Rapid EST isolation from chromosome 1R of rye

BMC Plant Biology

Volumn 8, Issue , 2008, Pages

  Zhou, Ruo Nan ^a,d   Shi, Rui ^a,e   Jiang, Shu Mei ^a,b   Yin, Wei Bo ^a   Wang, Huang Huang ^a   Chen, Yu Hong ^a   Hu, Jun ^a   Wang, Richard R C ^c   Zhang, Xiang Qi ^a   Hu, Zan Min ^a  

^a INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^b SOUTH CHINA SEA INSTITUTE OF OCEANOLOGY   (China)

^c UTAH STATE UNIVERSITY   (United States)

^d UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^e NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HORDEUM; POACEAE; SECALE CEREALE; TRITICUM AESTIVUM;

COMPLEMENTARY DNA; PLANT DNA;

ARTICLE; EXPRESSED SEQUENCE TAG; GENETICS; IMMUNOBLOTTING; PLANT CHROMOSOME; RYE;

CHROMOSOMES, PLANT; DNA, COMPLEMENTARY; DNA, PLANT; EXPRESSED SEQUENCE TAGS; IMMUNOBLOTTING; SECALE CEREALE;

EID: 42649083681     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-8-28     Document Type: Article

References (69)

1. Adams MD, Kelley JM, Goceyne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF, Kerlavage AR, McCombie WR, Venter JC: Complementary DNA sequencing: espressed sequence tags and human genome project. Science 1991, 252(5013):1651-1656.
2. Covitz PA, Smith LS, Long SR: Expressed sequence tags from a root-hair-enriched Medicago truncatula cDNA library. Plant Physiol 1998, 117:1325-1332.
3. Ewing RM, Kahla AB, Poirot O, Lopez F, Audic S, Claverie JM: Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res 1999, 9:950-959.
4. Fernandes J, Brendel V, Gai X, Lal S, Chandler VL, Elumalai RP, Galbraith DW, Pierson EA, Walbot V: Comparison of RNA expression profile based on maize expressed sequence tag frequency analysis and micro-array hybridization. Plant Physiol 2002, 128:896-910.
5. Hillier L, Lennon G, Becker M, Bonaldo MF, Chiapelli B, Chisoe S, Dietrich N, DuBuque T, Favello A, Gish W: Generation and analysis of 280,000 human expressed sequence tags. Genome Res 1996, 6:807-828.
6. Shoemaker R, Keim P, Vodkin L, Retzel E, Clifton SW, Waterston R, Smoller D, Coryell V, Khanna A, Erpelding J, Gai X, Brendel V, Raph-Schmidt C, Shoop EG, Vielweber CJ, Schmatz M, Pape D, Bowers Y, Theising B, Martin J, Dante M, Wylie T, Granger C: A compilation of soybean ESTs: generation and analysis. Genome 2002, 45:329-338.
7. Van der Hoeven R, Ronning C, Giovannoni J, Martin G, Tanksley S: Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of large expressed sequence tag collection and selective genomic sequencing. Plant Cell 2002, 14:1441-1456.
8. Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, Anderson OD, Akhunov ED, Dvoøák JA, Linkiewicz M, Ratnasiri A, Dubcovsky J, Bermudez-Kandianis CE, Greene RA, Kantety R, La Rota CM, Munkvold JD, Sorrells SF, Sorrells ME, Dilbirligi M, Sidhu D, Erayman M, Randhawa HS, Sandhu D, Bondareva SN, Gill KS, Mahmoud AA, Ma XF, Miftahudin, Gustafson JP, Conley EJ, Nduati V, Gonzalez-Hernandez JL, Anderson JA, Peng JH, Lapitan NLV, Hossain KG, Kalavacharla V, Kianian SF, Pathan MS, Zhang DS, Nguyen HT, Choi DW, Fenton RD, Close TJ, McGuire PE, Qualset CO, Gill BS: A Chromosome Bin Map of 16,000 Expressed Sequence Tag Loci and Distribution of Genes Among the Three Genomes of Polyploid Wheat. Genetics 2004, 168:701-712.
9. Hossain KG, Kalavacharla V, Lazo GR, Hegstad J, Wentz MJ, Simons K, Gehlhar S, Rust JL, Syamala RR, Obeori K, Suresh B, Karunadharma P, Chao S, Anderson OD, Qi LL, Echalier B, Gill BS, Linkiewicz AM, Ratnasiri A, Dubcovsky J, Akhunov ED, Dvorák J, Miftahudin, Ross K, Gustafson JP, Sidhu D, Dilbirligi M, Gill KS, Peng JH, Lapitan NLV, Greene RA, Bermudez-Kandianis CE, Sorrells ME, Feril O, Pathan MS, Nguyen HT, Gonzalez-Hernandez JL, Conley EJ, Anderson JA, Fenton D, Close TJ, McGuire PE, Qualset CO, Kianian SF: A chromosome bin map of 2148 expressed sequence tag loci of wheat homoeologous group 7. Genetics 2004, 168:687-699.
10. Linkiewicz AM, Qi LL, Gill BS, Echalier B, Chao S, Lazo GR, Hummel DD, Anderson OD, Akhunov ED, Dvorák J, Pathan MS, Nguyen HT, Peng JH, Lapitan NLV, Miftahudin, Gustafson JP, La Rota CM, Sorrells ME, Hossain KG, Kalavacharla V, Kianian SF, Sandhu D, Bondareva SN, Gill KS, Conley EJ, Anderson JA, Fenton RD, Close TJ, McGuire PE, Qualset CO, Dubcovsky J: A 2500-locus bin map of wheat homoeologous group 5 provides insights on gene distribution and colinearity with rice. Genetics 2004, 168:665-676.
11. Su YA, Trent JM, Guan XY, Meltzer PS: Direct isolation of genes encoded within a homogeneously staining region by chromosome microdissection. Proc Natl Acad Sci USA 1994, 91:9121-9125.
12. Zhang M, Yu L, Hu PR, Bi AD, Xia JH, Deng HX, Zhao SY: Isolation of the expression fragments with the probe pool of human chromosome 14q24.3 generated by microdissection. Acta Biologiae experimetalis sinica 1997, 30(3):241-246.
13. Gracia E, Ray ME, Polymeropoulos MH, Dehejia A, Meltzer PS, Trent JM: Isolation of chromosome-specific ESTs by microdissection-mediated cDNA capture. Genome Res 1997, 7:100-107.
14. Kim H, Kim C, Rhyu IJ, Kim JH, Lew DH, Chun YH, Park SH: Isolation of novel human fetal brain cDNAs mapped to human chromosome bands, 1q25 and 8q24.1. Mol Cells 2001, 11:257-262.
15. Albani D, Côté MJ, Armstrong KC, Chen QF, Segal A, Robert LS: PCR amplification of microdissected wheat chromosome arms in a 'single tube' reaction. Plant J 1993, 4(5):899-903.
16. Liu B, Segal G, Vega JM, Feldman M, Abbo S: Isolation and characterization of chromosome-specific DNA sequences from a chromosome arm genomic library of common wheat. Plant J 1997, 11(5):959-965.
17. Chen Q, Armstrong K: Characterization of a library from a single microdissected oat (Avena sativa L.) chromosome. Genome 1995, 38:706-714.
18. Busch W, Martin R, Herrmann RG, Hohmann U: Repeated DNA sequences isolated by microdissection I. Karyotyping of barley (Hordeum vulgare L.). Genome 1995, 38:1082-1090.
19. Jung C, Claussen U, Horsthemke B, Fis-cher F, Herrmann RG: A DNA library from an individual Beta patellaris chromosome conferring nematode resistance obtained by microdissection of meiotic metaphase chromosome. Plant Mol Biol 1992, 20:503-511.
20. Dang BY, Hu ZM, Zhou YH, Cui LH, Wang LL, Zhang TH, Li LC, Chen ZH: Isolation of single-chromosome DNA library from Lilium regale wilson. Chin Sci Bull 1998, 43(2):194-199.
21. Jiang SM, Hu J, Yin WB, Chen YH, Wang RRC, Hu ZM: Cloning of resistance gene analogs located on the alien chromosome in an addition line of wheat-Thinopyrum intermedium. Theor Appl Genet 2005, 111(5):923-931.
22. Jiang SM, Zhang L, Hu J, Shi R, Zhou G, Chen YH, Yin WB, Wang RRC, Hu ZM: Screening and analysis of differentially expressed genes from an alien addition line of wheat Thynopyrum intermedium induced by barley yellow dwarf virus infection. Genome 2004, 47:1114-1121.
23. Zhang FY, Yin WB, Shi R, Hu YK, Yan YM, Chen YH, Zhou YH, Hu J, Wang RRC, Hu ZM: Construction and characterization of chromosome 1B specific DNA library of wheat. Cana J Plant Sci 2005, 85:309-316.
24. Zhou YH, Dang BY, Wang H, Hu ZM, Wang LL, Chen ZH: Microdissection of a single chromosome and construction of t-he microclone library from soybean. Euphytica 2001, 121(2):129-135.
25. Zhou YH, Hu ZM, Dang BY, Wang H, Deng XD, Chen ZH: Microdissection and microloning of rye (Secale cereale L.) chromosome 1R. Chromosoma 1999, 108:250-255.
26. Kubaláková M, Valárik M, Bartoš J, Vrána J, Cíhalíková J, Molnár-Láng M, Doleže J: Analysis and sorting of rye (Secale cereale L.) chromosomes using flow cytometry. Genome 2003, 46:893-905.
27. van Kints TMC: Mildew of wheat. UK Cereal Pathogen Virulence Survey. Annual Report 1986:7-12.
28. Mago R, Spielmeyer W, Lawrence GJ, Ellis JG, Pryor AJ: Resistance genes for rye stem rust (SrR) and barley powdery mildew (Mla) are located in syntenic regions on short arm of chromosome. Genome 2004, 47:112-121.
29. Wehling P, Linz A, Hackauf B, Roux SR, Ruge B, Klocke B: Leaf-rust resistance in rye (Secale cereale L.). 1. Genetic analysis and mapping of resistance genes Pr1 and Pr2. Theor Appl Genet 2003, 107:432-438.
30. Shi ZX, Chen XM, Line RF, Leung H, Wellings CR: Development of resistance gene analog polymorphism markers for the Yr9 gene resistance to wheat stripe rust. Genome 2001, 44:509-516.
31. Wood EA, Sebesta EE, Starks KJ: Resistance of 'Gaucho' triticale to Schizaphis graminum. Environ Entomol 1974, 3:720-721.
32. Bennett MD, Gustafson JP, Smith JB: Variation on nuclear DNA in the genus Secale. Chromosoma 1977, 61:149-176.
33. Gaffney T, Friedrich L, Vernooij B, Negrotto D, Nye G, Uknes S, Ward E, Kessmann H, Rayls J: Requirement of salicylic acid for the induction of systemic acquired resistance. Science 1993, 261:754-756.
34. Draper J: Sugar import and metabolism during seed development. Trends Plant Sci 1997, 2:162-165.
35. Shirasu K, Nakajima H, Rajasekhar VK, Dixon RA, Lamb C: Salicylic Acid Potentiates an Agonist-Dependent Gain Control That Amplifies Pathogen Signals in the Activation of Defense Mechanisms. Plant Cell 1997, 9:261-270.
36. Lecerf F, Foggia L, Mulsant P, Bonnet A, Hatey F: A novel method to isolate the common fraction of two DNA samples: hybrid specific amplification (HSA). Nucleic Acids Res 2001, 29(17):e87.
37. Diatchenko L, Lau YF, Campbell AP, Chenchik A, Moqadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sverdlov ED, Siebert PD: Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 1996, 93:6025-6030.
38. Rogowsky PM, Langridge P, Shepherd KW: Polymerase chain reaction based mapping of rye involving repeated DNA sequences. Genome 1992, 35:621-626.
39. Clarke BC, Mukai Y, Appels R: The Sec-1 locus on the short arm of chromosome 1R of rye (Secale cereale L.). Chromosoma 1996, 105(5):269-275.
40. Juttner J, Olde D, Langridge P, Baumann U: Cloning and expression of a distinct subclass of plant thioredoxins. Eur J Biochem 2000, 267(24):7109-7117.
41. Ko JM, Do GS, Suh DY, Seo BB, Shin DC, Moon HP: Identification and chromosomal organization of two rye genome-specific RAPD products useful as introgression markers in wheat. Genome 2002, 45(1):157-164.
42. Gu YQ, Coleman-Derr D, Kong X, Anderson OD: Rapid Genome Evolution Revealed by Comparative Sequence Analysis of Orthologous Regions from Four Triticeae Genomes. Plant Physiol 2004, 135(1):459-470.
43. Kong XY, Gu YQ, You FM, Dubcovsky J, Anderson OD: Dynamics of the evolution of orthologous and paralogous portions of a complex locus region in two genomes of allopolyploid wheat. Plant Mol Biol 2004, 54(1):55-69.
44. Wissenbach M: New members of the barley Kas gene family encoding beta-ketoacyl-acyl carrier protein synthases. Plant Physiol 1994, 106(4):1711-1712.
45. Rousley S, Linx KK: Large scale sequencing of plant genome. Curr Opin Plant Biol 1998, 1(2):136-141.
46. Sasaki T: The rice genome project in Japan. Proc Natl Acad Sci USA 1998, 95(5):2027-2028.
47. Peñuela S, Danesh D, Young ND: Targeted isolation, sequence analysis, and physical mapping of nonTIR NBS-LRR genes in soybean. Theor Appl Genet 2002, 104:261-272.
48. Spielmeyer W, Huang L, Bariana H, Laroche A, Gill BS, Lagudah ES: NBS-LRR sequence is associated with leaf and stripe rust resistance on the end of homoeologous chromosome group 1S of wheat. Theor Appl Genet 2000, 101:1139-1144.
49. Yokoi H, Hadano S, Kogi M, Kang XL, Wakasa K, Joh-Elkeda: Isolation of expressed sequences encoded by the human Xq terminal portion using microclone probes generated by laser microdissection. Genomics 1994, 20:404-411.
50. Kao FT, Yu J, Tong S, Qi J, Patanjali SR, Weissman SM, Patterson D: Isolation and refined regional mapping of expressed sequences from human chromosome 21. Genomics 1994, 23:700-703.
51. Yu J: Gene identification and DNA sequence analysis in the GC-poor 20 megabase region of human chromosome 21. Proc Natl Acad Sci USA 1997, 94:6862-6867.
52. Wei J, Hodes ME, Wang Y, Feng Y, Ghetti B, Dlouhy SR: Direct cDNA selection with DNA microdissected from mouse chromosome 16: isolation of novel clones and construction of a partial transcription map of the C3–C4 region. Genome Res 1996, 6(8):678-687.
53. Yokoyama Y, Ohsugi K, Kozaki T, Sakuragawa N: Microdissection-mediated selection of chromosome region-specific cDNAs. Cytogenet Cell Genet 1997, 77(3–4):192-196.
54. Till BJ, Burtner C, Comai L, Henikoff S: Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res 2004, 32(8):2632-2641.
55. Hu ZM, Wang H, Chen YH, Shi R, Chen ZH: Studies on contamination of cytoplasm DNA and its control in plant chromosome microdissection. Acta Bot Sin 2003, 45(2):131-135.
56. Malamy J, Carr JP, Klessig DF, Raskin I: Salicylic acid: a likely endogenous signal in the resistance response of tobacco to viral infection. Science 1990, 250:1002-1004.
57. Yalpani N, León J, Lawton MA, Raskin I: Pathway of salicylic acid biosynthesis in healthy and virus-inoculated tobacco. Plant Physiol 1993, 103:315-321.
58. Hooft van Huijsduijnen RAM, Alblas SW, de Rijk RH, Bol JF: Induction by salicylic acid of pathogenesis-related proteins and resistance to alfalfa mosaic virus infection in various plant species. J Gen Virol 1986, 67:2135-2143.
59. Métraux JP, Signer H, Ryals J, Ward E, Wyss-Benz M, Gaudin J, Raschdorf K, Schmid E, Blum W, Inverardi B: Increase in salicylic acid at the onset of systemic acquired resistance in cucumber. Science 1990, 250:1004-1006.
60. Janda T, Szalai G, Tari I, Páldi E: Hydroponic treatment with salicylic acid decreases the effects of chilling injury in maize (Zea mays L.) plants. Planta 1999, 208:175-180.
61. Tan XP, Meyers BC, Kozik A, West ML, Morgante M, Clair DA, Bent AF, Michelmore RW: Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis. BMC Plant Biol 2007, 7:56.
62. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM: Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol 2006, 24:680-686.
63. Murray MG, Thompson WF: Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 1980, 8(19):4321-4325.
64. Nakata N, Yasumuro Y, Sasaki M: An acetocarmine-Giemsastaining of rye chromosomes. Japan J Genetics 1977, 52:315-318.
65. Telenius H, Carter NP, Bebb CE, Nordenskjöld M, Ponder BAJ, Tunnacliffe A: Degenerated Oligonucleotide-Primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 1992, 13:718-725.
66. Saghai-Maroof MA, Solman KM, Jorgensen RA, Allard RW: Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 1984, 81:8014-8018.
67. Chalaya T, Gogvadze E, Buzdin A, Kovalskaya E, Sverdlov ED: Improving specificity of DNA hybridization-based met hods. Nucleic Acids Res 2004, 32(16):e130.
68. Sambrook J, Russell DW: Molecular Cloning: A Laboratory Manual 3rd edition. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 2001.
69. GenBank [http://www.ncbi.nlm.nih.gov/]