Transcriptome and metabolome profiling of field-grown transgenic barley lack induced differences but show cultivar-specific variances

The aim of the present study was to assess possible adverse effects of transgene expression in leaves of field-grown barley relative to the influence of genetic background and the effect of plant interaction with arbuscular mycorrhizal fungi. We conducted transcript profiling, metabolome profiling, and metabolic fingerprinting of wild-type accessions and barley transgenics with seed-specific expression of (1,3-1, 4)-β-glucanase (GluB) in Baronesse (B) as well as of transgenics in Golden Promise (GP) background with ubiquitous expression of codon-optimized Trichoderma harzianum endochitinase (ChGP). We found more than 1,600 differential transcripts between varieties GP and B, with defense genes being strongly overrepresented in B, indicating a divergent response to subclinical pathogen challenge in the field. In contrast, no statistically significant differences between ChGP and GP could be detected based on transcriptome or metabolome analysis, although 22 genes and 4 metabolites were differentially abundant when comparing GluB and B, leading to the distinction of these two genotypes in principle component analysis. The coregulation of most of these genes in GluB and GP, as well as simple sequence repeat-marker analysis, suggests that the distinctive alleles in GluB are inherited from GP. Thus, the effect of the two investigated transgenes on the global transcript profile is substantially lower than the effect of a minor number of alleles that differ as a consequence of crop breeding. Exposing roots to the spores of the mycorrhizal Glomus sp. had little effect on the leaf transcriptome, but central leaf metabolism was consistently altered in all genotypes.

[1]  C. Lawrence,et al.  Genes from mycoparasitic fungi as a source for improving plant resistance to fungal pathogens. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Nigel W. Hardy,et al.  Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[3]  P. Puigdoménech,et al.  Lack of repeatable differential expression patterns between MON810 and comparable commercial varieties of maize , 2008, Plant Molecular Biology.

[4]  Welch Bl.  THE GENERALIZATION OF ‘STUDENT'S’ PROBLEM WHEN SEVERAL DIFFERENT POPULATION VARLANCES ARE INVOLVED , 1947 .

[5]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[6]  A. Smilde,et al.  Large-scale human metabolomics studies: a strategy for data (pre-) processing and validation. , 2006, Analytical chemistry.

[7]  U. Sonnewald,et al.  Ustilago maydis Infection Strongly Alters Organic Nitrogen Allocation in Maize and Stimulates Productivity of Systemic Source Leaves1[W][OA] , 2009, Plant Physiology.

[8]  Howard V. Davies,et al.  Comparison of Tuber Proteomes of Potato Varieties, Landraces, and Genetically Modified Lines1 , 2005, Plant Physiology.

[9]  A. Weber,et al.  The phenotype of the Arabidopsis cue1 mutant is not simply caused by a general restriction of the shikimate pathway. , 2003, The Plant journal : for cell and molecular biology.

[10]  U. Sonnewald,et al.  Tocopherol deficiency in transgenic tobacco (Nicotiana tabacum L.) plants leads to accelerated senescence. , 2009, Plant, cell & environment.

[11]  D. von Wettstein.  From analysis of mutants to genetic engineering. , 2007, Annual review of plant biology.

[12]  D. von Wettstein,et al.  Supplements of transgenic malt or grain containing (1,3-1,4)-ß-glucanase increase the nutritive value of barley-based broiler diets to that of maize , 2003, British poultry science.

[13]  Oliver Fiehn,et al.  Combining Genomics, Metabolome Analysis, and Biochemical Modelling to Understand Metabolic Networks , 2001, Comparative and functional genomics.

[14]  A. Lovegrove,et al.  A metabolomic study of substantial equivalence of field-grown genetically modified wheat. , 2006, Plant biotechnology journal.

[15]  T. Okita,et al.  The production of recombinant proteins in transgenic barley grains. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[16]  C. Manetti,et al.  A metabonomic study of transgenic maize (Zea mays) seeds revealed variations in osmolytes and branched amino acids. , 2006, Journal of experimental botany.

[17]  D. von Wettstein,et al.  Growth inhibition of the cereal root pathogens Rhizoctonia solani AG8, R. oryzae and Gaeumannomyces graminis var. tritici by a recombinant 42-kDa endochitinase from Trichoderma harzianum , 2006 .

[18]  Anna Coll,et al.  Gene expression profiles of MON810 and comparable non-GM maize varieties cultured in the field are more similar than are those of conventional lines , 2009, Transgenic Research.

[19]  J. Strauss,et al.  Mycoparasitic interaction relieves binding of the Cre1 carbon catabolite repressor protein to promoter sequences of the ech42 (endochitinase-encoding) gene in Trichoderma harzianum. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[20]  N. Benhamou,et al.  Cytochemical aspects of chitin breakdown during the parasitic action of a Trichoderma sp. on Fusarium oxysporum f.sp. radicis-lycopersici. , 1990 .

[21]  Søren Bak,et al.  Metabolic engineering of dhurrin in transgenic Arabidopsis plants with marginal inadvertent effects on the metabolome and transcriptome. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[22]  L. Harrier,et al.  Expression studies of plant genes differentially expressed in leaf and root tissues of tomato colonised by the arbuscular mycorrhizal fungus Glomus mosseae , 2003, Plant Molecular Biology.

[23]  S. Cohen,et al.  Using quaternary high-performance liquid chromatography eluent systems for separating 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate-derivatized amino acid mixtures , 1997 .

[24]  Sophia Sonnewald,et al.  Manipulation of plant innate immunity and gibberellin as factor of compatibility in the mutualistic association of barley roots with Piriformospora indica. , 2009, The Plant journal : for cell and molecular biology.

[25]  Falk Schreiber,et al.  VANTED: A system for advanced data analysis and visualization in the context of biological networks , 2006, BMC Bioinformatics.

[26]  H. Brinch-Pedersen,et al.  A Microarray-Based Comparative Analysis of Gene Expression Profiles During Grain Development in Transgenic and Wild Type Wheat , 2005, Transgenic Research.

[27]  G. Mikhaylenko,et al.  Improved barley broiler feed with transgenic malt containing heat-stable (1,3-1,4)-beta-glucanase. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[28]  E J Kok,et al.  Unintended effects and their detection in genetically modified crops. , 2004, Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association.

[29]  A. Pietro,et al.  CHITINOLYTIC ENZYMES PRODUCED BY TRICHODERMA HARZIANUM; ANTIFUNGAL ACTIVITY OF PURIFIED ENDOCHITINASE AND CHITOBIOSIDASE , 1993 .

[30]  R. Trethewey.  Metabolite profiling as an aid to metabolic engineering in plants. , 2004, Current opinion in plant biology.