Skip to main content
SpringerLink
Log in

Construction, Characterization, and Expressed Sequence Tag (EST) Analysis of Normalized cDNA Library of Thermo-Photoperiod-Sensitive Genic Male Sterile (TPGMS) Wheat from Spike Developmental Stages

  • Published:
Plant Molecular Biology Reporter Aims and scope Submit manuscript

Abstract

Thermo-photoperiod-sensitive genic male sterile (TPGMS) wheat is important in utilization of heterosis. To facilitate the use of such wheat line in agriculture, more knowledge about molecular mechanisms of TPGMS genes is required. In this study, we set up a normalized complementary DNA (cDNA) library based on the strategy of saturation hybridization with genomic DNA using TPGMS wheat line. This normalized cDNA library consists of cDNA from six directionally cloned cDNA libraries constructed with spike and anther tissues from spike developmental stages. From the normalized cDNA library, 3,264 single-pass expressed sequence tag (EST) were obtained. Exclusion of sequences shorter than 100 bp resulted in 3,223 vector-trimmed ESTs with a mean length of 926 bp. Clustering and assembly analysis resulted in 2,175 unique ESTs from 423 contigs and 1,752 singletons. Taking advantage of various tools and database, gene function classification showed that 60% of the ESTs were predicted to have putative gene function. Of the 2,175 unique ESTs, 264 (12%) displayed significant homology (BlastX E values <10−5) to genes previously reported to be involved in cold-response related processes. Among these, sequences encoding activities related to primary metabolism, signal transduction, and transcriptional regulation were observed. Finally, in the total EST sequences, 108 potential SSRs were found. The unigene dataset will now be used to fabricate biochips carrying all identified genes for TPGMS wheat functional genomic research.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

Abbreviations

CHA:

chemical hybridizing agents

CMS:

cytoplasmic male sterility

contigs:

contiguous consensus sequences

CSRD:

cold-stress-related database

EST:

expressed sequence tag

GO:

gene ontology

IP3:

inositol-1,4,5-triphosphate

MAP kinase:

mitogen- activated protein kinase

nr:

non-redundant

ROS:

reactive oxygen species

SSRs:

simple sequence repeats

TPGMS:

thermo-photoperiod-sensitive genic male sterile

TPGMSSUniGene:

TPGMS wheat Spike development related UniGene

TPP:

trehalose-6-phosphate phosphatase

References

  • Adams M, Kerlavage AR, Fleischmann RD, Fuldner RA, Bult CJ, Lee NH, et al. Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature 1995;377:173–4.

    Article  Google Scholar 

  • Ajay KG, Ju-Kon K, Thomas GO, Anil PR, Yang DC, Leon VK, et al. Trehalose accumulation in rice plants confers high tolerance levels to different abiotic stresses. Proc Natl Acad Sci U S A 2002;99(25):15898–903.

    Article  Google Scholar 

  • Ali MN, Koichiro T, Shuichi K, Yuki M, Masanori S, Masumi I, et al. EGassembler online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res 2006;34:459–62.

    Google Scholar 

  • Ana C, Stefan G, Juan Miguel GG, Javier T, Manuel T, Montserrat R. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005;21(18):3674–6.

    Article  Google Scholar 

  • Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, et al. The InterProScan database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 2001;29(1):37–40.

    Article  PubMed  CAS  Google Scholar 

  • Brent E, Phil G. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998;8:186–94.

    Google Scholar 

  • Cao SH, Guo XL, Liu DC, Zhang XQ, Zhang GM. Preliminary gene-mapping of photoperiod-temperature sensitive genic male sterility in wheat (Triticum aestivum L.). Acta Genetica Sinica 2004;31(3):293–8 (in Chinese with English abstract).

    PubMed  CAS  Google Scholar 

  • 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):847–54.

    PubMed  CAS  Google Scholar 

  • Chen RZ, Zhao X, Shao Z, Wei Z, Wang YY, Zhu LL, et al. Rice UDP-glucose pyrophosphorylase1 is essential for pollen callose deposition and its cosuppression results in a new type of thermosensitive genic male sterility. Plant Cell 2007;19:847–61.

    Article  PubMed  CAS  Google Scholar 

  • Chinnusamy V, Zhu JH, Zhu JK. Gene regulation during cold acclimation in plants. Physiol Plant 2006;126(1):52–61.

    Article  CAS  Google Scholar 

  • Chu ZH, Peng KM, Zhang LD, Zhou B, Wei J, Wang SP. Construction and characterization of a normalized whole-life-cycle cDNA library of rice. Chinese Sci Bull 2003;48:229–35.

    Article  CAS  Google Scholar 

  • Evgeni MZ, Rolf A. InterProScan—an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001;17(9):847–8.

    Article  Google Scholar 

  • Fowler S, Thomashow MF. Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 2002;14(8):1675–90.

    Article  PubMed  CAS  Google Scholar 

  • Guo RX, Sun DF, Tan ZB, Rong DF, Li CD. Two recessive genes controlling thermophotoperiod-sensitive male sterility in wheat. Theor Appl Genet 2006;112:1271–6.

    Article  PubMed  CAS  Google Scholar 

  • Hannah MA, Heyer AG, Hincha DK. A global survey of gene regulation during cold acclimation in arabidopsis thaliana. PLoS Genet 2005;1(2):e26.

    Article  PubMed  Google Scholar 

  • Jiang SY, Cai M, Ramachandran S. Oryza sativa MYOSIN XI B controls pollen development by photoperiod-sensitive protein localizations. Dev Biol 2007;304:579–92.

    Article  PubMed  CAS  Google Scholar 

  • Keiichi M, Kanako K, Etsuo S, Naoto K, Tadasu SI, Yuji K, et al. Tissue expression map of a large number of expressed sequence tags and its application to in silico screening of stress response genes in common wheat. Mol Gen Genomics 2006;276:304–12.

    Article  Google Scholar 

  • Ko MSH. An ‘equalized cDNA library’ by the reassociation of short double-stranded cDNA. Nucleic Acids Res 1990;118:5705–11.

    Article  Google Scholar 

  • Lazo GR, Chao S, Hummel H, Edwards H, Crossman CC, Lui N, et al. Development of an expressed eequence 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 2004;168:585–93.

    Article  PubMed  Google Scholar 

  • Li YF, Zhao CP, Zhang FT, Sun H, Sun DF. Fertility alteration in the photo-thermo-sensitive male sterile line BS20 of wheat (Triticum aestivum L.). Euphytica 2006;151:207–13.

    Article  Google Scholar 

  • Mohamed B, Jean D, Barbara B, Mario H, Fathey S. The CBF gene family in hexaploid wheat and its relationship to the phylogenetic complexity of cereal CBFs. Mol Genet Genomics 2007;277:533–54.

    Article  Google Scholar 

  • Murai K. Factors responsible for levels of male sterility in photoperiod-sensitive cytoplasmic male sterile (PCMS) wheat lines. Euphytica 2001;117:111–6.

    Article  Google Scholar 

  • Nathalie P, Charles P, Lee P, John AC, Marie JM, Janice C, et al. Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics 2005;6:144.

    Article  Google Scholar 

  • Ogihara Y, Mochida K, Nemoto Y, Murai K, Yamazaki Y, Shin IT, et al. 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 2003;33:1001–11.

    Article  PubMed  Google Scholar 

  • Ronning CM, Stegalkina SS, Ascenzi RA, Bougri O, Hart AL, Utterbach TR, et al. Comparative analyses of potato expressed sequence tag libraries. Plant Physiol 2003;131:419–29.

    Article  PubMed  Google Scholar 

  • Roosens NHCJ, Thu TT, Iskandar HM, Jacobs M. Isolation of the ornithine-δ-aminotransferase cDNA and effect of salt stress on its expression in Arabidopsis thaliana. Plant Physiol 1998;117:263–71.

    Article  PubMed  CAS  Google Scholar 

  • Sarhan F, Danyluk J. Engineering cold-tolerant crops-throwing the master switch. Trends Plant Sci 1998;3(8):289–91.

    Article  Google Scholar 

  • Satoh-Nagasawa N, Nagasawa N, Malcomber S, Sakai H, Jackson D. A trehalose metabolic enzyme controls inflorescence architecture in maize. Nature 2006;441:227–30.

    Article  PubMed  CAS  Google Scholar 

  • Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, et al. Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 2002;31(3):279–92.

    Article  PubMed  CAS  Google Scholar 

  • Soares MB, Bonaldo MF, Jelene P, Su L, Lawton L, Efstratiadis A. Construction and characterization of a normalized cDNA library. Proc Natl Acad Sci U S A 1994;91:9228–32.

    Article  PubMed  CAS  Google Scholar 

  • Stephen FA, Warren G, Webb M, Eugene WM, David JL. Basic local alignment search tool. J Mol Biol 1990;215:403–10.

    Google Scholar 

  • Stockinger EJ, Gilmour SJ, Thomashow MF. Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc Natl Acad Sci U S A 1997;94(3):1035–40.

    Article  PubMed  CAS  Google Scholar 

  • Viswanathan C, Zhu JK. Molecular genetic analysis of cold-regulated gene transcription. Philos Trans R Soc Lond B Biol Sci 2002;357(1423):877–86.

    Article  PubMed  CAS  Google Scholar 

  • Xin ZG, Browse J. Eskimo1 mutants of Arabidopsis are constitutively freezing-tolerant. Plant Biol 1998;95:7799–804.

    CAS  Google Scholar 

  • Zhang ZX, Zhang FD, Tang WH, Pi YJ, Zheng YL. Construction and characterization of normalized cDNA library of maize inbred MO17 from multiple tissues and developmental stages. Mol Biol 2005;39(2):177–84.

    Article  CAS  Google Scholar 

  • Zhao CP, Wang X, Zhang FT, Ye ZJ, Dai HJ. Advances of hybrid wheat and two-line system of photo-thermo sensitivity. Beijing Agric Sci 1999;17:3–5. (in Chinese with English abstract).

    Google Scholar 

  • Zhu JH, Dong CH, Zhu JK. Interplay between cold-responsive gene regulation, metabolism and RNA processing during plant cold acclimation. Curr Opin Plant Biol 2007;10:290–5.

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This study was supported by the Program of Beijing Basic Research and Innovation Platform for Agricultural Breeding (No. YZPT01-04), National “863” Program (no. 2006AA100102), and Excellence Scholar Fostered Program of Beijing Government.

Author information

Authors and Affiliations

  1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China

    D. Yang, Z. H. Tang & Y. L. Zheng

  2. Beijing Engineering and Technique Research Center of Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China

    Z. H. Tang, L. P. Zhang & C. P. Zhao

Authors
  1. D. Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Z. H. Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. L. P. Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. C. P. Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Y. L. Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to C. P. Zhao or Y. L. Zheng.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yang, D., Tang, Z.H., Zhang, L.P. et al. Construction, Characterization, and Expressed Sequence Tag (EST) Analysis of Normalized cDNA Library of Thermo-Photoperiod-Sensitive Genic Male Sterile (TPGMS) Wheat from Spike Developmental Stages. Plant Mol Biol Rep 27, 117–125 (2009). https://doi.org/10.1007/s11105-008-0050-7

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11105-008-0050-7

Keywords

Search

Navigation