Identification of differentially expressed proteins between hybrid and parents in wheat (Triticum aestivum L.) seedling leaves

Abstract

In spite of commercial use of heterosis in agriculture, the molecular basis of heterosis is poorly understood. To gain a better understanding of the molecular basis of wheat heterosis, we carried out a comparative proteomic analysis in seedling leaves between wheat hybrid and parents. Common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) Line 3338 and spelt wheat (Triticum spelta L., 2n = 6x = 42, AABBDD) Line 2463 were used to produce a heterotic F1 hybrid. The expression patterns of the total proteins were compared in seedling leaves between hybrid and its parents by using two-dimensional gel electrophoresis with two pH ranges for the first dimension separation. Among ~900 protein spots reproducibly detected, 49 protein spots were identified as being differentially expressed between hybrid and its parental lines (P < 0.05) for more than 1.5-folds. Six possible modes of differential expression were observed, including high- and low-parent dominance, underdominance, and overdominance, uniparent silencing and uniparent dominance. Moreover, 30 of the 49 differentially expressed protein spots were identified, which were involved in metabolism, signal transduction, energy, cell growth and division, disease and defense, secondary metabolism. These results indicated that wheat hybridization can cause protein expression differences between hybrid and its parents; these proteins were involved in diverse physiological process pathways, which might be responsible for the observed heterosis.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Abbreviations

ACN:

Acetonitrile

ADP:

Adenosine diphosphate

ATP:

Adenosine triphosphate

BPH:

Best-parent heterosis

CHA:

Chemical hybridizing agent

CHAPS:

3-[(3-Cholamidopropyl)-dimethylammonio]-1-propane sulfonate

CHCA:

A-cyano-4-hydroxycinnamic acid

DDRT:

Differential display reverse transcript

DRH:

Down-regulated in hybrid

DTT:

1,4-Dithio-DL-threitol

FBA:

Fructose-1,6-bisphosphate aldolase

GO:

Gene ontology

HDH:

High-dominant in hybrid

IEF:

Isoelectric focusing

LDH:

Low-dominant in hybrid

LDW:

Leaf dry weight

LFW:

Leaf fresh weight

LRR:

Leucine-rich repeat protein

MPH:

Mid-parent heterosis

MS:

Mass spectrometry

PMF:

Peptide map fingerprinting

PTM:

Post translational modification

RcbA:

Rubisco activase

RcbL:

Rubisco large subunit

SSH:

Suppression subtractive hybridization

2DE:

Two-dimensional gel electrophoresis

TFA:

Trifluoroacetic acid

TIR:

Toll/interleukin-1 receptor

TLN:

Total leaf number

TTN:

Total tiller number

UPF1:

Dominant expression of uniparental proteins in hybrids

UPnF1:

Dominant expression of uniparental proteins but not in hybrids

URH:

Up-regulated in hybrid

References

  1. Anderson L, Seilhamer J (1997) A comparison of selectedmRNA and protein abundances in human liver. Electrophoresis 18:533–537

    PubMed  Article  CAS  Google Scholar 

  2. Baginsky S, Kleffmann T, von Zychlinski A, Gruissem W (2005) Analysis of shotgun proteomics and RNA profiling data from Arabidopsis thaliana chloroplasts. J Proteome Res 4:637–640

    PubMed  Article  CAS  Google Scholar 

  3. Bevan M, Bancroft I, Bent E, Love K, Goodman H, Dean C, Bergkamp R, Dirkse W (1998) Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of the Arabidopsis thaliana. Nature 391:485–488

    PubMed  Article  CAS  Google Scholar 

  4. Broughton W-J, Dilworth M-J (1971) Control of leghaemoglobin synthesis in snake beans. Biochem J 125:1075–1080

    PubMed  CAS  Google Scholar 

  5. Corbin R-W, Paliy O, Yang F, Shabanowitz J, Platt M, Lyons C-E, Root K, McAuliffe J, Jordan M-I, Kustu S, Soupene E, Hunt D-F (2003) Toward a protein profile of Escherichia coli: comparison to its transcription profile. Proc Natl Acad Sci USA 100:9232–9237

    PubMed  Article  CAS  Google Scholar 

  6. Damerval C, Hebert Y, De Vienne D (1987) Is the polymorphism of protein amounts related to phenotypic variability? A comparison of two-dimensional electrophoresis data with morphological traits in maize. Theor Appl Genet 74:194–202

    Article  Google Scholar 

  7. Day D-A, Tuite M-F (1998) Post-transcriptional gene regulatory mechanisms in eukaryotes: an overview. J Endocrinol 157:361–371

    PubMed  Article  CAS  Google Scholar 

  8. Donnelly B-E, Madden R-D, Ayoubi P, Porter D-R, Dillwith J-W (2005) The wheat(Triticum aestivum L.) leaf proteome. Proteomics 5:1624–1633

    PubMed  Article  CAS  Google Scholar 

  9. Dunne A, Ejdebäck M, Ludidi P-L, O’Neill L-A, Gay N-J (2003) Structural complementarity of Toll/Interleukin-1 Receptor domains in Toll-like Receptors and the adaptors Mal and MyD88. J Biol Chem 278:41443–41451

    PubMed  Article  CAS  Google Scholar 

  10. Fedoroff N (2000) Transposons and genome evolution in plants. Proc Natl Acad Sci 97:7002–7007

    PubMed  Article  CAS  Google Scholar 

  11. Forsthoefel N-R, Cutler K, Port M-D, Yamamoto T, Vernon D-M (2005) PIRLs: a novel class of plant intracellular leucine-rich repeat proteins. Plant Cell Physiol 46:913–922

    PubMed  Article  CAS  Google Scholar 

  12. Frost D, Way H, Howles P, Luck J, Manners J, Hardham A, Finnegan J, Ellis J (2004) Tobacco Transgenic for the flax rust resistance gene L expresses allele-specific activation of defense responses. MPMI 17:224–232

    PubMed  Article  CAS  Google Scholar 

  13. Gonella J-A, Peterson P-A (1978) Isozyme relatedness of inbred lines of maize and performance of their hybrids. Maydica 23:55–61

    CAS  Google Scholar 

  14. Guo M, Rupe M-A, Zinselmeier C, Habben J, Bowen B-A, Smith O-S (2004) Allelic variation of gene expression in maize hybrids. Plant Cell 16:1707–1716

    PubMed  Article  CAS  Google Scholar 

  15. Gygi S-P, Rochon Y, Franza B-R, Aebersold R (1999) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19:1720–1730

    PubMed  CAS  Google Scholar 

  16. Hadjinov M-I, Scherbok V-S, Benko N-I, Gusev V-P, Sukhorzhevokaya T-B, Voronova L-P (1982) Interrelationships between isozymic diversity and combining ability in maize lines. Maydica 27:135–149

    Google Scholar 

  17. Heidrich-Sobrinho E, Cordeiro A-R (1975) Codominant isoenzymic allela as markers of genetic diversity correlated with heterosis in maize (Zea mays L.). Theor Appl Genet 46:197–199

    Article  CAS  Google Scholar 

  18. Holmes-Davis R, Tanaka C-K, Vensel W-H, HurkmanW-J McCormick S (2005) Proteome mapping of mature pollen of Arabidopsis thaliana. Proteomics 5:4864–4884

    PubMed  Article  CAS  Google Scholar 

  19. Huang Y, Li L-H, Chen Y, Li X-H, Xu C-G, Wang S-P, Zhang Q-F (2006) Comparative analysis of gene expression at early seedling stage between a rice hybrid and its parents using a cDNA microarray of 9198 uni-sequences. Sci China 49:519–529

    CAS  Google Scholar 

  20. Hunter R-B, Kannenberg L-W (1971) Isozyme characterization of corn (Zea mays) inbreds and its relationship to single cross hybrid performance. Can J Genet Cytol 13:197–199

    Google Scholar 

  21. Kashkush K, Feldman M, Levy A-A (2003) Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nature Genet 33:102–106

    PubMed  Article  CAS  Google Scholar 

  22. Kumar A, Bennetzen J-L (1999) Plant retrotransposon. Annu Rev Genet 33:479–532

    PubMed  Article  CAS  Google Scholar 

  23. Leonardi A, Damerval C, De Vienne D (1987) Inheritance of protein amounts: comparison of two-dimensional electrophoresis patterns of leaf sheath of two maize lines (Zeamays L.) and their hybrids. Genet Res 50:1–5

    Article  Google Scholar 

  24. Mack P-D, Kapelnikov A, Heifetz Y, Bender M (2006) Mating-responsive genes in reproductive tissues of female Drosophila melanogaster. Proc. Natl. Acad. Sci. 103:10358–10363

    PubMed  Article  CAS  Google Scholar 

  25. Martin T, Frommer W-B, Salanoubat M, Willmitzer L (1993) Expression of an Arabidopsis sucrose synthase gene indicates a role in metabolization of sucrose both during phloem loading and in sink organs. Plant J. 4:367–377

    PubMed  Article  CAS  Google Scholar 

  26. Matuschke I, Mishra RR, Qaim M (2007) Adoption and impact of hybrid wheat in India. World Dev 35:1422–1435

    Article  Google Scholar 

  27. Mills D-A, Richter M-L (1991) Nucleotide binding to the isolated β subunit of the chloroplast ATP synthase. J Biol Chem 266:7440–7444

    PubMed  CAS  Google Scholar 

  28. Mooney B-P, Miernyk J-A, Greenlief C-M, Thelen J-J (2006) Using quantitative proteomics of Arabidopsis roots and leaves to predict metabolic activity. Physiol Plant 128:237–250

    Article  CAS  Google Scholar 

  29. Nature Signaling Gateway (2007) Nature publishing group. http://www.signaling-gateway.org. Cited 29 Oct 2007

  30. Ni Z-F, Sun Q-X, Wu L-M, Xie C-J (2002) Differential gene expression between wheat hybrids and their parental inbreds in primary roots. Acta Bot Sin 44:457–462

    CAS  Google Scholar 

  31. Ni Z-F, Sun Q-X, Liu Z-Y (2000) Identification of a hybrid-specific expressed gene encoding novel RNA-binding protein in wheat seedling leaves using differential display of mRNA. Mol Gen Genet 263:934–938

    PubMed  Article  CAS  Google Scholar 

  32. Noir S, Brautigam A, Colby T, Schmidt J, Panstruga R (2005) A reference map of the Arabidopsis thaliana mature pollen proteome. Biochem Biophys Res Commun 337:1257–1266

    PubMed  Article  CAS  Google Scholar 

  33. Porubleva L, Velden K-V, Kothari S, Oliver D-J, Chitnis P-R (2001) The proteome of maize leaves: use of gene sequences and expressed sequence tag data for identification of proteins with peptide mass fingerprints. Electrophoresis 22:1724–1738

    PubMed  Article  CAS  Google Scholar 

  34. Ramagli L-S (1999) Quantifying protein in 2-D PAGE solubilization buffers. Methods Mol Biol 112:99–103

    PubMed  CAS  Google Scholar 

  35. Romagnoli S, Maddaloni M, Livini C, Motto M (1990) Relationship between gene expression and hybrid vigor in primary root tips of young maize. Theor Appl Genet 80:769–775

    Article  CAS  Google Scholar 

  36. Seo Y-S, Jeon J-SE, Rojas M-R, Gilbertson R-L (2007) Characterization of a novel Toll/interleukin-1 receptor (TIR)-TIR gene differentially expressed in common bean (Phaseolus vulgaris cv. Othello) undergoing a defence response to the geminivirus Bean dwarf mosaic virus. Mol Plant Pathol 8:151–162

    Article  CAS  Google Scholar 

  37. Song X, Ni Z-F, Yao Y-Y, Xie C-J, Li Z-X, Wu H-Y, Zhang Y-H, Sun Q-X (2007) Wheat (Triticum aestivum L.) root proteome and differentially expressed root proteins between hybrid and parents. Proteomics 7:3538–3557

    PubMed  Article  CAS  Google Scholar 

  38. Sun Q-X, Ni Z-F, Liu Z-Y (1999) Differential gene expression between wheat hybrids and their parental inbreds in seedling leaves. Euphytica 106:117–123

    Article  Google Scholar 

  39. Sun Q-X, Wu L-M, Ni Z-F, Meng F-R, Wang Z-K, Lin Z (2004) Differential gene expression patterns in leaves between hybrids and their parental inbreds are correlated with heterosis in a wheat diallel cross. Plant Sci 166:651–657

    Article  CAS  Google Scholar 

  40. Swanson-Wagner R-A, Jia Y, DeCook R, Borsuk L-A, Nettleton D, Schnable P-S (2006) All possible modes of gene action are observed in a global comparison of gene expression in a maize F 1 hybrid and its inbred parents. Proc Natl Acad Sci 103:6805–6810

    PubMed  Article  CAS  Google Scholar 

  41. Tsaftaris A-S (1987) Isozymes in plant breeding. In: Rattazzi MC, Scandalios GJ, Whitt GS (eds) Isozymes: current topics in biological and medical research. Alan R. Liss, New York, pp 103–119

    Google Scholar 

  42. Tsuyoshi M, Nobuaki H, Kazuko Y-S, Hiroshi K, Kazuo S (1994) Cloning and sequencing of a nove1 serine/threonine protein kinase in Arabidopsis thaliana. Plant Physiol 106:1229–1230

    Article  Google Scholar 

  43. Wang Z-K, Ni Z-F, Wu H-L, Nie X-L, Sun Q-X (2006) Heterosis in root development and differential gene expression between hybrids and their parental inbreds in wheat (Triticum aestivum L.). Theor Appl Genet 113:1283–1294

    PubMed  Article  CAS  Google Scholar 

  44. Wu L-M, Ni Z-F, Meng F-R, Lin Z, Sun Q-X (2003) Cloning and characterization of leaf cDNAs that are differentially expressed between wheat hybrids and their parents. Mol Gen Genet 270:281–286

    CAS  Google Scholar 

  45. Xia Q, Hendrickson E-L, Zhang Y, Wang T, Taub F, Moore B-C, Porat I, Whitman W-B, Hackett M, Leigh J-A (2006) Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR. Mol Cell Proteomics Feb 24:868–881

    Article  CAS  Google Scholar 

  46. Xiong L-Z, Yang G-P, Xu C-G, Zhang Q-F, Maroof M-A-S (1998) Relationships of differential gene expression in leaves with heterosis and heterozygosity in a rice diallel cross. Mol Breed 4:129–136

    Article  CAS  Google Scholar 

  47. Yao Y-Y, Ni Z-F, Zhang Y-H, Chen Y, Ding Y-H, Han Z-F, Liu Z-Y, Sun Q-X (2005) Identification of differentially expressed genes in leaf and root between wheat hybrid and its parental inbreds using PCR-based cDNA subtraction. Plant Mol Biol 58:367–384

    PubMed  Article  CAS  Google Scholar 

  48. Zhang Y-H, Ni Z-F, Yao Y-Y, Zhao J, Sun Q-X (2006) Analysis of genome-wide gene expression in root of wheat hybrid and its parents inbreds using Barley1 GeneChip. Prog Nat Sci 16:712–720

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The authors wish to thank Mr. Jidong Feng for his assistance in mass spectrometry analysis. This work was financially supported by National Basic Research Program of China (2007CB109000), National Natural Science Foundation of China (30671297), Program for New Century Excellent Talents in University (No. NCET-05-0131) and 863 Project of China.

Author information

Affiliations

Authors

Corresponding authors

Correspondence to Zhongfu Ni or Qixin Sun.

Additional information

X. Song and Z. Ni have equally contributed to this work.

Communicated by M. Kearsey.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Song, X., Ni, Z., Yao, Y. et al. Identification of differentially expressed proteins between hybrid and parents in wheat (Triticum aestivum L.) seedling leaves. Theor Appl Genet 118, 213 (2009). https://doi.org/10.1007/s00122-008-0890-4

Download citation

Keywords

  • Protein Spot
  • Differential Expression Pattern
  • Rubisco Activase
  • Wheat Hybrid
  • Differential Protein Expression