Transcriptome analysis of grain development in hexaploid wheat

Background

Hexaploid wheat is one of the most important cereal crops for human nutrition. Molecular understanding of the biology of the developing grain will assist the improvement of yield and quality traits for different environments. High quality transcriptomics is a powerful method to increase this understanding.

Results

The transcriptome of developing caryopses from hexaploid wheat (Triticum aestivum, cv. Hereward) was determined using Affymetrix wheat GeneChip^® oligonucleotide arrays which have probes for 55,052 transcripts. Of these, 14,550 showed significant differential regulation in the period between 6 and 42 days after anthesis (daa). Large changes in transcript abundance were observed which were categorised into distinct phases of differentiation (6–10 daa), grain fill (12–21 daa) and desiccation/maturation (28–42 daa) and were associated with specific tissues and processes. A similar experiment on developing caryopses grown with dry and/or hot environmental treatments was also analysed, using the profiles established in the first experiment to show that most environmental treatment effects on transcription were due to acceleration of development, but that a few transcripts were specifically affected. Transcript abundance profiles in both experiments for nine selected known and putative wheat transcription factors were independently confirmed by real time RT-PCR. These expression profiles confirm or extend our knowledge of the roles of the known transcription factors and suggest roles for the unknown ones.

Conclusion

This transcriptome data will provide a valuable resource for molecular studies on wheat grain. It has been demonstrated how it can be used to distinguish general developmental shifts from specific effects of treatments on gene expression and to diagnose the probable tissue specificity and role of transcription factors.

Effect of variety and environmental factors on gluten proteins: an analytical, spectroscopic, and rheological study

Four cultivars of winter wheat with contrasting qualities for breadmaking were selected to study the effects of environmental factors on grain protein composition and properties. They were grown in the field and under two controlled regimens designed to mimic typical "hot/dry" and "cold/wet" conditions experienced during grain development in the United Kingdom. The composition of the gluten proteins determined by SDS-PAGE and their size distribution determined by SE-HPLC were consistent with the presence of higher proportions of high M r polymers in the two varieties with good breadmaking performance (Spark and Soissons) with limited environmental effects on these parameters. Gluten protein fractions from three of the cultivars were analyzed by Fourier transform infrared (FTIR) spectroscopy and this, combined with creep measurements using a texture analyzer, showed that a conversion from beta-turns to beta-sheets occurred during extension, irrespective of the growth conditions. However, the breadmaking varieties Soissons and Spark showed greater differences related to environmental conditions than the variety Rialto, which has poorer processing quality.

Nematicidal effects of cysteine proteinases against sedentary plant parasitic nematodes

Cysteine proteinases from the fruit and latex of plants, such as papaya, pineapple and fig, have previously been shown to have substantial anthelmintic efficacy, in vitro and in vivo, against a range of animal parasitic nematodes. In this paper, we describe the in vitro effects of these plant extracts against 2 sedentary plant parasitic nematodes of the genera Meloidogyne and Globodera. All the plant extracts examined caused digestion of the cuticle and decreased the activity of the tested nematodes. The specific inhibitor of cysteine proteinases, E-64, blocked this activity completely, indicating that it was essentially mediated by cysteine proteinases. In vitro, plant cysteine proteinases are active against second-stage juveniles of M. incognita and M. javanica, and some cysteine proteinases also affect the second-stage juveniles of Globodera rostochiensis. It is not known yet whether these plant extracts will interfere with, or prevent invasion of, host plants.

Characterization of the emulsification properties of 2S albumins from sunflower seed

The ability of 2S albumins from sunflower seeds to stabilize oil-in-water emulsions has been investigated, demonstrating that one of the proteins (SFA8) effectively stabilizes emulsions, while another (SF-LTP) does not stabilize emulsions. The surface tension and surface dilation viscosity of these two proteins were measured, rationalizing the emulsifying ability of SFA8 in terms of its ability to form a strongly elastic monolayer at interfaces. The secondary structure changes that occur upon adsorption of SFA8 to the oil/water interface have also been studied by fluorescence, circular dichroism (CD), and Fourier-transform infrared (FT-IR) spectroscopy. It was found that the beta-sheet content of the protein increased upon adsorption at the expense of alpha-helix and random structure. Moreover, FT-IR measurements indicate the presence of intermolecular beta-sheet formation upon adsorption. Fluorescence studies with an oil-soluble fluorescence quencher indicate that the single tryptophan residue present in SFA8 may become located in the oil-phase of the emulsion. This residue is thought to be partially buried in the native protein, and these data suggest that changes in the polypeptide region flanking this residue may play an important role in the molecular rearrangement that occur on or following adsorption to the oil/water interface.

D hordeins of Hordeum chilense: a novel source of variation for improvement of wheat

The high molecular weight subunits of wheat (Triticum aestivum L.) glutenin (HMW-GS) are important in determining the bread-making quality of flour and dough. There is therefore interest in transferring orthologous HMW-GS present in other grass species into wheat by wide crossing in order to extend the range of end use properties. In this work, we have isolated and characterized two genes encoding D hordeins from Hordeum chilense (Roem. et Schult.) lines H1 and H7, representing two ecotypes. The fragments were 4,305 bp for line H1 and 4,227 for line H7 and contained the promoter, coding and terminator regions. Both sequences differ in the presence of single base changes (SNPs) and insertions/deletions in the open reading frame (ORF). The encoded proteins comprise 870 and 896 amino acids for lines H1 and H7, respectively. The primary structure is similar to those of D hordeins of cultivated barley (H. vulgare L.) and HMW-GS from wheat. However, the D hordeins from H. chilense are significantly larger than those from cultivated barley due to the presence of longer repetitive regions. The H. chilense D hordeins also differ from those of cultivated barley in the distribution of the cysteine residues: whereas the D hordeins of cultivated barley contain ten cysteines with four in the repetitive domain, only nine are present in the H. chilense proteins with two in the repetitive domain. As in the HMW-GS, the central part of the D hordein proteins comprises repeated sequences based on short peptide motifs. The repetitive domain is divided in three regions named as R1 (N-terminal repeats), R2 (central degenerate repeats) and R3 (C-terminal repeats). Hexapeptide motifs are present throughout the repetitive domains of D hordeins with a consensus motif of PFQGQQ in R1 and R2 and PHQGQQ in R3. In addition, the tetrapeptide motif TTVS, which is characteristic of D hordeins of cultivated barley is present in the repetitive domain close to the protein C-terminus.

In vitro fermentation by human fecal microflora of wheat arabinoxylans

The fermentation of three arabinoxylan (AX) fractions from wheat by the human fecal microflora was investigated in vitro. Three AX fractions, with average molecular masses of 354, 278, and 66 kDa, were incorporated into miniature-scale batch cultures (with inulin as a positive prebiotic control) with feces from three healthy donors, aged 23-29. Microflora changes were monitored by the culture-independent technique, fluorescent in situ hybridization, and short chain fatty acid (SCFA) and lactic acid production were measured by high-performance liquid chromatography. Total cell numbers increased significantly in all treated cultures, and the fermentation of AX was associated with a proliferation of the bifidobacteria, lactobacilli, and eubacteria groups. Smaller but statistically significant increases in bacteroides and clostridia groups were also observed. All AX fractions had comparable bifidogenic impacts on the microflora at 5 and 12 h, but the 66 kDa AX was particularly selective for lactobacilli. Eubacteria increased significantly on all AX fractions, particularly on 66 kDa AX. As previously reported, inulin gave a selective increase in bifidobacteria. All supplemented cultures showed significant rises in total SCFA production, with a particularly high proportion of butyric acid being produced from AX fermentation. The prebiotic effect, that is, the selectivity of AX for bifidobacteria and lactobacilli groups, increased as the molecular mass of the AX decreased. This suggests that molecular mass may influence the fermentation of AX in the colon.

A novel bioinformatics approach identifies candidate genes for the synthesis and feruloylation of arabinoxylan

Arabinoxylans (AXs) are major components of graminaceous plant cell walls, including those in the grain and straw of economically important cereals. Despite some recent advances in identifying the genes encoding biosynthetic enzymes for a number of other plant cell wall polysaccharides, the genes encoding enzymes of the final stages of AX synthesis have not been identified. We have therefore adopted a novel bioinformatics approach based on estimation of differential expression of orthologous genes between taxonomic divisions of species. Over 3 million public domain cereal and dicot expressed sequence tags were mapped onto the complete sets of rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) genes, respectively. It was assumed that genes in cereals involved in AX biosynthesis would be expressed at high levels and that their orthologs in dicotyledonous plants would be expressed at much lower levels. Considering all rice genes encoding putative glycosyl transferases (GTs) predicted to be integral membrane proteins, genes in the GT43, GT47, and GT61 families emerged as much the strongest candidates. When the search was widened to all other rice or Arabidopsis genes predicted to encode integral membrane proteins, cereal genes in Pfam family PF02458 emerged as candidates for the feruloylation of AX. Our analysis, known activities, and recent findings elsewhere are most consistent with genes in the GT43 families encoding beta-1,4-xylan synthases, genes in the GT47 family encoding xylan alpha-1,2- or alpha-1,3-arabinosyl transferases, and genes in the GT61 family encoding feruloyl-AX beta-1,2-xylosyl transferases.

Promoter analysis and immunolocalisation show that puroindoline genes are exclusively expressed in starchy endosperm cells of wheat grain

The purolindolines are small cysteine-rich proteins which are present in the grain of wheat. They have a major impact on the utilisation of the grain as they are the major determinants of grain texture, which affects both milling and baking properties. Bread and durum wheats were transformed with constructs comprising the promoter regions of the Puroindoline a (Pina) and Puroindoline b (Pinb) genes fused to the uidA (GUS) reporter gene. Nine lines showing 3:1 segregation for the transgene and comprising all transgene/species combinations were selected for detailed analysis of transgene expression during grain development. This showed that transgene expression occurred only in the starchy endosperm cells and was not observed in any other seed or vegetative tissues. The location of the puroindoline proteins in these cells was confirmed by tissue printing of developing grain, using a highly specific monoclonal antibody for detection and an antibody to the aleurone-localised 8S globulin as a control. This provides clear evidence that puroindolines are only synthesised and accumulated in the starchy endosperm cells of the wheat grain.

The effect of environment on endosperm cell-wall development in Triticum aestivum during grain filling: an infrared spectroscopic imaging study

One of the major factors contributing to the failure of new wheat varieties is seasonal variability in end-use quality. Consequently, it is important to produce varieties which are robust and stable over a range of environmental conditions. Recently developed sample preparation methods have allowed the application of FT-IR spectroscopic imaging methods to the analysis of wheat endosperm cell wall composition, allowing the spatial distribution of structural components to be determined without the limitations of conventional chemical analysis. The advantages of the methods, described in this paper, are that they determine the composition of endosperm cell walls in situ and with minimal modification during preparation. Two bread-making wheat cultivars, Spark and Rialto, were selected to determine the impact of environmental conditions on the cell-wall composition of the starchy endosperm of the developing and mature grain, focusing on the period of grain filling (starting at about 14 days after anthesis). Studies carried out over two successive seasons show that the structure of the arabinoxylans in the endosperm cell walls changes from a highly branched form to a less branched form. Furthermore, during development the rate of restructuring was faster when the plants were grown at higher temperature with restricted water availability from 14 days after anthesis with differences in the rate of restructuring occurring between the two cultivars.

Isolation and characterization of Viviparous-1 genes in wheat cultivars with distinct ABA sensitivity and pre-harvest sprouting tolerance

Pre-harvest sprouting (PHS) of wheat reduces the quality and economic value of grain, and increasing PHS tolerance is one of the most important traits in wheat breeding. Two new Vp-1B alleles related to PHS tolerance were identified on the 3BL chromosome of bread wheat and were designated Vp-1Bb and Vp-1Bc. Sequence analysis showed that Vp-1Bb has a 193 bp insertion and Vp-1Bc has a 83 bp deletion located in the third intron region of the Vp-1B gene, and that they shared 95.43% and 97.89% similarity, respectively, with the sequence of AJ400713 (Vp-1Ba) at the nucleotide level. Their sequences were deposited in the GenBank under the accession numbers DQ517493 and DQ517494. Semi-quantitative RT-PCR analysis showed that alternatively spliced transcripts of the Vp-1A, Vp-1B, and Vp-1D homologues were present and there were no differences in the splicing patterns or abundances of Vp-1A and Vp-1D from embryos 35 d after pollination between PHS-tolerant and -susceptible cultivars. Although Vp-1Ba, Vp-1Bb, and Vp-1Bc could each produce a set of transcripts, only one was correctly spliced and had the capacity to encode the full-length VP1 protein and was more highly expressed with Vp-1Bb and Vp-1Bc than with Vp-1Ba. Comparison of the expression patterns of Vp-1Ba, Vp-1Bb, and Vp-1Bc on different days after pollination also revealed that the expression of these genes was developmentally regulated. Furthermore, genotypes with different levels of tolerance to PHS respond differently to ABA exposure and differences in transcript levels of Vp-1Ba, Vp-1Bb, and Vp-1Bc were observed after ABA treatment. The results indicated that insertion or deletion in the third intron region might affect the expression of the Vp-1B gene and its sensitivity to ABA, and thus resistance to PHS.

Properties and exploitation of oleosins

Oleosins stabilize oil bodies in seeds and other tissues and contain a unique hydrophobic domain which appears to be inserted into the oil matrix as an alpha-helical hairpin. The oleosin proteins may be exploited to stabilize emulsions while the ease of oil body preparation has led to the expression of bioactive proteins as oleosin fusions in molecular farming.

Formation of high levels of acrylamide during the processing of flour derived from sulfate-deprived wheat

When wheat was grown under conditions of severe sulfate depletion, dramatic increases in the concentration of free asparagine were found in the grain of up to 30 times as compared to samples receiving the normal levels of sulfate fertilizer. The effect was observed both in plants grown in pots, where the levels of nutrients were carefully controlled, and in plants grown in field trials on soil with poor levels of natural nutrients where sulfate fertilizer was applied at levels from 0 to 40 kg sulfur/Ha. Many of the other free amino acids were present at higher levels in the sulfate-deprived wheat, but the levels of free glutamine showed increases similar to those observed for asparagine. In baked cereal products, asparagine is the precursor of the suspect carcinogen acrylamide, and when flours from the sulfate-deprived wheat were heated at 160 degrees C for 20 min, levels of acrylamide between 2600 and 5200 microg/kg were found as compared to 600-900 microg/kg in wheat grown with normal levels of sulfate fertilization.

An optimal pooling strategy applied to high-throughput screening for rare marker-free transformants

An optimal pooling system, called Accurate and Fast Target Screening, has been developed for high-throughput identifying the rare marker-free transformants. This system can identify targets between 10- and 100-fold more efficiently than analysis of individual samples. By calculating the efficiency for different proportions of targets and the optimal group size in a worst case scenario, we are able to estimate an upper limit for the number of tests that are required. The application of this system to determine the transgene in an artificially constructed population of transgenic and non-transgenic wheat lines successfully identified the 10 positive samples located randomly with 990 negative samples using only 92 PCR reactions. The same approach was also applied to determine transgene expression by SDS-PAGE of seed proteins. This system gives unambiguous positive or negative results and should facilitate marker-free transformation.

The potential allergenicity of two 2S albumins from soybean (Glycine max): a protein microarray approach

BACKGROUND

The 2S albumins are a group of storage proteins that occur widely in seeds of dicotyledonous plants. The widespread distribution and stability to digestion of allergenic 2S albumins raise the question of why some members of this family present in important food sources, such as soybean, are not regarded as major allergens.

METHODS

The pepsinolytic stability of two 2S albumins from soybean seed was determined using simulated gastric fluid. Using a new protein microarray system, IgE binding to these soybean 2S albumins was studied with the sera from 23 European individuals allergic to soybean. In order to validate the microarray result, two of the sera were selected and further tested using the micro-ELISA and UniCAP system.

RESULTS

Both albumins exhibited high stability to digestion similar to other allergenic members of the 2S albumin, trypsin/amylase inhibitor and lipid transfer protein superfamily. None of the patients was found to have IgE specific to soybean 2S albumins by the microarray system, and this result was in agreement with the results from the micro-ELISA and UniCAP system.

CONCLUSIONS

The results from microarray, micro-ELISA and UniCAP system suggested that the 2S albumins from soybean are not major allergens within the patient population analyzed.

Transgenesis has less impact on the transcriptome of wheat grain than conventional breeding

Detailed global gene expression profiles have been obtained for a series of transgenic and conventionally bred wheat lines expressing additional genes encoding HMW (high molecular weight) subunits of glutenin, a group of endosperm-specific seed storage proteins known to determine dough strength and therefore bread-making quality. Differences in endosperm and leaf transcriptome profiles between untransformed and derived transgenic lines were consistently extremely small, when analysing plants containing either transgenes only, or also marker genes. Differences observed in gene expression in the endosperm between conventionally bred material were much larger in comparison to differences between transgenic and untransformed lines exhibiting the same complements of gluten subunits. These results suggest that the presence of the transgenes did not significantly alter gene expression and that, at this level of investigation, transgenic plants could be considered substantially equivalent to untransformed parental lines.

A metabolomic study of substantial equivalence of field-grown genetically modified wheat

The 'substantial equivalence' of three transgenic wheats expressing additional high-molecular-weight subunit genes and the corresponding parental lines (two lines plus a null transformant) was examined using metabolite profiling of samples grown in replicate field trials on two UK sites (Rothamsted, Hertfordshire and Long Ashton, near Bristol) for 3 years. Multivariate comparison of the proton nuclear magnetic resonance spectra of polar metabolites extracted with deuterated methanol-water showed a stronger influence of site and year than of genotype. Nevertheless, some separation between the transgenic and parental lines was observed, notably between the transgenic line B73-6-1 (which had the highest level of transgene expression) and its parental line L88-6. Comparison of the spectra showed that this separation resulted from increased levels of maltose and/or sucrose in this transgenic line, and that differences in free amino acids were also apparent. More detailed studies of the amino acid composition of material grown in 2000 were carried out using gas chromatography-mass spectrometry. The most noticeable difference was that the samples grown at Rothamsted consistently contained larger amounts of acidic amino acids (glutamic, aspartic) and their amides (glutamine, asparagine). In addition, the related lines, L88-6 and B73-6-1, both contained larger amounts of proline and gamma-aminobutyric acid when grown at Long Ashton than at Rothamsted. The results clearly demonstrate that the environment affects the metabolome and that any differences between the control and transgenic lines are generally within the same range as the differences observed between the control lines grown on different sites and in different years.

Aphid alarm pheromone produced by transgenic plants affects aphid and parasitoid behavior

The alarm pheromone for many species of aphids, which causes dispersion in response to attack by predators or parasitoids, consists of the sesquiterpene (E)-beta-farnesene (Ebetaf). We used high levels of expression in Arabidopsis thaliana plants of an Ebetaf synthase gene cloned from Mentha x piperita to cause emission of pure Ebetaf. These plants elicited potent effects on behavior of the aphid Myzus persicae (alarm and repellent responses) and its parasitoid Diaeretiella rapae (an arrestant response). Here, we report the transformation of a plant to produce an insect pheromone and demonstrate that the resulting emission affects behavioral responses at two trophic levels.

Comparative field performance over 3 years and two sites of transgenic wheat lines expressing HMW subunit transgenes

A series of transgenic wheat lines expressing additional high molecular weight (HMW) subunit genes and the corresponding control lines were grown in replicate field trials at two UK sites (Rothamsted Research, approximately 50 km north of London and Long Ashton, near Bristol) over 3 years (1998, 1999, 2000), with successive generations of the transgenic lines (T3, T4, T5) being planted. Four plots from each site were used to determine grain dry weight, grain nitrogen, dough strength (measured as peak resistance by Mixograph analysis) and the expression levels of the endogenous and "added" subunits. Detailed statistical analyses showed that the transgenic and non-transgenic lines did not differ in terms of stability of HMW subunit gene expression or in stability of grain nitrogen, dry weight or dough strength, either between the 3 years or between sites and plots. These results indicate that the transgenic and control lines can be regarded as substantially equivalent in terms of stability of gene expression between generations and environments.

Comparison of Repetitive Sequences Derived from High Molecular Weight Subunits of Wheat Glutenin, an Elastomeric Plant Protein

A strategy has been developed to create repetitive peptides incorporating substitutions in the PGQGQQGYYPTSLQQ consensus repeat sequence of high molecular weight subunits in order to investigate natural sequence variations in elastomeric proteins of wheat gluten. After introduction of glutamic and aspartic acid residues, the peptide behaved similarly to the unmodified form at low pH, but became readily water soluble at pH > 6. Substitution of Gln for Leu at position 13 resulted in only small changes to the secondary structure of the water-insoluble peptides, as did Tyr8His and Thr11Ala. The effects of proline substitutions depended on their location: Leu13Pro substitution had little effect on solubility and structure, but Gln6Pro substitution resulted in dramatic changes. Peptides with two Gln6Pro substitutions had similar properties to the water-insoluble parental peptide, but those with 6 or 10 substitutions were readily soluble. The results indicated that specific sequences influence noncovalent intermolecular interactions in wheat gluten proteins.

Nanomechanical force measurements of gliadin protein interactions

The strength and nature of interactions between monomeric gliadin proteins involving alpha-alpha, omega-omega, and alpha-omega interactions in 0.01M acetic acid, and the effect of urea has been investigated. It was shown by means of nanomechanical force measurements that the stretching events in the separation curve after adhesive phenomena originated from proteins. These stretching events displayed different responses of the alpha- and omega-gliadins to urea. While 2M urea caused the more globular alpha-gliadins to unfold, the beta-turn-rich omega-gliadins remained fairly stable even in 8M urea. This suggests different roles for gliadins in the formation of dough; while the omega-gliadins are still in a compact structure being responsible for the viscous flow, the alpha-gliadins have already started to participate in forming the network in dough.