Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.)

BMC Plant Biology

Volumn 10, Issue , 2010, Pages

  Qiu, Lijun ^a,c   Yang, Chun ^a   Tian, Bo ^a   Yang, Jun Bo ^b   Liu, Aizhong ^a  

^a CHINESE ACADEMY OF SCIENCES   (China)

^b KUNMING INSTITUTE OF BOTANY   (China)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

EUPHORBIA; EUPHORBIACEAE; RICINUS COMMUNIS;

MICROSATELLITE DNA;

ARTICLE; EXPRESSED SEQUENCE TAG; GENETIC DATABASE; GENETIC POLYMORPHISM; GENETICS; PLANT GENE; POLYMERASE CHAIN REACTION; RICINUS COMMUNIS;

CASTOR BEAN; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; GENES, PLANT; MICROSATELLITE REPEATS; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC;

EID: 78650092243     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-10-278     Document Type: Article

References (51)

1. Hayes WC. The Scepter of Egypt II. 1953, Cambridge, Mass. USA: Harvard University Press.
2. Weiss EA. Castor bean, Sesame, and safflower. 1971, London, Leonard Hill.
3. Govaerts R, Frodin DG, Radcliffe-Smith A. World checklist and bibliography of Euphorbiaceae (with Pandaceae). 2000, Trowbridge, Wiltshire, Redwood Books Limited.
4. Atsmon D. Castor. Oilcrops of the World, Their Breeding and Utilization 1989, 438-447. New York, McGraw-Hill, Robbelen G, Downey RK, Ashri A.
5. Sujatha M, Reddy TP, Mahasi MJ. Role of biotechnological interventions in the improvement of castor bean (Ricinus communis L.) and Jatropha curcas L. Biotechnol Adv 2008, 26:424-435. 10.1016/j.biotechadv.2008.05.004, 18579331.
6. Weiss EA. Oilseed crops. 2000, London, Blackwell.
7. Li FJ, Wang CL, Wang YF, Chen ZQ, Chen MH, Gao LF. Fatty acid composition of the castor bean seed of nine castor bean hybrids. China Oils and Fats 2008, 33:62-64.
8. Meinders HC, Jones MD. Pollen shedding and dispersal in the castor bean plant Ricinus communis L. J Agron 1950, 4:206-209.
9. Brigham RD. Natural outcrossing in dwarf-internode castor bean, Ricinus communis L. Crop Sci 1967, 7:353-355.
10. Allard RW, Alvim P, Ashri A, Barton JH. Managing global genetic resources; the U. S. national plant germplasm system: elements of the national plant germplasm system. 1991, 43-86. Washington DC, The National Academies Press.
11. Gupta PK, Varshney RK. The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 2000, 113:163-185.
12. Chakrabarty SK, Banu SS. Genetic diversity in pistillate lines of castor bean (Ricinus communis). Indian J Agric Sci 1999, 69:729-730.
13. Allan G, Williams A, Rabinowicz PD, Chan AP, Ravel J, Keim P. Worldwide genotyping of castor bean germplasm (Ricinus communis L.) using AFLPs and SSRs. Genet Resour Crop Evol 2008, 55:365-378.
14. Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 1996, 2:225-238.
15. Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK. An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts. Euphytica 2005, 142:169-196.
16. Zane L, Bargelloni L, Patarnello T. Strategies for microsatellite isolation: a review. Mol Ecol 2002, 11:1-16. 10.1046/j.0962-1083.2001.01418.x, 11903900.
17. Squirrell J, Hollingsworth PM, Woodhead M, Russell J, Lowe AJ, Gibby M, Powell W. How much effort is required to isolate nuclear microsatellites from plants?. Mol Ecol 2003, 12:1339-1348. 10.1046/j.1365-294X.2003.01825.x, 12755865.
18. Ellis JR, Burke JM. EST-SSRs as a resource for population genetics analysis. Heredity 2007, 99:125-132. 10.1038/sj.hdy.6801001, 17519965.
19. Cordeiro GM, Casu R, McIntyre CL, Manners JM, Henry RJ. Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant Sci 2001, 160:1115-1123. 10.1016/S0168-9452(01)00365-X, 11337068.
20. Varshney RK, Sigmund R, Börner A, Korzum V, Stein N, Sorrells ME, Langridge P, Graner A. Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Sci 2005, 168:195-202.
21. Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R. Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 2000, 156:847-854. 1461288, 11014830.
22. Tóth G, Gáspári Z, Jurka J. Microsatellites in different eukaryotic genomes: Survey and analysis. Genome Res 2000, 10:967-981. 10.1101/gr.10.7.967, 310925, 10899146.
23. Morgante M, Hanafey M, Powell W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 2002, 30:194-200. 10.1038/ng822, 11799393.
24. Nicot N, Chiquet V, Gandon B, Amilhat L, Legeai F, Leroy P, Bernard M, Sourdille P. Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor Appl Genet 2004, 109:800-805. 10.1007/s00122-004-1685-x, 15146317.
25. Kota R, Varshney RK, Thiel T, Dehmer KJ, Graner A. Generation and comparison of EST-derived SSRs and SNPs in barley (Houdeum vulgare L.). Hereditas 2001, 135:145-151. 10.1111/j.1601-5223.2001.00145.x, 12152327.
26. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential. Genome Res 2001, 11:1441-1452. 10.1101/gr.184001, 311097, 11483586.
27. Thiel T, Michalek W, Varshney RK, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 2003, 106:411-422.
28. Holton TA, Christopher JT, McClure L, Harker N, Henry RJ. Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat. Mol Breed 2002, 9:63-71.
29. Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS Henry RJ. Analysis of SSRs derived from grape ESTs. Theor Appl Genet 2000, 100:723-726.
30. Areshchenkova T, Ganal MW. Comparative analysis of polymorphism and chromosomal location of tomato microsatellite markers isolated from different sources. Theor Appl Genet 2002, 104:229-235. 10.1007/s00122-001-0775-2, 12582691.
31. Bhat PR, Krishnakumar V, Hendre PS, Rajendrakumar P, Varshney RK, Aggarwal RK. Identification and characterization of gene-derived EST-SSR markers from robusta coffee variety 'CxR' (an interspecific hybrid of Coffea canephora x Coffea congensis). Mol Ecol Notes 2005, 5:80-83.
32. Poncet V, Rondeau M, Tranchant C, Cayrel A, Hamon S, de Kochko A, Hamon P. SSR mining in coffee tree EST databases: potential use of EST-SSRs as markers for the Coffea genus. Mol Genet Genomics 2006, 276:436-449. 10.1007/s00438-006-0153-5, 16924545.
33. Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krishnakumar V, Singh L. Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theor Appl Genet 2007, 114:359-372. 10.1007/s00122-006-0440-x, 17115127.
34. Low ETL, Alias H, Boon SH, Shariff EM, Tan CYA, Ooi LCL, Cheah SC, Raha AR, Wan KL, Singh R. Oil palm (Elaeis guineensis Jacq.) tissue culture ESTs: Identifying genes associated with callogenesis and embryogenesis. BMC Plant Biol 2008, 8:62. 10.1186/1471-2229-8-62, 2442076, 18507865.
35. Feng SP, Li WG, Huang HS, Wang JY, Wu YT. Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis). Mol Breed 2009, 23:85-97.
36. Varshney RK, Thiel T, Stein N, Langridge P, Graner A. In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 2002, 7:537-546.
37. Arumuganathan K, Earle ED. Nuclear DNA content of some important plant species. Plant Mol Biol Report 1991, 9:211-215.
38. Kantety RV, La Rota M, Matthews DE, Sorrells ME. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 2002, 48:501-510. 10.1023/A:1014875206165, 11999831.
39. Metzgar D, Bytof J, Wills C. Selection against frame shift mutations limits microsatellite expansion in coding DNA. Genome Res 2000, 10:72-80. 310501, 10645952.
40. Bajay MM, Pinheiro JB, Batista CEA, Nobrega MBM, Zucchi MI. Development and characterization markers for castor bean (Ricinus communis L.), an important oleaginous species for biodiesel production. Conservation Genet Resour 2009, 1:237-239.
41. Raji AA, Anderson VJ, Kolade AO, Ugwu DC, Dixon GA, Ingelbrecht LI. Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility. BMC Plant Biol 2009, 9:118. 10.1186/1471-2229-9-118, 2758884, 19747391.
42. Wurdack KJ, Hoffmann P, Chase MW. Molecular phylogenetic analysis of uniovulate Euphorbiaceae (Euphorbiaceae sensu stricto) using plastid rbcL and trnL-F DNA sequences. Am J Bot 2005, 92:1397-1420.
43. Moshkin VA. History and origin of castor bean. Castor bean 1986, 6-10. New Delhi, Oxonian, Moshkin VA.
44. Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 1987, 19:11-15.
45. van de Loo FJ, Broun P, Turner S, Ville CS. An oleate 12-hydroxylase from Ricinus communis L. is a fatty acyl desaturase homolog. Proc Natl Acad Sci USA 1995, 92:6743-6747. 10.1073/pnas.92.15.6743, 41405, 7624314.
46. Doering-Saad C, Newbury HJ, Couldridge CE, Bale JS, Pritchard J. A phloem-enriched cDNA library from Ricinus: insights into phloem function. J Exp Bot 2006, 57:3183-3193. 10.1093/jxb/erl082, 16936221.
47. Lu C, Wallis JG, Browse J. An analysis of expressed sequence tags of developing castor bean endosperm using a full-length cDNA library. BMC Plant Biol 2007, 7:42. 10.1186/1471-2229-7-42, 1950504, 17672910.
48. Li WZ, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659. 10.1093/bioinformatics/btl158, 16731699., http://bioinformatics.ljcrf.edu/cd-hi/
49. Rozen S, Skaletsky HJ. Primer3 on the WWW for general users and for biologist programmers. Bioinformatics Methods and Protocols: Methods in Molecular Biology 2000, 365-386. Humana Press, Totowa NJ., http://frodo.wi.mit.edu/primer3/primer3_code.html
50. Lewis PO, Zaykin D. Genetic data analysis: computer program for the analysis of allelic data. 2001, , http://lewis.eeb.uconn.edu/lewishome/software.html
51. Swofford DL. PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4b. 2001, Sunderland, MA: Sinauer Associates.