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Analysis of hexaploid bread wheat homoeologous gene expression using nullisomic-tetrasomic lines. (A) Schematic illustrating the group 1 homoeologous chromosomes in hexaploid bread wheat, the derived nullisomic-tetrasomic lines and the A and D genome diploids. A single homoeologue-specific variant (HSV) diagnostic for each of A (red), B (blue) and D (green) homoeologous chromosomes is shown. (B) Two sets of three homoeologue-specific haplotypes of BE497595, a gene encoding a chloroplast thylakoidal peptidase-like protein and which has 24 HSVs (inverted triangles) diagnostic for either 5A (red), 5B (blue) or 5D (green) homoeologues. RNA-Seq reads are aligned to a degenerate reference sequence shown in grey containing genetic ambiguity codes at HSV locations. Double ended arrows illustrate candidate sequence regions for haplotype quantification. (C,D) RNA-Seq read frequencies from roots for the nullitetras and A and D genome diploids (C) and in two biological replicates of euploid wheat (D) for each homoeologue-specific haplotype given in the boxed region shown in (B). The homoeologous expression pattern in euploid wheat roots is indicated below the pie chart.
Source publication
Bread wheat (Triticum aestivum) has a large, complex and hexaploid genome consisting of A, B and D homoeologous chromosome sets. Therefore each wheat gene potentially exists as a trio of A, B and D homoeoloci, each of which may contribute differentially to wheat phenotypes. We describe a novel approach combining wheat cytogenetic resources (chromos...
Contexts in source publication
Context 1
... each nullitetra line, lack ('nulli') of one homoeologue is compensated by an extra set of either of the remaining homoeologous chromosomes, thus restoring the hexaploid state. For example, N1AT1B lacks chromo- some 1A but has two sets ('tetra') of chromosome 1B ( Figure 1A). The nullitetras have historically been used for determining presence of wheat genes on specific homoeo- logous chromosomes [59][60][61], and we reasoned that, in combination with next generation sequencing, they could be used to develop a systematic understanding of the relative contributions of individual homoeoloci to overall wheat gene expression. ...Context 2
... therefore obtained mRNA-Seq datasets [62] from non-normalized cDNA libraries created from shoot and root tissues of the euploid bread wheat cultivar Chinese Spring, from which the nullitetra lines are derived [58], from complete sets of chromosome 1 and 5 nullitetras, and from extant relatives of the diploid A (Triticum urartu) and D (Aegilops tauschii) genome donors, herein referred to as A and D genome diploids ( Figure 1A; see Additional file 1: Table S1). In the then absence of a T. aestivum genome sequence, we exploited an extensive wheat 'expressed sequence tags' (ESTs) resource to con- struct a reference transcriptome sequence (see Additional file 2: Table S2). ...Context 3
... ESTs from chromosomes 1 (1,123) and 5 (1,247), we created a wheat group 1 and 5 partial reference transcriptome consisting of 2,354 ESTs (see Methods). Since the mean length of these ESTs (hereafter referred to as 'genes') was 455 ± 133 bp (see Additional file 3: Figure S1), the genes in our reference are representative of fragments of sequence transcribed from entire genes in their subgenome of origin. Assuming the diploid wheat genome contains approximately ~32,000 genes [40], this reference set represents ~5-10% of the total wheat gene content. ...Context 4
... HSVs that were 'diagnostic' (i.e., specific) for a particular homoeolo- gue were confirmed by the presence of the diagnostic base at a particular site in all nullitetra lines except for those lines lacking the corresponding homoeologous chromo- some. For example, Figure 1A illustrates a notional ' A/ T' homoeologue-specific variant at the tip of the short arm of chromosome 1, where the A base is diagnostic for the A homoeologue, as distinct from the T base present on the B and D homoeologues. Such 'diagnostic' sequences were used to infer the expression (and there- fore presence) of a particular gene on a specific homo- eologous chromosome. ...Context 5
... next combined HSVs co-locating within a region of gene sequence less than the 51 base pair length of an individual sequence read to produce haplotypes. Figure 1B illustrates this process for BE497595, a gene with 24 HSVs distinguishing three homoeoloci on chro- mosomes 5A, 5B and 5D. The boxed region shows three homoeologue-specific haplotypes defined by two A- diagnostic HSVs and a single B-diagnostic HSV. ...Context 6
... three homoeolocus-specific haplotypes can be distin- guished, despite the absence either of individual 3-allele HSVs or 2-allele diagnostic HSVs for all three homoeo- loci. The homoeolocus-specificity of each haplotype is confirmed by its absence in the nullitetra line lacking the respective homoeologous chromosome and by its presence in all other samples ( Figure 1C), allowing esti- mation of the number of homoeoloci of an individual gene that are detectably expressed (e.g., exactly three A, B and D homoeoloci of gene BE497595; Figure 1D). For the majority of sequences, haplotypes in the diploids are identical to the corresponding homoeologous haplo- types in euploid wheat ( Figure 1C). ...Context 7
... three homoeolocus-specific haplotypes can be distin- guished, despite the absence either of individual 3-allele HSVs or 2-allele diagnostic HSVs for all three homoeo- loci. The homoeolocus-specificity of each haplotype is confirmed by its absence in the nullitetra line lacking the respective homoeologous chromosome and by its presence in all other samples ( Figure 1C), allowing esti- mation of the number of homoeoloci of an individual gene that are detectably expressed (e.g., exactly three A, B and D homoeoloci of gene BE497595; Figure 1D). For the majority of sequences, haplotypes in the diploids are identical to the corresponding homoeologous haplo- types in euploid wheat ( Figure 1C). ...Context 8
... homoeolocus-specificity of each haplotype is confirmed by its absence in the nullitetra line lacking the respective homoeologous chromosome and by its presence in all other samples ( Figure 1C), allowing esti- mation of the number of homoeoloci of an individual gene that are detectably expressed (e.g., exactly three A, B and D homoeoloci of gene BE497595; Figure 1D). For the majority of sequences, haplotypes in the diploids are identical to the corresponding homoeologous haplo- types in euploid wheat ( Figure 1C). ...Context 9
... we could not be certain that each homoeolocus exists in single copy on each homoeologous chromosome, we could assess the relative contribution from each homoeologous subgenome. To do this we aligned reads using novoalign [64] to a degenerative ref- erence sequence (shown in grey in Figure 1B). For se- quence regions with exactly three homoeologue-specific haplotypes, for example those marked by arrows in Figure 1B, reads with A, B and D sequences were quan- tified and compared using chi-square to a 1:1:1 expect- ation. ...Context 10
... do this we aligned reads using novoalign [64] to a degenerative ref- erence sequence (shown in grey in Figure 1B). For se- quence regions with exactly three homoeologue-specific haplotypes, for example those marked by arrows in Figure 1B, reads with A, B and D sequences were quan- tified and compared using chi-square to a 1:1:1 expect- ation. Regions with more than three haplotypes were ignored as they most likely contained additional sequence alignments from paralogous genes. ...Context 11
... such genes, we combined the two replicates for ana- lysis of the significance of differential expression in each tissue (see Additional file 9: Table S3). For example, in Figure 1D, BE497595 showed a 'B > A = D' pattern in roots for both replicates in both illustrated regions with three homoeolocus-specific haplotypes. This pattern was signifi- cant at p < .001, ...Context 12
... observed highly similar homoeo- locus expression patterns from the two replicates of each tissue, with less than 7% of 'unknown' cases in either shoots (14/217 genes) or roots (15/249 genes) caused by conflicting patterns of expression. Note that while we do not focus on the expression of homoeoloci in the nullitetras here, Figure 1C shows that for BE497595, all the nullitetras except for N5BT5A show an expression pattern consistent with a dosage response to the extra copies of the 'tetra' genome. N5BT5A shows the oppos- ite response, a negative dosage compensation in which the contribution from the 'tetra' genome (A) is lower than that of the other 'diploid' genome (D). ...Context 13
... homoeoloci contribute disproportionately to wheat gene expression B subgenome homoeoloci not only exceed A or D homo- eoloci in number but also contribute more to the bread wheat transcriptome ( Figure 3C). Significantly more genes are expressed from B homoeoloci of groups 1 or 5 than from either A or D homoeoloci, both in shoots (A(1,134), B (1,205), D (1,110), chi-square, p = .046) and in roots (A(1,188), B(1,262), D(1,158), p = .036). ...Context 14
... more genes are expressed from B homoeoloci of groups 1 or 5 than from either A or D homoeoloci, both in shoots (A(1,134), B (1,205), D (1,110), chi-square, p = .046) and in roots (A(1,188), B(1,262), D(1,158), p = .036). Among genes expressed from a single homoeolocus, significantly more are expressed from B (6-10% genes) than from ei- ther A or D chromosomes (4-6% genes), both in shoots ( Figure 3C, chi-square, p = .013 ...Similar publications
Storage proteins of wheat, rye, barley and, to a lesser extent, oats contain epitopes responsible for triggering the celiac disease (CD). In recent decades an increased frequency of CD has been observed, and though the reasons for this increase are unclear, modern plant breeding has attracted criticism attributing to the new varieties a part of the...
Citations
... It belongs to the Triticeae tribe, which also includes barley, rye, and triticale. Among the species, wheat has the largest and most complex hexaploid genome (2n = 6x = 42), which consists of the three homoeologous subgenomes A, B, and D. Each gene present as homologues A, B, and D could retain its original function or, as a result of independent evolution, develop heterogeneous expression, and/or one or two copies may be silenced or deleted [2,3]. ...
Members of the TaCKX gene family (GFMs) encode the cytokinin oxygenase/dehydrogenase enzyme (CKX), which irreversibly degrades cytokinins in the organs of wheat plants; therefore, these genes perform a key role in the regulation of yield-related traits. The purpose of the investigation was to determine how expression patterns of these genes, together with the transcription factor-encoding gene TaNAC2-5A, and yield-related traits are inherited to apply this knowledge to speed up breeding processes. The traits were tested in 7 days after pollination (DAP) spikes and seedling roots of maternal and paternal parents and their F2 progeny. The expression levels of most of them and the yield were inherited in F2 from the paternal parent. Some pairs or groups of genes cooperated, and some showed opposite functions. Models of up- or down-regulation of TaCKX GFMs and TaNAC2-5A in low-yielding maternal plants crossed with higher-yielding paternal plants and their high-yielding F2 progeny reproduced gene expression and yield of the paternal parent. The correlation coefficients between TaCKX GFMs, TaNAC2-5A, and yield-related traits in high-yielding F2 progeny indicated which of these genes were specifically correlated with individual yield-related traits. The most common was expressed in 7 DAP spikes TaCKX2.1, which positively correlated with grain number, grain yield, spike number, and spike length, and seedling root mass. The expression levels of TaCKX1 or TaNAC2-5A in the seedling roots were negatively correlated with these traits. In contrast, the thousand grain weight (TGW) was negatively regulated by TaCKX2.2.2, TaCKX2.1, and TaCKX10 in 7 DAP spikes but positively correlated with TaCKX10 and TaNAC2-5A in seedling roots. Transmission of TaCKX GFMs and TaNAC2-5A expression patterns and yield-related traits from parents to the F2 generation indicate their paternal imprinting. These newly shown data of nonmendelian epigenetic inheritance shed new light on crossing strategies to obtain a high-yielding F2 generation.
... Gene disruption compared to their orthologous counterparts, premature stop codons, and other factors can cause gene losses [42] and rapid genome reorganization during polyploidization and diploidization processes [43][44][45]. Previous studies have indicated that polyploidization events may result in the loss of homologous genes or changes in gene expression levels, or both [46][47][48][49]. Within four phylogenetic clades, phylogenetic analysis revealed considerable similarity and monophyletic distribution among Gossypium species, which may support the conservative evolution style of PC genes. ...
Phytocyanins (PCs) are a class of plant-specific blue copper proteins that have been
demonstrated to play a role in electron transport and plant development. Through analysis of
the copper ligand residues, spectroscopic properties, and domain architecture of the protein, PCs
have been grouped into four subfamilies: uclacyanins (UCs), stellacyanins (SCs), plantacyanins
(PLCs), and early nodulin-like proteins (ENODLs). The present study aimed to identify and charac�terise the PCs present in three distinct cotton species (Gossypium hirsutum, Gossyium arboreum, and
Gossypium raimondii) through the identification of 98, 63, and 69 genes respectively. We grouped PCs
into four clades by using bioinformatics analysis and sequence alignment, which exhibit variations
in gene structure and motif distribution. PCs are distributed across all chromosomes in each of the
three species, with varying numbers of exons per gene and multiple conserved motifs, and with a
minimum of 1 and maximum of 11 exons found on one gene. Transcriptomic data and qRT-PCR
analysis revealed that two highly differentiated PC genes were expressed at the fibre initiation stage,
while three highly differentiated PCs were expressed at the fibre elongation stage. These findings
serve as a foundation for further investigations aimed at understanding the contribution of this gene
family in cotton fibre production.
... The increased production of cereals such as wheat is urgently needed to meet the demand gap for global food supply by the year 2050 (Tester and Langridge, 2010) when 60%-70% increase in the food production is required to feed the projected rapid increase in population (Silva, 2018). Allohexaploid bread wheat (Triticum aestivum, 2n = 6x = 42, AABBDD) is of relatively recent origin, having evolved ~8,500 years ago following two separate interspecific hybridization events involving three diploid donor species (n = 7; Leach et al., 2014). First, the tetraploid (pasta) wheat (T. ...
Transposable elements (TEs) constitute ~80% of the complex bread wheat genome and contribute significantly to wheat evolution and environmental adaptation. We studied 52 TE insertion polymorphism markers to ascertain their efficiency as a robust DNA marker system for genetic studies in wheat and related species. Significant variation was found in miniature inverted-repeat transposable element (MITE) insertions in relation to ploidy with the highest number of “full site” insertions occurring in the hexaploids (32.6 ± 3.8), while the tetraploid and diploid progenitors had 22.3 ± 0.6 and 15.0 ± 3.5 “full sites,” respectively, which suggested a recent rapid activation of these transposons after the formation of wheat. Constructed phylogenetic trees were consistent with the evolutionary history of these species which clustered mainly according to ploidy and genome types (SS, AA, DD, AABB, and AABBDD). The synthetic hexaploids sub-clustered near the tetraploid species from which they were re-synthesized. Preliminary genotyping in 104 recombinant inbred lines (RILs) showed predominantly 1:1 segregation for simplex markers, with four of these markers already integrated into our current DArT-and SNP-based linkage map. The MITE insertions also showed stability with no single excision observed. The MITE insertion site polymorphisms uncovered in this study are very promising as high-potential evolutionary markers for genomic studies in wheat.
... Combining of the three subgenomes of wheat during polyploidization resulted in chromatin and DNA methylation changes that correlate with altered gene expression (Yuan et al., 2020). Leach et al. observed that~55% of the wheat genes are expressed either from one or two homeoloci through a combination of extensive transcriptional silencing and homoeolocus loss (Leach et al., 2014). Similarly, Gardiner et al. observed differential methylation between the three subgenomes of wheat and a correlation between the subgenomespecific promoter methylation and decreased gene expression levels (Gardiner et al., 2015). ...
Transcriptional gene silencing (TGS) can offer a straightforward tool for functional analysis of plant genes, particularly in polyploid species such as wheat, where genetic redundancy poses a challenge in applying mutagenesis approaches, including CRISPR gene editing. In this study, we demonstrate efficient TGS in wheat, mediated by constitutive RNA expression of a promoter inverted repeat (pIR). pIR‐mediated TGS of two anther‐specific genes, TaMs45 and TaMs1, abolished their function resulting in male sterility. While TGS of TaMs45 required transcriptional silencing of all three homeologs, a B‐genome specific pIR for TaMs1 was sufficient to confer male sterility. We further show that the pIRs effect TGS of TaMs45 gene through DNA methylation of homologous promoter sequence, successfully suppressing transcription of all three homeologs. Applying pIR‐mediated TGS in wheat, we have generated a dominant male fertility system for production of hybrid seed and demonstrated the efficacy of this system under greenhouse and field conditions. This report describes the first successful TGS in wheat, while providing a dominant negative approach as alternative to gene knockout strategies for hybrid wheat breeding and seed production.
... Our results showed that the m 6 A methylation of peaks and peak-related genes on different sub-genomes (A, B, D) are different in wheat grain different developmental stages, which is similar to genome-specific DNA methylation (Gardiner et al. 2015). Several studies showed differential expression across the three sub-genomes, with as much as onethird of genes being ascribed to expression from only one of the sub-genomes (Leach et al. 2014). Leach et al. (2014) observed that B sub-genome homoeoloci not only exceed A or D homoeoloci in number but also contribute more to the bread wheat transcriptome and concluded that B-genome homoeoloci tend to contribute more to wheat gene expression than do A or D genome homoeoloci in wheat root and shoot tissues. ...
... Several studies showed differential expression across the three sub-genomes, with as much as onethird of genes being ascribed to expression from only one of the sub-genomes (Leach et al. 2014). Leach et al. (2014) observed that B sub-genome homoeoloci not only exceed A or D homoeoloci in number but also contribute more to the bread wheat transcriptome and concluded that B-genome homoeoloci tend to contribute more to wheat gene expression than do A or D genome homoeoloci in wheat root and shoot tissues. It was reported that the numbers of high confidence protein-coding genes were nearly equal on the three subgenomes, pseudogenes were obviously highest on B, followed by on A and D subgenome in hexaploid wheat (Guan et al. 2020). ...
Main conclusion
More methylation changes occur in late interval than in early interval of wheat seed development with protein and the starch synthesis-related pathway enriched in the later stages.
Abstract
Wheat seed development is a critical process to determining wheat yield and quality, which is controlled by genetics, epigenetics and environments. The N6-methyladenosine (m⁶A) modification is a reversible and dynamic process and plays regulatory role in plant development and stress responses. To better understand the role of m⁶A in wheat grain development, we characterized the m⁶A modification at 10 day post-anthesis (DPA), 20 DPA and 30 DPA in wheat grain development. m⁶A-seq identified 30,615, 30,326, 27,676 high confidence m⁶A peaks from the 10DPA, 20DPA, and 30DPA, respectively, and enriched at 3'UTR. There were 29,964, 29,542 and 26,834 unique peaks identified in AN0942_10d, AN0942_20d and AN0942_30d. One hundred and forty-two genes were methylated by m⁶A throughout seed development, 940 genes methylated in early grain development (AN0942_20d vs AN0942_10d), 1542 genes in late grain development (AN0942_30d vs AN0942_20d), and 1190 genes between early and late development stage (AN0942_30d vs AN0942_10d). KEGG enrichment analysis found that protein-related pathways and the starch synthesis-related pathway were significantly enriched in the later stages of seed development. Our results provide novel knowledge on m⁶A dynamic changes and its roles in wheat grain development.
... Gene losses can be the result of premature stop codon, disruption of genes as compared to their orthologous [37], and rapid genome re-organization during polyploidization and diploidization process [38][39][40]. Previous studies have evidenced that polyploidization processes may result in losing of homologous members or altered expression profiles of the homologous genes or both [31,[41][42][43]. Similar phenomenon was noticed in the expression profiling of homologous OMT genes between A t and D t in G. hirsutum, which clued that these genes might have experienced abovementioned events during evolution processes. ...
Background: O-methyltransferases (OMTs) are an important group of enzymes that catalyze the transfer of a methyl group from S-adenosyl-L-methionine to their acceptor substrates. OMTs are divided into several groups according to their structural features. In Gossypium species, they are involved in phenolics and flavonoid pathways. Phenolics defend the cellulose fiber from dreadful external conditions of biotic and abiotic stresses, promoting strength and growth of plant cell wall. Results: An OMT gene family, containing a total of 192 members, has been identified and characterized in three main Gossypium species, G. hirsutum, G. arboreum and G. raimondii. Cis-regulatory elements analysis suggested important roles of OMT genes in growth, development, and defense against stresses. Transcriptome data of different fiber developmental stages in Chromosome Substitution Segment Lines (CSSLs), Recombination Inbred Lines (RILs) with excellent fiber quality, and standard genetic cotton cultivar TM-1 demonstrate that up-regulation of OMT genes at different fiber developmental stages, and abiotic stress treatments have some significant correlations with fiber quality formation, and with salt stress response. Quantitative RT-PCR results revealed that GhOMT10_Dt and GhOMT70_At genes had a specific expression in response to salt stress while GhOMT49_At, GhOMT49_Dt, and GhOMT48_At in fiber elongation and secondary cell wall stages. Conclusions: Our results indicate that O-methyltransferase genes have multi-responses to salt stress and fiber development in Gossypium species and that they may contribute to salt tolerance or fiber quality formation in Gossypium.
... Incomplete compensation is generally presumed to occur between the different homeologous sub-genomes of wheat (Leach et al., 2014). However, in our study, we found that the compensatory transcriptional effects following chromosome substitution were detectable across homeologous chromosomes from the intact sub-genomes as well as in almost all the other wheat chromosomes (Figure 1D). ...
Even frequently used in wheat breeding, we still have an insufficient understanding of the biology of the products via distant hybridization. In this study, a transcriptomic analysis was performed for six Triticum aestivum-Thinopyrum elongatum substitution lines in comparison with the host plants. All the six disomic substitution lines showed much stronger “transcriptomic-shock” occurred on alien genomes with 57.43–69.22% genes changed expression level but less on the recipient genome (2.19–8.97%). Genome-wide suppression of alien genes along chromosomes was observed with a high proportion of downregulated genes (39.69–48.21%). Oppositely, the wheat recipient showed genome-wide compensation with more upregulated genes, occurring on all chromosomes but not limited to the homeologous groups. Moreover, strong co-upregulation of the orthologs between wheat and Thinopyrum sub-genomes was enriched in photosynthesis with predicted chloroplastic localization, which indicates that the compensation happened not only on wheat host genomes but also on alien genomes.
... Only genes that showed fold change (FC) ≥ 2 or FC ≤ -2, when TPM values were compared under pathogen inoculation versus mock (control), were considered differentially expressed. Further, to analyze the expression patterns of the differentially expressed CGs (DECGs) in different wheat tissues during development, relevant expression datasets available at the expVIP platform were used (Gillies et al. 2012;Leach et al. 2014;Li et al. 2013;Pfeifer et al. 2014;Ramírez-González et al. 2018). Heatmaps were then generated using Morpheus (https:// softw are. ...
Unlabelled:
In wheat, meta-QTLs (MQTLs) and candidate genes (CGs) were identified for multiple disease resistance (MDR). For this purpose, information was collected from 58 studies for mapping QTLs for resistance to one or more of the five diseases. As many as 493 QTLs were available from these studies, which were distributed in five diseases as follows: septoria tritici blotch (STB) 126 QTLs; septoria nodorum blotch (SNB), 103 QTLs; fusarium head blight (FHB), 184 QTLs; karnal bunt (KB), 66 QTLs; and loose smut (LS), 14 QTLs. Of these 493 QTLs, only 291 QTLs could be projected onto a consensus genetic map, giving 63 MQTLs. The CI of the MQTLs ranged from 0.04 to 15.31 cM with an average of 3.09 cM per MQTL. This is a ~ 4.39 fold reduction from the CI of QTLs, which ranged from 0 to 197.6 cM, with a mean of 13.57 cM. Of 63 MQTLs, 60 were anchored to the reference physical map of wheat (the physical interval of these MQTLs ranged from 0.30 to 726.01 Mb with an average of 74.09 Mb). Thirty-eight (38) of these MQTLs were verified using marker-trait associations (MTAs) derived from genome-wide association studies. As many as 874 CGs were also identified which were further investigated for differential expression using data from five transcriptome studies, resulting in 194 differentially expressed candidate genes (DECGs). Among the DECGs, 85 genes had functions previously reported to be associated with disease resistance. These results should prove useful for fine mapping and cloning of MDR genes and marker-assisted breeding.
Supplementary information:
The online version contains supplementary material available at 10.1007/s11032-022-01282-z.
... The availability of high-quality genome sequences recently allowed detailed study of gene expression patterns in the polyploid wheat. Polyploidization often results in homoeolog expression bias that, in many cases, were caused by epigenetic modifications including DNA methylation and histone modifications [15,16]. A significant portion of triads (1:1:1 homoeologs from three subgenomes) exhibit homoeolog expression bias [15]. ...
... A significant portion of triads (1:1:1 homoeologs from three subgenomes) exhibit homoeolog expression bias [15]. These unbalanced expressions of homoeologs often affect plant growth, development, and stress responses in wheat [16][17][18]. Despite this, much remains unknown about their potential biological contributions to grains at early development. ...
Grain development, as a vital process in the crop’s life cycle, is crucial for determining crop quality and yield. The wheat grain expanding phase is the early process involving the rapid morphological changes and initiation of grain filling. However, little is known about the molecular basis of grain development at this stage. Here, we provide a time-series transcriptome profile of developing wheat grain at 0, 2, 4, 6, 8, and 10 days after pollination of the wheat landrace Chinese Spring. A total of 26,892 differentially expressed genes, including 1468 transcription factors, were found between adjacent time points. Co-expression cluster analysis and Gene Ontology enrichment revealed dynamic expressions of cell division and starch biosynthesis related structural genes and transcription factors. Moreover, diverse, differential and drastically varied expression trends of the key genes related to hormone metabolism were identified. Furthermore, ~30% of triads showed unbalanced expression patterns enriching for genes in multiple pivotal metabolic pathways. Hormone metabolism related genes, such as YUC10 (YUCCA flavin-containing monooxygenase 10), AOS2 (allene oxide synthase 2), CYP90D2 (cytochrome P450 90D2), and CKX1 (cytokinin dehydrogenase 1), were dominantly contributed by A or D homoeologs of the triads. Our study provided a systematic picture of transcriptional regulation of wheat grains at the early grain expanding phase which should deepen our understanding of wheat grain development and help in wheat yield improvement.
... Differential expression of distinct homoeoloci was studied in detail in wheat (Leach et al., 2014). In that study, around 45% of genes on wheat chromosomes 1 and 5 were expressed as three distinct homoeoloci in both shoot and root tissues, with most of these genes displaying a bias towards a Since the aleurone was the tissue where RHT-1-TaIDD11 interaction was identified, grain tissue-specific TaIDD11 expression was investigated (Table 4.1). ...
... Expression of TaERF-B5 and TaERF-D5 genes is 4.1-and 3.4-fold higher than the expression of TaERF-B5a and TaERF-D5a, respectively, whereas the expression of TaERF-A5 is 22.9-fold higher than that of TaERF-A5a. At least 45% of genes in wheat were found to be expressed unequivocally from all three homoeoloci and when two homoeologues equally dominate total gene expression, A and D or B and D homoeologues dominance is much more common (Leach et al., 2014). This appears to be the case as for TaERF5 all three homoeologues contribute to the transcript levels, whereas for TaERF5a, TaERF-B5a and TaERF-D5a dominance is observed. ...
Germinating embryos release gibberellins (GAs), which act on aleurone cells to promote the expression of hydrolytic enzymes via the transcription factor (TF) GAMYB. GAs promote the degradation of DELLA proteins, which in the aleurone results in the upregulation of GAMYB expression. Although it is known that DELLAs negatively regulate GAMYB activity, the molecular mechanisms underlying this response are currently unclear. Recent studies have demonstrated that DELLAs do not contain a DNA-binding domain and they regulate transcription by acting as coactivators or corepressors of TFs. It was therefore hypothesised that the regulation of GAMYB by DELLA may be indirect, by working in a complex with other TF/TFs. A yeast two-hybrid (Y2H) screen of the wheat aleurone cDNA library revealed that wheat DELLA protein, RHT-1, interacts with different classes of TFs. Two TFs were selected for further analysis: INDETERMINATE DOMAIN 11 (TaIDD11) and ETHYLENE RESPONSE FACTOR 5 (TaERF5). The interactions between RHT-1 and TaIDD11 and TaERF5 were confirmed in Y2H assays and in planta. Reverse genetics approach was applied to understand the roles of identified TFs in the regulation of GA response. TaIDD11 was found to be a positive regulator of GA-mediated growth and floral transition, as the Taidd11 (triple knockout mutant) displayed reduced growth and delayed transition to flowering. The transcript levels of GA3ox, GA20ox and GID1b, the genes positively regulating GA biosynthesis and signalling, were enhanced in the mutant, which resulted in enhanced levels of bioactive GA1. The TaERF5 has a close paralogue in wheat (TaERF5a), which shows high level of conservation and is hypothesized to have redundant function. Genome editing using CRISPR/Cas9 was applied to generate sextuple Taerf5 Taerf5a mutant, and the Cas9-free T3 seeds are now awaiting phenotypic analysis. Together, this study identified a novel component of GA signalling that regulates GA-mediated growth and development, possibly via interaction with RHT-1.
