Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas)
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- 作者：Zhangying Wang (1)
Jun Li (2)
Zhongxia Luo (1)
Lifei Huang (1)
Xinliang Chen (1)
Boping Fang (1)
Yujun Li (1)
Jingyi Chen (1)
Xiongjian Zhang (1) - 刊名：BMC Plant Biology
- 出版年：2011
- 出版时间：December 2011
- 年：2011
- 卷：11
- 期：1
- 全文大小：403KB
- 参考文献：1. The Food and Agriculture Organization [http://faostat.fao.org/]
2. Jim C, G C, Albert K, Kenneth V, Maria A, Robert O, Bryon R: Development of a genetic linkage map and identification of homologous linkage groups in sweetpotato using multiple-dose AFLP markers. / Molecular Breeding 2008,21(4):511鈥?32. CrossRef
3. Kriegner A, Cervantes JC, Burg K, Mwanga ROM, Zhang D: A genetic linkage map of sweetpotato [Ipomoea batatas (L.) Lam.] based on AFLP markers. / Molecular Breeding 2003,11(3):169鈥?85. CrossRef
4. Li AX, Liu QC, Wang QM, Zhang LM, Hong Z, Liu SZ: Establishment of Molecular Linkage Maps Using SRAP Markers in Sweet Potato. / ACTA AGRONOMICA SINICA 2010,36(8):1286鈥?295.
5. Morgante M, Hanafey M, Powell W: Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. / Nat Genet 2002,30(2):194鈥?00. CrossRef
6. Taramino G, Tarchini R, Ferrario S, Lee M, Pe ME: Characterization and mapping of simple sequence repeats (SSRs) in Sorghum bicolor. / Theoretical and Applied Genetics 1997, 95:66鈥?2. CrossRef
7. La Rota M, Kantety RV, Yu JK, Sorrells ME: Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. / BMC Genomics 2005,6(1):23. CrossRef
8. Edwards K, Barker J, Daly A, Jones C, Karp A: Microsatellite libraries enriched for several microsatellite sequences in plants. / Biotechniques 1996,20(5):758鈥?60.
9. Hamilton M, Pincus E, Di-Fiore A, Fleischer R: Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. / Biotechniques 1999,27(3):500鈥?07.
10. Wen M, Wang H, Xia Z, Zou M, Lu C, Wang W: Developmenrt of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha Curcas L. / BMC Res Notes 2010, 3:42. CrossRef
11. Nunome T, Negoro S, Kono I, Kanamori H, Miyatake K, Yamaguchi H, Ohyama A, Fukuoka H: Development of SSR markers derived from SSR-enriched genomic library of eggplant (Solanum melongena L.). / Theor Appl Genet 2009,119(6):1143鈥?153. CrossRef
12. Iniguez-Luy FL, Voort AV, Osborn TC: Development of a set of public SSR markers derived from genomic sequence of a rapid cycling Brassica oleracea L. genotype. / Theor Appl Genet 2008,117(6):977鈥?85. CrossRef
13. Saha MC, Cooper JD, Mian MA, Chekhovskiy K, May GD: Tall fescue genomic SSR markers: development and transferability across multiple grass species. / Theor Appl Genet 2006,113(8):1449鈥?458. CrossRef
14. Wang YW, Samuels TD, Wu YQ: Development of 1,030 genomic SSR markers in switchgrass. / Theor Appl Genet 2011,122(4):677鈥?86. CrossRef
15. Gupta PK, Rustgi S: Molecular markers from the transcribed/expressed region of the genome in higher plants. / Funct Integr Genomics 2004,4(3):139鈥?62. CrossRef
16. 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鈥?26. CrossRef
17. Eujayl I, Sledge MK, Wang L, May GD, Chekhovskiy K, Zwonitzer JC, Mian MA: Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. / Theor Appl Genet 2004,108(3):414鈥?22. CrossRef
18. Zhang LY, Bernard M, Leroy P, Feuillet C, Sourdille P: High transferability of bread wheat EST-derived SSRs to other cereals. / Theor Appl Genet 2005,111(4):677鈥?87. CrossRef
19. Varshney RK, Graner A, Sorrells ME: Genic microsatellite markers in plants: features and applications. / Trends Biotechnol 2005,23(1):48鈥?5. CrossRef
20. Varshney RK, Sigmund R, B枚rner A, Korzun 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鈥?02. CrossRef
21. Jarret RL, Bowen N: Simple Sequence Repeats (SSRs) for sweetpotato germplasm characterization. / Plant Genet Res Newslett 1994, 100:9鈥?1.
22. Buteler MI, Jarret RL, LaBonte DR: Sequence characterization of microsatellites in diploid and polyploid Ipomoea. / Theor Appl Genet 1999, 99:123鈥?32. CrossRef
23. Buteler MI, Bonte DRL, Jarret RL, Macchiavelli RE: Microsatellite-based paternity analysis in polyploidy sweetpotato. / J Am Soc Hort Sci 2002, 127:392鈥?96.
24. Zhang DP, Carbajulca D, Ojeda L, Rossel G, Milla S, Herrera C, Ghislain M: Microsatellite Analysis of Genetic Diversity in Sweetpotato Varieties from Latin America. / "CIP Program Report 1999鈥?000" International Potato Center, Lima, Peru P295鈥?01 2001.
25. Hwang SY, Tseng YT, Lo HF: Application of simple sequence repeats in determining the genetic relationships of cultivars used in sweet potato polycross breeding in Taiwan. / Scientia Horticulturae 2002,93(3鈥?):215鈥?24. CrossRef
26. Hu J, Nakatani M, Mizuno K, Fujimura T: Development and Characterization of Microsatellite Markers in Sweetpotato. / Breeding Science 2004, 54:177鈥?88. CrossRef
27. Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang L, Chen X, Li Y: De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). / BMC Genomics 2010, 11:726. CrossRef
28. Schafleitner R, Tincopa LR, Palomino O, Rossel G, Robles RF, Alagon R, Rivera C, Quispe C, Rojas L, Pacheco JA, / et al.: A sweetpotato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers. / BMC Genomics 2010,11(1):604. CrossRef
29. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, / et al.: TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. / Bioinformatics 2003,19(5):651鈥?52. CrossRef
30. Liang X, Chen X, Hong Y, Liu H, Zhou G, Li S, Guo B: Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species. / BMC Plant Biol 2009, 9:35. CrossRef
31. 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(5鈥?):501鈥?10. CrossRef
32. Zeng S, Xiao G, Guo J, Fei Z, Xu Y, Roe BA, Wang Y: Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. / BMC Genomics 2010, 11:94. CrossRef
33. 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(2):847鈥?54.
34. Kumpatla SP, Mukhopadhyay S: Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. / Genome 2005,48(6):985鈥?98. CrossRef
35. Gao L, Tang J, Li H, Jia J: Analysis of microsatellites in major crops assessed by computational and experimental approaches. / Mol Breed 2003,12(3):245鈥?61. CrossRef
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(2A):537鈥?46.
37. 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(3):411鈥?22.
38. Gao LF, Jing RL, Huo NX, Li Y, Li XP, Zhou RH, Chang XP, Tang JF, Ma ZY, Jia JZ: One hundred and one new microsatellite loci derived from ESTs (EST-SSRs) in bread wheat. / Theor Appl Genet 2004,108(7):1392鈥?400. CrossRef
39. La Rota M, Kantety RV, Yu JK, Sorrells ME: Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. / BMC Genomics 2005, 6:23. CrossRef
40. Saha MC, Mian MA, Eujayl I, Zwonitzer JC, Wang L, May GD: Tall fescue EST-SSR markers with transferability across several grass species. / Theor Appl Genet 2004,109(4):783鈥?91. CrossRef
41. 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(6):1115鈥?123. CrossRef
42. Yu JK, Dake TM, Singh S, Benscher D, Li W, Gill B, Sorrells ME: Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat. / Genome 2004,47(5):805鈥?18. CrossRef
43. Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS: Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. / Mol Genet Genomics 2003,270(4):315鈥?23. CrossRef
44. Rungis D, Berube Y, Zhang J, Ralph S, Ritland CE, Ellis BE, Douglas C, Bohlmann J, Ritland K: Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags. / Theor Appl Genet 2004,109(6):1283鈥?294. CrossRef
45. Russell J, Booth A, Fuller J, Harrower B, Hedley P, Machray G, Powell W: A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome. / Genome 2004,47(2):389鈥?98. CrossRef
46. 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(2):359鈥?72. CrossRef
47. Guo W, Wang W, Zhou B, Zhang T: Cross-species transferability of G. arboreum-derived EST-SSRs in the diploid species of Gossypium. / Theor Appl Genet 2006,112(8):1573鈥?581. CrossRef
48. Chavarriaga-Aguirre PP, Maya MM, Bonierbale MW, Kresovich S, Fregene MA, Tohme J, G K: Microsatellites in Cassava (Manihot esculenta Crantz): discovery, inheritance and variability. / Theoretical and Applied Genetics 1998,97(3):493鈥?01. CrossRef
49. Wang YW, Samuels TD, Wu YQ: Development of 1,030 genomic SSR markers in switchgrass. / Theor Appl Genet 2010.
50. Chakraborty R, Kimmel M, Stivers DN, Davison LJ, Deka R: Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci. / Proc Natl Acad Sci USA 1997,94(3):1041鈥?046. CrossRef
51. Schug MD, Hutter CM, Wetterstrand KA, Gaudette MS, Mackay TF, Aquadro CF: The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster. / Mol Biol Evol 1998,15(12):1751鈥?760.
52. Stewart CN Jr, Via LE: A rapid CTAB DNA isolation technique useful for RAPD fingerprinting and other PCR applications. / Biotechniques 1993,14(5):748鈥?50.
53. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. / Nucleic Acids Res 1997,25(17):3389鈥?402. CrossRef - 作者单位：Zhangying Wang (1)
Jun Li (2)
Zhongxia Luo (1)
Lifei Huang (1)
Xinliang Chen (1)
Boping Fang (1)
Yujun Li (1)
Jingyi Chen (1)
Xiongjian Zhang (1)
1. Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
2. College of Life Science, China West Normal University, Nanchong, 637002, China
文摘
Background Currently there exists a limited availability of genetic marker resources in sweetpotato (Ipomoea batatas), which is hindering genetic research in this species. It is necessary to develop more molecular markers for potential use in sweetpotato genetic research. With the newly developed next generation sequencing technology, large amount of transcribed sequences of sweetpotato have been generated and are available for identifying SSR markers by data mining. Results In this study, we investigated 181,615 ESTs for the identification and development of SSR markers. In total, 8,294 SSRs were identified from 7,163 SSR-containing unique ESTs. On an average, one SSR was found per 7.1 kb of EST sequence with tri-nucleotide motifs (42.9%) being the most abundant followed by di- (41.2%), tetra- (9.2%), penta- (3.7%) and hexa-nucleotide (3.1%) repeat types. The top five motifs included AG/CT (26.9%), AAG/CTT (13.5%), AT/TA (10.6%), CCG/CGG (5.8%) and AAT/ATT (4.5%). After removing possible duplicate of published EST-SSRs of sweetpotato, a total of non-repeat 7,958 SSR motifs were identified. Based on these SSR-containing sequences, 1,060 pairs of high-quality SSR primers were designed and used for validation of the amplification and assessment of the polymorphism between two parents of one mapping population (E Shu 3 Hao and Guang 2k-30) and eight accessions of cultivated sweetpotatoes. The results showed that 816 primer pairs could yield reproducible and strong amplification products, of which 195 (23.9%) and 342 (41.9%) primer pairs exhibited polymorphism between E Shu 3 Hao and Guang 2k-30 and among the 8 cultivated sweetpotatoes, respectively. Conclusion This study gives an insight into the frequency, type and distribution of sweetpotato EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated sweetpotato. These EST-SSR markers could enrich the current resource of molecular markers for the sweetpotato community and would be useful for qualitative and quantitative trait mapping, marker-assisted selection, evolution and genetic diversity studies in cultivated sweetpotato and related Ipomoea species.