wang J, Wu Y, Ren G, Guo Q, Liu J, et al. (2011) Genetic differentiation and delimitation between ecologically diverged Populus euphratica and P. pruinosa. PLoS ONE 6: e26530. Available: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0026530.Accessed 6 March 2013.
11. Jacob JJ, Lindpaintner K, Lincoln SE, Kusumi K, Bunker RK, et al. (1991) Genetic mapping of a gene causing hypertension in the stroke-prone spontaneously hypertensive rat. Cell 67: 213-224.
12. Edwards AL, Civitello A, Hammond HA, Caskey CT, (1991) DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am J Hum Genet 49: 746-756.
13. Tautz D, (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17: 6463-6471.
14. Litt M, Luty JA, (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44: 397-401.
15. Zane L, Bargelloni L, Patarnello T, (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11: 1-16.
16. Kelkar YD, Strubczewski N, Hile SE, Chiaromonte F, Eckert KA, et al. (2010) What is a microsatellite: A computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats. Genome Biol Evol 2: 620-635.
17. Guichoux E, Lagache L, Wagner S, Chaumeil P, Léger P, et al. (2011) Current trends in microsatellite genotyping. Mol Ecol Res 11: 591-611.
18. Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK, (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177: 309-334.
19. Scott KD, Eggler P, Seaton G, et al. (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100: 723-726.
20. Karagyozov L, Kalcheva ID, Chapman VM, (1993) Construction of random small-insert genomic libraries highly enriched for simple sequence repeats. Nucleic Acids Res 21: 3911-3912.
21. Armour JAL, Neumann R, Gobert S, Jeffreys AJ, (1994) Isolation of human simple repeat loci by hybridization selection. Hum Mol Genet 3: 599-605.
22. Kandpal RP, Kandpal G, Weissman SM, (1994) Construction of libraries enriched for sequence repeats and jumping clones, and hybridization selection for region-specific markers. Proc Natl Acad Sci U S A 91: 88-92.
23. Kijas JM, Fowler JC, Garbett CA, Thomas MR, (1994) Enrichment of microsatellites from the citrus genome using biotinylated oligonucleotide sequences bound to streptavidin-coated magnetic particles. Biotechniques 16: 656-660.
24. Durand J, Bodenes C, Chancerel E, Frigerio J-M, Vendramin G, et al. (2010) A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. BMC Genomics 11: 570. Available: http://www.biomedcentral.com/1471-2164/11/570.Accessed 6 March 2013.
25. McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, et al. (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA research 9: 199-207.
26. Kantety RV, La Rota M, Matthews DE, Sorrells ME, (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48: 501-510.
27. Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, et al. (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics 270: 315-323.
28. Blenda A, Scheffler J, Scheffler B, Palmer M, Lacape JM, et al. (2006) CMD: a Cotton Microsatellite Database resource for Gossypium genomics. BMC Genomics 7: 132. Available: http://www.biomedcentral.com/1471-2164/7/132/.Accessed 6 March 2013.
29. Poncet V, Rondeau M, Tranchant C, Cayrel A, Hamon S, et al. (2006) SSR mining in coffee tree EST databases: potential use of EST-SSRs as markers for the Coffea genus. Mol Genet Genomics 276: 436-449.
30. Ueno S, Moriguchi Y, Uchiyama K, Ujino-Ihara T, Futamura N, et al. (2012) A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica. BMC Genomics 13: 136. Available: http://www.biomedcentral.com/1471-2164/13/136/.Accessed 6 March 2013.
31. Feng SP, Li WG, Huang HS, Wang JY, Wu YT, (2009) Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis). Mol Breed 23: 85-97.
32. Tuskan GA, Gunter LE, Yang ZK, Yin TM, Sewell MM, et al. (2004) Characterization of microsatellites revealed by genomic sequencing of Populus trichocarpa. Can J For Res 34: 85-93.
33. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604.
34. Qiu Q, Ma T, Hu Q, Liu B, Wu Y, et al. (2011) Genome-scale transcriptome analysis of the desert poplar, Populus euphratica. Tree Physiol 31: 452-461.
35. Huang Y, Niu B, Gao Y, Fu L, Li W, (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26: 680-682.
36. Thiel T, Michalek W, Varshney R, Graner A, (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106: 411-422.
37. Botstein D, White RL, Skolnick M, Davis RW, (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32: 314-331.
38. Yin TM, Zhang XY, Gunter LE, Li SX, Wullschleger SD, et al. (2009) Microsatellite primer resource for Populus developed from the mapped sequence scaffolds of the Nisqually-1 genome. New Phytol 181: 498- 503.
39. Li S, Yin T, Wang M, Tuskan GA, (2011) Characterization of microsatellites in the coding regions of the Populus genome. Mol Breed 27: 59-66.
40. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
41. Ueno S, Tsumura Y, (2008) Development of ten microsatellite markers for Quercus mongolica var. crispula by database mining. Conserv Genet 9: 1083-1085.
42. Varshney RK, Graner A, Sorrells ME, (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23: 48-55.
43. Maia LC, Palmieri DA, Souza VQ, Kopp MM, Carvalho FIF, et al. (2008) SSR Locator: Tool for simple sequence repeat discovery integrated with primer design and PCR simulation. Int J Plant Genomics Article ID 412696. Available: http:// http://www.hindawi.com/journals/ijpg/2008/412696/.Accessed 6 March 2013.
44. Victoria FC, da Maia LC, de Oliveira AC (2011) In silico comparative analysis of SSR markers in plants.BMC Plant Biol 11: 15. Available: http://www.biomedcentral.com/1471-2229/11/15.Accessed 6 March 2013.
45. Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, et al. (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156: 847-854.
46. Varshney RK, Thiel T, Stein N, Langridge P, Graner A, (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 7: 537-546.
47. Metzgar D, Bytof J, Wills C, (2000) Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res 10: 72-80.
48. Grover A, Aishwarya V, Sharma PC, (2007) Biased distribution of microsatellite motifs in the rice genome. Mol Genet Genomics 277: 469-480.
49. Morgante M, Hanafey M, Powell W, (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30: 194-200.
50. Qiu L, Yang C, Tian B, Yang JB, Liu A (2010) Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.). BMC Plant Biol 10: 278. Available: http://www.biomedcentral.com/1471-2229/10/278.Accessed 6 March 2013.
51. van der Schoot J, Pospíšková M, Vosman B, Smulders MJM, (2000) Development and characterization of microsatellite markers in black poplar (Populus nigra L.). Theor Appl Genet 101: 317-322.
52. Smulders MJM, Van Der Schoot J, Arens P, Vosman B, (2001) Trinucleotide repeat microsatellite markers for black poplar (Populus nigra L.). Mol Ecol Notes 1: 188-190.
53. Schuelke M, (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18: 233-234.
54. Brandström M, Ellegren H, (2008) Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias. Genome Res 18: 881-887.
55. Yu JK, La Rota M, Kantety RV, Sorrells ME, (2004) EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genomics 271: 742-751.
56. Jayashree B, Punna R, Prasad P, Bantte K, Hash CT, et al. (2006) A database of simple sequence repeats from cereal and legume expressed sequence tags mined in silico: survey and evaluation. In Silico Biol 6: 607-620.
57. Shirasawa K, Asamizu E, Fukuoka H, Ohyama A, Sato S, et al. (2010) An interspecific linkage map of SSR and intronic polymorphism markers in tomato. Theor Appl Genet 121: 731-739.
58. Xu F, Feng SS, Wu RL, Du KF, (2013) Two highly validated SSR multiplexes (8-plex) for Euphrates' poplar, Populus euphratica (Salicaceae). Mol Ecol Res 13: 144-153.
59. Rozen S, Skaletsky H, (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
60. Peakall ROD, Smouse PE, (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6: 288-295.
61. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 28: 2731-2739.