Use of a large-scale Triticeae expressed sequence tag resource to reveal gene expression profiles in hexaploid wheat (Triticum aestivum L.)

Genome

Volumn 49, Issue 5, 2006, Pages 531-544

  Chao, S ^a,b,k   Lazo, G R ^a   You, F ^a,b   Crossman, C C ^a   Hummel, D D ^a   Lui, N ^a   Laudencia Chingcuanco, D ^a   Anderson, J A ^c   Close, T J ^d   Dubcovsky, J ^b   Gill, B S ^e   Gill, K S ^f   Gustafson, J P ^g   Kianian, S F ^h   Lapitan, N L V ⁱ   Nguyen, H T ^g   Sorrells, M E ^j   McGuire, P E ^b   Qualset, C O ^b   Anderson, O D ^a  

^a WESTERN REGIONAL RESEARCH CENTER   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF MINNESOTA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e KANSAS STATE UNIVERSITY   (United States)

^f WASHINGTON STATE UNIVERSITY   (United States)

^g UNIVERSITY OF MISSOURI   (United States)

^h NORTH DAKOTA STATE UNIVERSITY   (United States)

ⁱ Department of Environmental and Radiological Health Sciences   (United States)

^j Department of Obstetrics Gynecology   (United States)

^k USDA ARS Red River Valley Agricultural Research Center   (United States)

more..

Author keywords

Ests; Expressed sequence tags; Gene expression profiles; Triticeae; Wheat

Indexed keywords

ARTICLE; CLUSTER ANALYSIS; CONTIG MAPPING; EXPRESSED SEQUENCE TAG; GENE; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETIC DATABASE; GENETICS; GROWTH, DEVELOPMENT AND AGING; INFORMATION PROCESSING; METABOLISM; PHYLOGENY; POLYPLOIDY; TISSUE DISTRIBUTION; WHEAT;

CLUSTER ANALYSIS; CONTIG MAPPING; DATA COLLECTION; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE LIBRARY; GENES, PLANT; PHYLOGENY; POLYPLOIDY; TISSUE DISTRIBUTION; TRITICUM;

AEGILOPS SPELTOIDES; SECALE CEREALE; TRITICEAE; TRITICUM AESTIVUM;

EID: 33747841661     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G06-003     Document Type: Article

References (26)

1. Adams, M.D., Kelley, J. M., Gocayne, J.D., Dubnick, M., Polymeropoulos, M.H., Xiao, H., et al. 1991. Complementary DNA sequencing: expressed sequence tags and human genome project. Science (Washington, D.C.) 252: 1651-1656.
2. Akhunov, E.D., Akhunov, A.R., Linkiewicz, A.M., Dubcovsky, J, Hummel, D., Lazo, G.R., et al. 2003a. Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates. Proc. Acad. Natl. Sci. U.S.A. 100: 10836-10841.
3. Akhunov, E.D., Goodyear, J.A., Geng, S., Qi, L.L., Echalier, B., Gill, B.S., et al. 2003b. The organization and rate of evolution of the wheat genomes are correlated with recombination rates along chromosome arms. Genome Res. 13: 753-763.
4. Anderson, O.D., and Greene, F.C. 1989. The characterization and comparative analysis of high-molecular-weight glutenin genes from genomes A and B of a hexaploid bread wheat. Theor. Appl. Genet. 77(5): 689-700.
5. Audic, S., and Claverie, J.-M. 1997. The significance of digital gene expression profiles. Genome Res. 7: 986-995.
6. Clarke, B.C., Hobbs, M., Skylas, D., and Appels, R. 2000. Genes active in developing wheat endosperm. Funct. Integr. Genomics, 1: 44-55.
7. Cooper, B., Clarke, J.D., Budworth, P., Kreps, J., Hutchison, D., Park, S. et al. 2003. A network of rice genes associated with stress response and seed development. Proc. Natl. Acad. Sci. U.S.A. 100: 4945-4950.
8. Dvorak, J., and Akhunov, E.D. 2005. Tempos of gene locus deletions and duplications and their relationship to recombination rate during diploid and polyploid evolution in the Aegilops-Triticum alliance. Genetics, 171: 323-332.
9. Eisen, M.B., Spellman, P.T., Brown, P.O., and Bostein, D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U.S.A. 95: 14863-14868.
10. Ewing, R.M., Kahla, A.B., Poirot, O., Lopez, F., Audic, S., and Claverie, J.-M. 1999. Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res. 9: 950-959.
11. Gustafson, J.P., McGuire, P.E., and Qualset, C.O. 2004. Genomic resources: moving wheat into the mainstream in plant genomics. Genetics, 168: 583-584.
12. Hamel, F., Breton, C., and Houde, M. 1998. Isolation and characterization of wheat aluminum-regulated genes: possible involvement of aluminum as a pathogen response elicitor. Planta, 205: 531-538.
13. Kreps, J.A., Wu, Y., Chang, H.-S., Zhu, T., Wang, X., and Harper, J.F. 2002. Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol. 130: 2129-2141.
14. Kruger, W.M., Pritsch, C., Chao, S., and Muehlbauer, G.J. 2002. Functional and comparative bioinformatics analysis of expressed genes from wheat spikes infected with Fusarium graminearum. Mol. Plant-Microbe Interact. 15: 454-455.
15. Lazo, G.R., Chao, S., Hummel, D.D., Edwards, H., Crossman, C.C., Lui, N., et al. 2004. Development of an expressed sequence tag (EST) resource for wheat (Triticum aestivum L.): EST generation, unigene analysis, probe selection, and bioinformatics for a 16,000-locus bin-delineated map. Genetics, 168: 585-593.
16. Ogihara, Y., Mochida, K., Nemoto, Y., Murai, K., Yamazaki, Y., Shin-I, T., and Kohara, Y. 2003. Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags. Plant J. 33: 1001-1011.
17. Ohlrogge, J., and Benning, C. 2000. Unraveling plant metabolism by EST analysis. Curr. Opin. Plant Biol. 3: 224-228.
18. Okubo, K., Hori, N., Matoba, R., Niiyama, T., Fukushima, A., Kojima, Y., and Matsubara, K. 1992. Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression. Nat. Genet. 2: 173-179.
19. Ozturk, Z.N., Talame, V., Deyholos, M., Michalowski, C.B., Galbraith, D.W., Gozukirmizi, N., Tuberosa, R., and Bohnert, H.J. 2002. Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barley. Plant Mol. Biol. 48: 551-573.
20. Qi, L.L., Echalier, B., Chao, S., Lazo, G.R., Butler, G.E., Anderson, O.D., et al. 2004. A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics, 168: 701-712.
21. Ronning, C.M., Stegalkina, S.S., Ascenzi, R.A., Bougri, O., Hart, A.L., Utterbach, T.R., et al. 2003. Comparative analyses of potato expressed sequence tag libraries. Plant Physiol. 131: 419-429.
22. Rubin, G.M., Hong, L., Brokstein, P., Evans-Holm, M., Frise, E., Stapleton, M., and Harvey, D.A. 2000. A Drosophila complementary DNA resource. Science (Washington, D.C.), 287: 2222-2224.
23. Sorrells, M.E., La Rota, M., Bermudez-Kandianis, C.E., Greene, R.A., Kantety, R., Munkvold, J.D., et al. 2003. Comparative DNA sequence analysis of wheat and rice genomes. Genome Res. 13: 1818-1827.
24. Whetten, R., Sun, Y.-H., Zhang, Y., and Sederoff, R. 2001. Functional genomics and cell wall biosynthesis in loblolly pine. Plant Mol. Biol. 47: 275-291.
25. Zhang, D., Choi, D.W., Wanamaker, S., Fenton, R.D., Chin, A., Malatrasi, M., et al. 2004. Construction and evaluation of cDNA libraries for large-scale expressed sequence tag sequencing in wheat (Triticum aestivum, L.). Genetics, 168: 595-608.
26. Zhu, J.-K. 2002. Salt and drought stress signal transduction in plants. Annu. Rev. Plant Biol. 53: 247-273.