Transcript profiles of genes expressed in endosperm tissue are altered by high temperature during wheat grain development

Genetic variation for terminal heat stress tolerance in winter wheat

In many regions worldwide wheat (Triticum aestivum L.) plants experience terminal high temperature stress during the grain filling stage, which is a leading cause for single seed weight decrease and consequently for grain yield reduction. An approach to mitigate high temperature damage is to develop tolerant cultivars using the conventional breeding approach which involves identifying tolerant lines and then incorporating the tolerant traits in commercial varieties. In this study, we evaluated the terminal heat stress tolerance of 304 diverse elite winter wheat lines from wheat breeding programs in the US, Australia, and Serbia in controlled environmental conditions. Chlorophyll content and yield traits were measured and calculated as the percentage of non-stress control. The results showed that there was significant genetic variation for chlorophyll retention and seed weight under heat stress conditions. The positive correlation between the percent of chlorophyll content and the percent of single seed weight was significant. Two possible mechanisms of heat tolerance during grain filling were proposed. One represented by wheat line OK05723W might be mainly through the current photosynthesis since the high percentage of single seed weight was accompanied with high percentages of chlorophyll content and high shoot dry weight, and the other represented by wheat Line TX04M410164 might be mainly through the relocation of reserves since the high percentage of single seed weight was accompanied with low percentages of chlorophyll content and low shoot dry weight under heat stress. The tolerant genotypes identified in this study should be useful for breeding programs after further validation.

Heat shock exposure during early wheat grain development can reduce maximum endosperm cell number but not necessarily final grain dry mass

Post-anthesis heat shocks, which are expected to increase in frequency under climate change, may affect wheat grain development and lead to significant decreases in grain yield. Grain development occurs in three phases, the lag-phase, the filling-phase, and maturation. The growth of the three main compartments of the grain (outer layers (OLs), endosperm, embryo) is staggered, so that heat shocks affect time- and tissue-specific growth processes differentially depending on their timing. We hypothesized that heat shocks during the lag-phase may reduce final grain size, resulting from a reduction in endosperm cell number and/or a restricted OLs growth. Plants were heated for four consecutive days during the lag-phase or the filling-phase or both phases (lag- and filling-). Heat shocks consisted in four hours a day at 38°C and 21°C for the rest of the day. Controlled plants were maintained at 21/14°C (day/night). For each temperature treatment, kinetics of whole grain and compartment masses and dimensions were measured as well as the endosperm cell number. An early heat shock reduced endosperm cell proliferation. However, the growth patterns neither of endosperm nor of OLs were modified compared to controls, resulting in no differences in final grain size. Furthermore, compared to controls, a single heat shock during the filling-phase reduced both the duration and rate of dry mass accumulation into grains, whereas two consecutive shocks reduced the duration but enhanced the rate of dry mass of accumulation, even when endosperm cell number was reduced. The mean endosperm cell size was shown to be larger after early heat shocks. All together, these results suggest a compensatory mechanism exists to regulate endosperm cell size and number. This process might be a new mechanistic target for molecular studies and would improve our understanding of post-anthesis wheat tolerance to heat-shocks.

Amylase Trypsin Inhibitors (ATIs) in a Selection of Ancient and Modern Wheat: Effect of Genotype and Growing Environment on Inhibitory Activities

Wheat amylase-trypsin inhibitors (ATIs) are a family of plant defense proteins with an important role in human health for their involvement in allergies, celiac disease and non-celiac wheat sensitivity. Information about the differences in ATI activities among wheat genotypes and the influence of the growing environment is scarce. Therefore, ten selected wheat accessions with different ploidy level and year of release, previously characterized for their ATI gene sequences, were grown during three consecutive crop years at two growing areas and used for in vitro ATI activities. The contributions of the genotype and the crop year were significant for both activities. The hexaploid wheat genotypes showed the highest inhibitory activities. Einkorn had a peculiar behavior showing the lowest alpha-amylase inhibitory activity, but the highest trypsin inhibitory activity. It was not possible to observe any trend in ATI activities as a function of the release year of the wheat samples. The two inhibitory activities were differently affected by the growing conditions and were negatively correlated with the protein content. This information can be important in understanding the extent of variation of ATI inhibitory properties in relation to the wheat genotype and the growing environment and the impact of ATIs, if any, on human health and nutrition.

Grain Transcriptome Dynamics Induced by Heat in Commercial and Traditional Bread Wheat Genotypes

High temperature (HT) events have negative impact on wheat grains yield and quality. Transcriptome profiles of wheat developing grains of commercial genotypes (Antequera and Bancal) and landraces (Ardito and Magueija) submitted to heatwave-like treatments during grain filling were evaluated. Landraces showed significantly more differentially expressed genes (DEGs) and presented more similar responses than commercial genotypes. DEGs were more associated with transcription and RNA and protein synthesis in Antequera and with metabolism alterations in Bancal and landraces. Landraces upregulated genes encoding proteins already described as HT responsive, like heat shock proteins and cupins. Apart from the genes encoding HSP, two other genes were upregulated in all genotypes, one encoding for Adenylate kinase, essential for the cellular homeostasis, and the other for ferritin, recently related with increased tolerance to several abiotic stress in Arabidopsis. Moreover, a NAC transcription factor involved in plant development, known to be a negative regulator of starch synthesis and grain yield, was found to be upregulated in both commercial varieties and downregulated in Magueija landrace. The detected diversity of molecular processes involved in heat response of commercial and traditional genotypes contribute to understand the importance of genetic diversity and relevant pathways to cope with these extreme events.

Feeling the heat: developmental and molecular responses of wheat and barley to high ambient temperatures

The increasing demand for global food security in the face of a warming climate is leading researchers to investigate the physiological and molecular responses of cereals to rising ambient temperatures. Wheat and barley are temperate cereals whose yields are adversely affected by high ambient temperatures, with each 1 °C increase above optimum temperatures reducing productivity by 5-6%. Reproductive development is vulnerable to high-temperature stress, which reduces yields by decreasing grain number and/or size and weight. In recent years, analysis of early inflorescence development and genetic pathways that control the vegetative to floral transition have elucidated molecular processes that respond to rising temperatures, including those involved in the vernalization- and photoperiod-dependent control of flowering. In comparison, our understanding of genes that underpin thermal responses during later developmental stages remains poor, thus highlighting a key area for future research. This review outlines the responses of developmental genes to warmer conditions and summarizes our knowledge of the reproductive traits of wheat and barley influenced by high temperatures. We explore ways in which recent advances in wheat and barley research capabilities could help identify genes that underpin responses to rising temperatures, and how improved knowledge of the genetic regulation of reproduction and plant architecture could be used to develop thermally resilient cultivars.

High post-anthesis temperature effects on bread wheat (Triticum aestivum L.) grain transcriptome during early grain-filling

BACKGROUND

High post-anthesis (p.a) temperatures reduce mature grain weights in wheat and other cereals. However, the causes of this reduction are not entirely known. Control of grain expansion by the maternally derived pericarp of the grain has previously been suggested, although this interaction has not been investigated under high p.a. temperatures. Down-regulation of pericarp localised genes that regulate cell wall expansion under high p.a. temperatures may limit expansion of the encapsulated endosperm due to a loss of plasticity in the pericarp, reducing mature grain weight. Here the effect of high p.a. temperatures on the transcriptome of the pericarp and endosperm of the wheat grain during early grain-filling was investigated via RNA-Seq and is discussed alongside grain moisture dynamics during early grain development and mature grain weight.

RESULTS

High p.a. temperatures applied from 6-days after anthesis (daa) and until 18daa reduced the grain's ability to accumulate water, with total grain moisture and percentage grain moisture content being significantly reduced from 14daa onwards. Mature grain weight was also significantly reduced by the same high p.a. temperatures applied from 6daa for 4-days or more, in a separate experiment. Comparison of our RNA-Seq data from whole grains, with existing data sets from isolated pericarp and endosperm tissues enabled the identification of subsets of genes whose expression was significantly affected by high p.a. temperature and predominantly expressed in either tissue. Hierarchical clustering and gene ontology analysis resulted in the identification of a number of genes implicated in the regulation of cell wall expansion, predominantly expressed in the pericarp and significantly down-regulated under high p.a. temperatures, including endoglucanase, xyloglucan endotransglycosylases and a β-expansin. An over-representation of genes involved in the 'cuticle development' functional pathway that were expressed in the pericarp and affected by high p.a. temperatures was also observed.

CONCLUSIONS

High p.a. temperature induced down-regulation of genes involved in regulating pericarp cell wall expansion. This concomitant down-regulation with a reduction in total grain moisture content and grain weight following the same treatment period, adds support to the theory that high p.a. temperatures may cause a reduction in mature grain weight as result of decreased pericarp cell wall expansion.

Association and genome analyses to propose putative candidate genes for malt quality traits

BACKGROUND

We studied the genetics of nine malt quality traits using association genetics in a panel of North Dakota, ICARDA, and Ethiopian barley lines. Grain samples harvested from Bekoji in 2011 and 2012 were used.

RESULTS

The mapping panel revealed strong population structure explained by inflorescence-type, geographic origin, and breeding history. North Dakota germplasm were superior in malt quality traits and they can be donors to improve malt quality properties. We identified 106 marker-trait associations (MTAs) for the nine traits, representing 81 genomic regions across all barley chromosomes. Chromosomes 3H, 5H, and 7H contained most of the MTAs (58.5%). Nearly 18.5% of these genomic regions contained two to three malt quality traits. Within ±250 kb of 81 genomic regions, we recovered 348 barley genes, with some potential impacting malt quality. These include invertase, β-fructofuranosidase, α-glucosidase, serine carboxypeptidase, and bidirectional sugar transporter SWEET14-like protein. Eighteen of these genes were also previously reported in the Hordeum Toolbox, and 17 of them highly expressed during the germination process.

CONCLUSION

The results from this study invite further follow-up functional characterization experiments to relate the genes with individual malt quality traits with higher confidence. It also provides germplasm resources for malt barley improvement. © 2018 Society of Chemical Industry.

Genome-Wide Association Studies to Identify Loci and Candidate Genes Controlling Kernel Weight and Length in a Historical United States Wheat Population

Although kernel weight (KW) is a major component of grain yield, its contribution to yield genetic gain during breeding history has been minimal. This highlights an untapped potential for further increases in yield via improving KW. We investigated variation and genetics of KW and kernel length (KL) via genome-wide association studies (GWAS) using a historical and contemporary soft red winter wheat population representing 200 years of selection and breeding history in the United States. The observed changes of KW and KL over time did not show any conclusive trend. The population showed a structure, which was mainly explained by the time and location of germplasm development. Cluster sharing by germplasm from more than one breeding population was suggestive of episodes of germplasm exchange. Using 2 years of field-based phenotyping, we detected 26 quantitative trait loci (QTL) for KW and 27 QTL for KL with -log₁₀(p) > 3.5. The search for candidate genes near the QTL on the wheat genome version IWGSCv1.0 has resulted in over 500 genes. The predicted functions of several of these genes are related to kernel development, photosynthesis, sucrose and starch synthesis, and assimilate remobilization and transport. We also evaluated the effect of allelic polymorphism of genes previously reported for KW and KL by using Kompetitive Allele Specific PCR (KASP) markers. Only TaGW2 showed significant association with KW. Two genes, i.e., TaSus2-2B and TaGS-D1 showed significant association with KL. Further physiological studies are needed to decipher the involvement of these genes in KW and KL development.

Molecular characterization and evolutionary origins of farinin genes in Brachypodium distachyon L

Farinins are one of the oldest members of the gluten family in wheat and Aegilops species, and they influence dough properties. Here, we performed the first detailed molecular genetic study on farinin genes in Brachypodium distachyon L., the model species for Triticum aestivum. A total of 51 b-type farinin genes were cloned and characterized, including 27 functional and 24 non-functional pseudogenes from 14 different B. distachyon accessions. All genes were highly similar to those previously reported from wheat and Aegilops species. The identification of deduced amino acid sequences showed that b-type farinins across Triticeae genomes could be classified as b1-, b2-, b3-, and b4-type farinins; however, B. distachyon had only b3- and b4-type farinins. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) revealed that farinin genes are transcribed into mRNA in B. distachyon at much lower levels than in Triticeae, despite the presence of cis-acting elements in promoter regions. Phylogenetic analysis suggested that Brachypodium farinins may have closer relationships with common wheat and further confirmed four different types of b-type farinins in Triticeae and Brachypodium genomes, corresponding to b1, b2, b3 (group 1), and b4 (group 2). A putative evolutionary origin model of farinin genes in Brachypodium, Triticum, and the related species suggests that all b-type farinins diverged from their common ancestor ~3.2 million years ago (MYA). The b3 and b4 types could be considered older in the farinin family. The results explain the loss of b1- and b2-type farinin alleles in Brachypodium.

Differential Expression of Durum Wheat Gluten Proteome under Water Stress during Grain Filling

Environmental stress during grain filling may affect wheat protein composition, thus influencing its final quality. A proteomic approach was used to evaluate changes in storage protein composition under water stress of two Italian durum wheat (Triticum turgidum ssp. durum) cultivars, Ciccio and Svevo. The high-molecular-weight glutenin region increased progressively in both cultivars and under two water regimens. The L48-35 region, corresponding to low-molecular-weight (LMW) glutenin subunits, increased slightly during grain development and decreased under water stress in both cultivars. In particular, an s-type LMW related to superior technological quality was down-expressed in the early-mid period in Svevo and in the mid-late period in Ciccio. Finally, the L<35 region, corresponding to gliadin-like proteins, decreased slightly during grain development and increased under stress in both cultivars. Several α-gliadins, associated with immunological potential, increased their expression under water stress, especially in Svevo in the early-mid stage of grain filling.

Thermal stress effects on grain yield in Brachypodium distachyon occur via H2A.Z-nucleosomes

BACKGROUND

Crop plants are highly sensitive to ambient temperature, with a 1 ºC difference in temperature sufficient to affect development and yield. Monocot crop plants are particularly vulnerable to higher temperatures during the reproductive and grain-filling phases. The molecular mechanisms by which temperature influences grain development are, however, unknown. In Arabidopsis thaliana, H2A.Z-nucleosomes coordinate transcriptional responses to higher temperature. We therefore investigated whether the effects of high temperature on grain development are mediated by H2A.Z-nucleosomes.

RESULTS

We have analyzed the thermal responses of the Pooid grass, Brachypodium distachyon, a model system for crops. We find that H2A.Z-nucleosome occupancy is more responsive to increases in ambient temperature in the reproductive tissue of developing grains compared withvegetative seedlings. This difference correlates with strong phenotypic responses of developing grain to increased temperature, including early maturity and reduced yield. Conversely, temperature has limited impact on the timing of transition from the vegetative to generative stage, with increased temperature unable to substitute for long photoperiod induction of flowering. RNAi silencing of components necessary for H2A.Z-nucleosome deposition is sufficient to phenocopythe effects of warmer temperature on grain development.

CONCLUSIONS

H2A.Z-nucleosomes are important in coordinating the sensitivity of temperate grasses to increased temperature during grain development. Perturbing H2A.Z occupancy, through higher temperature or genetically, strongly reduces yield. Thus, we provide a molecular understanding of the pathways through which high temperature impacts on yield. These findings may be useful for breeding crops resilient to thermal stress.

Molecular mechanisms of HMW glutenin subunits from 1S(l) genome of Aegilops longissima positively affecting wheat breadmaking quality

A wheat cultivar “Chinese Spring” chromosome substitution line CS-1S^l(1B), in which the 1B chromosome was substituted by 1S^l from Aegilops longissima, was developed and found to possess superior dough and breadmaking quality. The molecular mechanism of its super quality conformation is studied in the aspects of high molecular glutenin genes, protein accumulation patterns, glutenin polymeric proteins, protein bodies, starch granules, and protein disulfide isomerase (PDI) and PDI-like protein expressions. Results showed that the introduced HMW-GS 1S^l×2.3* and 1S^ly16* in the substitution line possesses long repetitive domain, making both be larger than any known x- and y-type subunits from B genome. The introduced subunit genes were also found to have a higher level of mRNA expressions during grain development, resulting in more HMW-GS accumulation in the mature grains. A higher abundance of PDI and PDI-like proteins was observed which possess a known function of assisting disulfide bond formation. Larger HMW-GS deposited in protein bodies were also found in the substitution line. The CS substitution line is expected to be highly valuable in wheat quality improvement since the novel HMW-GS are located on chromosome 1S^l, making it possible to combine with the known superior D×5+Dy10 subunits encoded by Glu-D1 for developing high quality bread wheat.

Cloning, expression, and evolutionary analysis of α-gliadin genes from Triticum and Aegilops genomes

Fifteen novel α-gliadin genes were cloned and sequenced from Triticum and related Aegilops genomes by allele-specific polymerase chain reaction (AS-PCR). Sequence comparison displayed high diversities in the α-gliadin gene family. Four toxic epitopes and glutamine residues in the two polyglutamine domains facilitated these α-gliadins to be assigned to specific chromosomes. Five representative α-gliadin genes were successfully expressed in Escherichia coli, and their amount reached a maximum after 4 h induced by isopropyl-β-D-thiogalactoside (IPTG), indicating a high level of expression under the control of T7 promoter. The transcriptional expression of α-gliadin genes during grain development detected by quantitative real-time polymerase chain reaction (qRT-PCR) showed a similar up-down regulation pattern in different genotypes. A neighbor-joining tree constructed with both full-open reading frame (ORF) α-gliadin genes and pseudogenes further revealed the origin and phylogenetic relationships among Triticum and related Aegilops genomes. The evolutionary analysis demonstrated that α-gliadin genes evolved mainly by synonymous substitutions under strong purifying selection during the evolutionary process.

Identification and characterization of high temperature stress responsive genes in bread wheat (Triticum aestivum L.) and their regulation at various stages of development

To elucidate the effect of high temperature, wheat plants (Triticum aestivum cv. CPAN 1676) were given heat shock at 37 and 42°C for 2 h, and responsive genes were identified through PCR-Select Subtraction technology. Four subtractive cDNA libraries, including three forward and one reverse subtraction, were constructed from three different developmental stages. A total of 5,500 ESTs were generated and 3,516 high quality ESTs submitted to Genbank. More than one-third of the ESTs generated fall in unknown/no hit category upon homology search through BLAST analysis. Differential expression was confirmed by cDNA macroarray and by northern/RT-PCR analysis. Expression analysis of wheat plants subjected to high temperature stress, after 1 and 4 days of recovery, showed fast recovery in seedling tissue. However, even after 4 days, recovery was negligible in the developing seed tissue after 2 h of heat stress. Ten selected genes were analyzed in further detail including one unknown protein and a new heat shock factor, by quantitative real-time PCR in an array of 35 different wheat tissues representing major developmental stages as well as different abiotic stresses. Tissue specificity was examined along with cross talk with other abiotic stresses and putative signalling molecules.

Proteomic approaches for qualitative and quantitative characterisation of food allergens

Food allergy is an IgE-mediated hypersensitive reaction estimated to affect up to 4% of infants and adults in developed countries. Proteins termed allergens are mostly responsible for food allergic reactions, consisting of mild to severe systemic reactions. Proteomics include multi-dimensional separation and protein identification by mass spectrometry, followed by data analysis by bioinformatic tools. Proteomics have increasingly been used in the allergy field to (i) identify the genetic and phenotypic variability of allergens in crops, (ii) obtain well-characterised allergens as reported within the EC-funded Integrated Project EuroPrevall, (iii) detect and quantify allergens, either in their native form or in forms resulting from food processing, in complex foods such as bread, cookies, etc., as considered by the EC-funded MoniQA project. These approaches are helping to improve food allergy diagnosis, therapy, and allergenic risk assessment. In the future, the development of more cost effective and sensitive technologies will further enhance the value of proteomics to the allergy field allowing routine use of this approach. We review the applications of proteomics in the field of food allergy.

Transcriptomic analysis of starch biosynthesis in the developing grain of hexaploid wheat

The expression of genes involved in starch synthesis in wheat was analyzed together with the accumulation profiles of soluble sugars, starch, protein, and starch granule distribution in developing caryopses obtained from the same biological materials used for profiling of gene expression using DNA microarrays. Multiple expression patterns were detected for the different starch biosynthetic gene isoforms, suggesting their relative importance through caryopsis development. Members of the ADP-glucose pyrophosphorylase, starch synthase, starch branching enzyme, and sucrose synthase gene families showed different expression profiles; expression of some members of these gene families coincided with a period of high accumulation of starch while others did not. A biphasic pattern was observed in the rates of starch and protein accumulation which paralleled changes in global gene expression. Metabolic and regulatory genes that show a pattern of expression similar to starch accumulation and granule size distribution were identified, suggesting their coinvolvement in these biological processes.

Effect of environmental stress during grain filling on the soluble proteome of wheat (Triticum aestivum) dough liquor

The influence of genotype and environment on a soluble wheat dough liquor proteome was studied for four cultivars grown under field conditions and under hot/dry and cool/wet regimes by two-dimensional electrophoresis followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry or quadrupole time-of-flight mass spectrometry. Although the four cultivars had similar patterns, differences in the relative abundances of some components were observed. Similarly, some differences were observed between the control samples and the samples grown under cool/wet and hot/dry conditions. These included differences in the abundances of storage proteins belonging to the 7S globulin (vicilin-like) and alpha-globulin families and of protective proteins including members of the serpin, described as allergens, and chitinase families. A number of novel annotations were made as compared to previous work on the dough liquor of cv. Hereward, including two 19 kDa alpha-globulins, precursors of endochitinases A and C, and several polypeptides belonging to the 7S globulin (vicilin-like) family.

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.

The Triticum aestivum non-specific lipid transfer protein (TaLtp) gene family: comparative promoter activity of six TaLtp genes in transgenic rice

Plant non-specific lipid transfer proteins (nsLTPs) are encoded by a multigene family and support physiological functions, which remain unclear. We adapted an efficient ligation-mediated polymerase chain reaction (LM-PCR) procedure that enabled isolation of 22 novel Triticum aestivum nsLtp (TaLtp) genes encoding types 1 and 2 nsLTPs. A phylogenetic tree clustered the wheat nsLTPs into ten subfamilies comprising 1-7 members. We also studied the activity of four type 1 and two type 2 TaLtp gene promoters in transgenic rice using the 1-Glucuronidase reporter gene. The activities of the six promoters displayed both overlapping and distinct features in rice. In vegetative organs, these promoters were active in leaves and root vascular tissues while no beta-Glucuronidase (GUS) activity was detected in stems. In flowers, the GUS activity driven by the TaLtp7.2a, TaLtp9.1a, TaLtp9.2d, and TaLtp9.3e gene promoters was associated with vascular tissues in glumes and in the extremities of anther filaments whereas only the TaLtp9.4a gene promoter was active in anther epidermal cells. In developing grains, GUS activity and GUS immunolocalization data evidenced complex patterns of activity of the TaLtp7.1a, TaLtp9.2d, and TaLtp9.4a gene promoters in embryo scutellum and in the grain epicarp cell layer. In contrast, GUS activity driven by TaLtp7.2a, TaLtp9.1a, and TaLtp9.3e promoters was restricted to the vascular bundle of the embryo scutellum. This diversity of TaLtp gene promoter activity supports the hypothesis that the encoded TaLTPs possess distinct functions in planta.

Transcriptional profiling of wheat caryopsis development using cDNA microarrays

The expression of 7,835 genes in developing wheat caryopses was analyzed using cDNA arrays. Using a mixed model analysis of variance (ANOVA) method, 29% (2,237) of the genes on the array were identified to be differentially expressed at the 6 different time-points examined, which covers the developmental stages from coenocytic endosperm to physiological maturity. Comparison of genes differentially expressed between two time-points revealed a dynamic transcript accumulation profile with major re-programming events that occur at 3-7, 7-14 and 21-28 DPA. A k-means clustering algorithm grouped the differentially expressed genes into 10 clusters, revealing co-expression of genes involved in the same pathway such as carbohydrate and protein synthesis or preparation for desiccation. Functional annotation of genes that show peak expression at specific time-points correlated with the developmental events associated with the respective stages. Results provide information on the temporal expression during caryopsis development for a significant number of differentially expressed genes with unknown function.