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Summary The AGAMOUS‐LIKE6 (AGL6)‐like genes are ancient MADS‐box genes and are functionally studied in a few model plants. The knowledge of these genes in wheat remains limited. Here, by studying a ‘double homoeolog mutant’ of the AGL6 gene in tetraploid wheat, we showed that AGL6 was required for the development of all four whorls of floral organs with dosage‐dependent effect on floret fertility. Yeast two‐hybrid analyses detected interactions of AGL6 with all classes of MADS‐box proteins in the ABCDE model for floral organ development. AGL6 was found to interact with several additional proteins, including the G protein β and γ (DEP1) subunits. Analysis of the DEP1‐B mutant showed a significant reduction in spikelet number per spike in tetraploid wheat, while overexpression of AGL6 in common wheat increased the spikelet number per spike and hence the grain number per spike. RNA‐seq analysis identified the regulation of several meristem activity genes by AGL6, such as FUL2 and TaMADS55. Our work therefore extensively updated the wheat ABCDE model and proposed an alternative approach to improve wheat grain yield by manipulating the AGL6 gene.

Auxin signaling is essential for the development of grain size and grain weight, two important components for crop yield. However, no auxin/indole acetic acid repressor (Aux/IAA) has been functionally characterized to be involved in the development of wheat (Triticum aestivum L.) grains to date. Here, we identified a wheat Aux/IAA gene, TaIAA21, and studied its regulatory pathway. We found that TaIAA21 mutation significantly increased grain length, grain width, and grain weight. Cross-sections of mutant grains revealed elongated outer pericarp cells compared to those of the wild type, where the expression of TaIAA21 was detected by in situ hybridization. Screening of auxin response factor (ARF) genes highly expressed in early developing grains revealed that TaARF25 interacts with TaIAA21. In contrast, mutation of the tetraploid wheat (Triticum turgidum) ARF25 gene significantly reduced grain size and weight. RNA sequencing analysis revealed upregulation of several ethylene response factor genes (ERFs) in taiaa21 mutants which carried auxin response cis-elements in their promoter. One of them, ERF3, was upregulated in the taiaa21 mutant and downregulated in the ttarf25 mutant. Transactivation assays showed that ARF25 promotes ERF3 transcription, while mutation of TtERF3 resulted in reduced grain size and weight. Analysis of natural variations identified three TaIAA21-A haplotypes with increased allele frequencies in cultivars relative to landraces, a signature of breeding selection. Our work demonstrates that TaIAA21 works as a negative regulator of grain size and weight development via the ARF25-ERFs module and is useful for yield improvement in wheat.

The Q gene in common wheat encodes an APETALA2 (AP2) transcription factor that causes the free threshing attribute. Wheat spikelets bearing several florets are subtended by a pair of soft glumes that allow free liberation of seeds. In wild species, the glumes are tough and rigid, making threshing difficult. However, the nature of these “soft glumes”, caused by the domestication allele Q is not clear. Here, we found that over expression of Q in common wheat leads to homeotic florets at glume positions. We provide phenotypic, microscopy, and marker genes evidence to demonstrate that the soft glumes of common wheat are in fact lemma-like organs, or so-called sterile-lemmas. By comparing the structures subtending spikelets in wheat and other crops such as rice and maize, we found that AP2 genes may play conserved functions in grasses by manipulating vestigial structures, such as floret-derived soft glumes in wheat and empty glumes in rice. Conversion of these seemingly vegetative organs to reproductive organs may be useful in yield improvement of crop species. Keywords: Floret development, Spike morphology, Sterile lemma, Wheat

The RNAi technology takes advantage of the intrinsic RNA interference (RNAi) mechanism that exists in nearly all eukaryotes in which target mRNAs are degraded or functionally suppressed. Significant progress has been made in recent years where RNAi technology is applied to several crops and economic plants for protection against diseases like fungi, pests, and nematode. RNAi technology is also applied in controlling pathogen damages in wheat, one of the most important crops in the world. In this review, we first give a brief introduction of the RNAi technology and the underneath mechanism. We then review the recent progress of its utilization in crops, particular wheat. Finally, we discuss the existing challenges and prospect future development of this technology in crop protection.

DNA methylation is dynamically involved in plant immunity, but little information is known about its roles in plant interactions with biotrophic fungi, especially in temperate grasses such as wheat (Triticum aestivum). Using wheat diploid progenitor Aegilops tauschii accession AL8/78, the genome of which has been sequenced, we assessed the extent of DNA methylation in response to infection with Blumeria graminis f. sp. tritici (Bgt), which causes powdery mildew. Upon Bgt infection, ARGONAUTE4a (AGO4a) was significantly downregulated in A. tauschii, which was accompanied by a substantial reduction in AGO4a‐sorted 24‐nt siRNA levels, especially for genes near transposable elements (TAGs). Bisulfite sequencing revealed abundant differentially methylated regions (DMRs) with CHH hypomethylation. TAGs bearing CHH‐hypomethylated DMRs were enriched for ‘response to stress’ functions, including receptor kinase, peroxidase, and pathogenesis‐related genes. Virus‐induced gene silencing (VIGS) of a DOMAINS REARRANGED METHYLASE 2 (DRM2) homolog enhanced plant resistance to Bgt. The effect of CHH hypomethylation was exemplified by the upregulation of a pathogenesis‐related β‐1,3‐glucanse gene implicated in Bgt defense. These findings support the idea that dynamic DNA methylation represents a regulatory layer in the complex mechanism of plant immunity, which could be exploited to improve disease resistance in common wheat.

Bread wheat is not only an important cereal crop but also a model for study of an allopolyploid plant with a large, highly repetitive genome. Advances in next-generation sequencing (NGS) technology provide needed throughput to conquer the enormous size of the wheat genome. Multiple high quality reference genome sequences will soon be available. Full-scale wheat functional genomics studies are dawning. In this review we highlight the available tools and methodologies for wheat functional genomics research developed with the assistance of NGS technology and recent progress, particularly the concerted effort in generating multiple reference genomes, strategies to attain genome-wide genetic variation, genome-wide association studies, mutant population generation, and NGS-supported gene cloning and functional characterization. These resources and platforms lay a solid foundation for wheat research, leading to a new era of wheat functional genomics that will bridge the gap between genotype and phenotype. Dissection of wheat genomes and gene functions should assist in genomics-assisted selection and facilitate breeding of elite varieties for sustainable agriculture in China and the world.

Appropriate flowering timing is crucial for plant reproductive success. The florigen, FLOWERING LOCUS T (FT), interacts with 14-3-3 proteins and the bZIP transcription factor FD, functioning at core nodes in multiple flowering pathways. There are two FT homologues, FT1 and FT2, in Brachypodium distachyon. Here we show that FT2 undergoes age-dependent alternative splicing (AS), resulting in two splice variants (FT2α and FT2β). The FT2β-encoded protein cannot interact with FD or 14-3-3s but is able to form heterodimers with FT2α and FT1, thereby interfering with the florigen-mediated assembly of the flowering initiation complex. Notably, transgenic plants overproducing FT2β exhibit delayed flowering, while transgenic plants in which FT2β is silenced by an artificial microRNA display accelerated flowering, demonstrating a dominant-negative role of FT2β in flowering induction. Furthermore, we show that the AS splicing of FT2 is conserved in important cereal crops, such as barley and wheat. Collectively, these findings reveal a novel posttranscriptional mode of FT regulation in temperate grasses., The correct timing of transition from the vegetative to reproductive stage is critical during the plant life cycle. Here the authors show that age dependent alternative splicing of FLOWERING LOCUS T mRNA regulates phase transitions in Brachypodium distachyon.

The wheat AP2-like transcription factor gene Q has played a major role in domestication by conferring the free-threshing character and pleiotropically affecting numerous other traits. However, little information is known regarding the molecular mechanisms associated with the regulation of these traits by Q, especially for the structural determination of threshability. Here, transcriptome analysis of immature spike tissues in three lines nearly isogenic for Q revealed over 3000 differentially expressed genes (DEGs) involved in a number of pathways. Using phenotypic, microscopic, transcriptomic, and tissue-specific gene expression analyses, we demonstrated that Q governs threshability through extensive modification of wheat glumes including their structure, cell wall thickness, and chemical composition. Critical DEGs and pathways involved in secondary cell wall synthesis and regulation of the chemical composition of glumes were identified. We also showed that the mutation giving rise to the Q allele synchronized the expression of genes for micro-sporogenesis that affected pollen fertility, and may determine the final grain number for wheat spikes. Transcriptome dissection of genes and genetic pathways regulated by Q should further our understanding of wheat domestication and improvement.

Background Hexaploid bread wheat (Triticum aestivum L) arose by two polyploidisation events from three diploid species with homoeologous genomes. Nullisomic-tetrasomic (nulli-tetra or NT) lines are aneuploid wheat plants lacking two and adding two of six homoeologous chromosomes. These plants can grow normally, but with significantly morphological variations because the adding two chromosomes or the remaining four chromosomes compensate for those absent. Despite these interesting phenomena, detailed molecular mechanisms underlying dosage deletion and compensation in these useful genetic materials have not been determined. Results By sequencing the transcriptomes of leaves in two-week-old seedlings, we showed that the profiles of differentially expressed genes between NT stocks for homoeologous group 7 and the parent hexaploid Chinese Spring (CS) occurred throughout the whole genome with a subgenome and chromosome preference. The deletion effect of nulli-chromosomes was compensated partly by the tetra-chromosomes via the dose level of expressed genes, according to the types of homoeologous genes. The functions of differentially regulated genes primarily focused on carbon metabolic process, photosynthesis process, hormone metabolism, and responding to stimulus, and etc., which might be related to the defective phenotypes that included reductions in plant height, flag leaf length, spikelet number, and kernels per spike. Conclusions The perturbation of the expression levels of transcriptional genes among the NT stocks for homoeologous group 7 demonstrated the gene dosage effect of the subgenome at the genome-wide level. The gene dosage deletion and compensation can be used as a model to elucidate the functions of the subgenomes in modern polyploid plants. Electronic supplementary material The online version of this article (10.1186/s12864-018-5421-3) contains supplementary material, which is available to authorized users.

The TCP family genes are plant-specific transcription factors and play important roles in plant development. TCPs have been evolutionarily and functionally studied in several plants. Although common wheat (Triticum aestivum L.) is a major staple crop worldwide, no systematic analysis of TCPs in this important crop has been conducted. Here, we performed a genome-wide survey in wheat and found 66 TCP genes that belonged to 22 homoeologous groups. We then mapped these genes on wheat chromosomes and found that several TCP genes were duplicated in wheat including the ortholog of the maize TEOSINTE BRANCHED 1. Expression study using both RT-PCR and in situ hybridization assay showed that most wheat TCP genes were expressed throughout development of young spike and immature seed. Cis-acting element survey along promoter regions suggests that subfunctionalization may have occurred for homoeologous genes. Moreover, protein–protein interaction experiments of three TCP proteins showed that they can form either homodimers or heterodimers. Finally, we characterized two TaTCP9 mutants from tetraploid wheat. Each of these two mutant lines contained a premature stop codon in the A subgenome homoeolog that was dominantly expressed over the B subgenome homoeolog. We observed that mutation caused increased spike and grain lengths. Together, our analysis of the wheat TCP gene family provides a start point for further functional study of these important transcription factors in wheat.

Common wheat (Triticum aestivum) is an allohexaploid (AABBDD), with Triticum urartu (AA) and Aegilops tauschii (DD) as its A and D genome donors. Squamosa Promoter Binding Protein-Like (SPL) genes play important roles in plant development; however, a systematic study of this gene family in wheat is still lacking. Here, we mined the wheat genomes for SPLs and found 19 SPL genes each from the T. urartu and Ae. tauschii genomes. We also identified 58 SPL genes from the hexaploid wheat genome. We then compared the conservation and divergence of SPLs between the two diploid species in gene structures, tissuespecific expression patterns and responses to salt stress, drought and low temperature. For functional studies, two hexaploid wheat SPLs, TaSPL3 (with miR156 site mutated) and TaSPL6, were overexpressed in Arabidopsis and found to be involved in flowering time and biomass accumulation. In addition, a mutant allele (TaSPL6-D R ) with a 47 bp duplication upstream of the SBP domain was found to be associated with maturity date and grain number per spike among landraces from a Chinese wheat mini-core collection. Collectively, our work provides useful knowledge on the sequences and functions of wheat SPL genes that may help future functional studies and molecular breeding.

Bread wheat (or common wheat, Triticum aestivum) is an allohexaploid (AABBDD, 2n = 6x = 42) that arose by hybridization between a cultivated tetraploid wheat T. turgidum (AABB, 2n = 4x = 28) and the wild goatgrass Aegilops tauschii (DD, 2n = 2x = 14). Polyploidization provided niches for rigorous genome modification at cytogenetic, genetic, and epigenetic levels, rendering a broader spread than its progenitors. This review summarizes the latest advances in understanding gene regulation mechanisms in newly synthesized allohexaploid wheat and possible correlation with polyploid growth vigor and adaptation. Cytogenetic studies reveal persistent association of whole-chromosome aneuploidy with nascent allopolyploids, in contrast to the genetic stability in common wheat. Transcriptome analysis of the euploid wheat shows that small RNAs are driving forces for homoeo-allele expression regulation via genetic and epigenetic mechanisms. The ensuing non-additively expressed genes and those with expression level dominance to the respective progenitor may play distinct functions in growth vigor and adaptation in nascent allohexaploid wheat. Further genetic diploidization of allohexaploid wheat is not random. Regional asymmetrical gene distribution, rather than subgenome dominance, is observed in both synthetic and natural allohexaploid wheats. The combinatorial effects of diverged genomes, subsequent selection of specific gene categories, and subgenome-specific traits are essential for the successful establishment of common wheat.

Early reproductive development in cereals is crucial for final grain number per spike and hence the yield potential of the crop. To date, however, no systematic analyses of gene expression profiles during this important process have been conducted for common wheat (Triticum aestivum). Here, we studied the transcriptome profiles at four stages of early wheat reproductive development, from spikelet initiation to floral organ differentiation. K-means clustering and stage-specific transcript identification detected dynamically expressed homeologs of important transcription regulators in spikelet and floral meristems that may be involved in spikelet initiation, floret meristem specification, and floral organ patterning, as inferred from their homologs in model plants. Small RNA transcriptome sequencing discovered key microRNAs that were differentially expressed during wheat inflorescence development alongside their target genes, suggesting that miRNA-mediated regulatory mechanisms for floral development may be conserved in cereals and Arabidopsis. Our analysis was further substantiated by the functional characterization of the ARGONAUTE1d (AGO1d) gene, which was initially expressed in stamen primordia and later in the tapetum during anther maturation. In agreement with its stage-specific expression pattern, the loss of function of the predominantly expressed B homeolog of AGO1d in a tetraploid durum wheat mutant resulted in smaller anthers with more infertile pollens than the wild type and a reduced grain number per spike. Together, our work provides a first glimpse of the gene regulatory networks in wheat inflorescence development that may be pivotal for floral and grain development, highlighting potential targets for genetic manipulation to improve future wheat yields.

Nascent allohexaploid wheat may represent the initial genetic state of common wheat (Triticum aestivum), which arose as a hybrid between Triticum turgidum (AABB) and Aegilops tauschii (DD) and by chromosome doubling and outcompeted its parents in growth vigor and adaptability. To better understand the molecular basis for this success, we performed mRNA and small RNA transcriptome analyses in nascent allohexaploid wheat and its following generations, their progenitors, and the natural allohexaploid cultivar Chinese Spring, with the assistance of recently published A and D genome sequences. We found that nonadditively expressed protein-coding genes were rare but relevant to growth vigor. Moreover, a high proportion of protein-coding genes exhibited parental expression level dominance, with genes for which the total homoeolog expression level in the progeny was similar to that in T. turgidum potentially participating in development and those with similar expression to that in Ae. tauschii involved in adaptation. In addition, a high proportion of microRNAs showed nonadditive expression upon polyploidization, potentially leading to differential expression of important target genes. Furthermore, increased small interfering RNA density was observed for transposable element-associated D homoeologs in the allohexaploid progeny, which may account for biased repression of D homoeologs. Together, our data provide insights into small RNA-mediated dynamic homoeolog regulation mechanisms that may contribute to heterosis in nascent hexaploid wheat.

Calcium-dependent protein kinases (CPKs) are important Ca2+ signalling components involved in complex immune and stress signalling networks; but the knowledge of CPK gene functions in the hexaploid wheat is limited. Previously, TaCPK2 was shown to be inducible by powdery mildew (Blumeria graminis tritici, Bgt) infection in wheat. Here, its functions in disease resistance are characterized further. This study shows the presence of defence-response and cold-response cis-elements on the promoters of the A subgenome homoeologue (TaCPK2-A) and D subgenome homoeologue (TaCPK2-D), respectively. Their expression patterns were then confirmed by quantitative real-time PCR (qRT-PCR) using genome-specific primers, where TaCPK2-A was induced by Bgt treatment while TaCPK2-D mainly responded to cold treatment. Downregulation of TaCPK2-A by virus-induced gene silencing (VIGS) causes loss of resistance to Bgt in resistant wheat lines, indicating that TaCPK2-A is required for powdery mildew resistance. Furthermore, overexpression of TaCPK2-A in rice enhanced bacterial blight (Xanthomonas oryzae pv. oryzae, Xoo) resistance. qRT-PCR analysis showed that overexpression of TaCPK2-A in rice promoted the expression of OsWRKY45-1, a transcription factor involved in both fungal and bacterial resistance by regulating jasmonic acid and salicylic acid signalling genes. The opposite effect was found in wheat TaCPK2-A VIGS plants, where the homologue of OsWRKY45-1 was significantly repressed. These data suggest that modulation of WRKY45-1 and associated defence-response genes by CPK2 genes may be the common mechanism for multiple disease resistance in grass species, which may have undergone subfunctionalization in promoters before the formation of hexaploid wheat.

Seed shattering is one of the major domestication traits of crops. In wheat, except for the Q gene whose mutation renders free threshing and changing of rachis fragility, not much is known about the molecular mechanism for this process. We report here the cloning and characterization of TaqSH1, the ortholog of the rice seed shattering gene qSH1. TaqSH1 encodes a BEL1-like protein that is conserved between monocots and eudicots. TaqSH1 was located on the homoeologous group 3, a potential new genetic locus for seed threshability in wheat. Over expression of TaqSH1 in Arabidopsis resulted in dwarfed plants. The inflorescences of transgenic plants were more compact with larger pedicel angles. Scanning Electron Microscopy (SEM) showed that the transgenic siliques had a narrower replum where the dehiscence zone was altered. In addition, abscission of petals was significantly delayed due to delayed abscission zone development. Real-time PCR assays showed that over expression of TaqSH1 down regulated known Arabidopsis abscission related genes IDA, HAESA, KNAT1/6 and SHP1/2 in the transgenic plants. Taken together, our data suggest that TaqSH1 may represent another example of conserved mechanisms across monocots and eudicots for fruit/grain abscission and should have potential application in genetic manipulation of wheat seed shattering.

Gene duplication contributes to the expansion of gene families and subsequent functional diversification. Calcium-dependent protein kinases (CDPKs) are members of an important calcium sensor family involved in abiotic and biotic stress signaling in plants. We report here the molecular evolution and expression analysis of a pair of duplicated CDPK genes CPK7 and CPK12 that arose in the common ancestor of grass species. With higher nonsynonymous/synonymous ratios (dN/dS, or ω), CPK12 genes appear to diverge more rapidly than CPK7s, suggesting relaxed selection constraints on CPK12s. Sliding window analysis revealed increased dN and ω values at N-terminal regions and the calcium-binding EF hand loops. Likelihood analyses using various models in PAML 4.0 showed purifying selection on both CPK7 and CPK12 lineages. In addition to the divergence in cis-element combinations on their promoters, functional divergence of CPK7 and CPK12 genes was also observed in wheat where TaCPK7 was found to respond to drought (PEG), salt (NaCl), cold, and hydrogen peroxide (H(2)O(2)) while TaCPK12 responded only to the treatment of ABA, a feature that may complement or expand TaCPK7-mediated stress signaling networks of wheat. The contrasting expression patterns of CPK7 and CPK12 genes under stress conditions were also observed in rice, suggesting conservative functional evolution of these genes. Since no positive selection was detected between the two lineages, the divergence of CPK7 and CPK12 genes should be ascribed to subfunctionalization, rather than neofunctionalization. Thus, our work demonstrates another case of evolutionary employment of duplicated genes via subfunctionalization for better adaptation.

Abscisic acid (ABA) plays pivotal roles in plant biotic and abiotic stress responses, where calcium ions are important second messengers. Calcium/calmodulin-dependent protein kinase (CCaMK) is essential for nodulation in legumes, but whether it will perceive calcium signals from abiotic stresses is not clear, especially in non-legume plants. Here we report the isolation and characterization of the D-genome copy of wheat CCaMK gene TaCCaMK. TaCCaMK was predominantly expressed in root tissues of wheat seedlings, and its proteins were located both on the cytoplasm membrane and in the nucleus as shown in the onion epidermis cells. Quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) assay showed that the expression of TaCCaMK was downregulated by ABA, as well as NaCl and PEG treatments in wheat seedling roots. A DNA fragment of 1,119 bp upstream of the start codon of the TaCCaMK gene (pTaCCaMK) was isolated by thermal asymmetric interlaced PCR (TAIL-PCR), on which six ABA-responsive cis-elements were predicted. pTaCCaMK can drive GUS reporter gene expression in the root and stem stalk of the transgenic Arabidopsis plants which can be repressed by ABA treatments, consistent with the observation in the qRT-PCR assay in wheat. Overexpressing TaCCaMK in Arabidopsis plants reduced their sensitivity to ABA treatment during seed germination and root elongation. Under high-salt conditions, the transgenic plants also conferred enhanced seed germination rate and became hypersensitive with increased chlorosis. Therefore, our data suggest that TaCCaMK is a negative regulator for ABA signaling which may participate in abiotic stress responses in wheat.

Highlight A tobacco (Nicotiana tobaccum) SVP family MADS-box gene is identified as a new regulator working in pedicel elongation for optimal inflorescence architecture by directly regulating an Arabidopsis BP homologue NtBPL, Optimal inflorescence architecture is important for plant reproductive success by affecting the ultimate number of flowers that set fruits and for plant competitiveness when interacting with biotic or abiotic conditions. The pedicel is one of the key contributors to inflorescence architecture diversity. To date, knowledge about the molecular mechanisms of pedicel development is derived from Arabidopsis. Not much is known regarding other plants. Here, an SVP family MADS-box gene, NtSVP, in tobacco (Nicotiana tabacum) that is required for pedicel elongation was identified. It is shown that knockdown of NtSVP by RNA interference (RNAi) caused elongated pedicels, while overexpression resulted in compact inflorescences with much shortened pedicels. Moreover, an Arabidopsis BREVIPEDECELLUS/KNAT1 homologue NtBP-Like (NtBPL) was significantly up-regulated in NtSVP-RNAi plants. Disruption of NtBPL decreased pedicel lengths and shortened cortex cells. Consistent with the presence of a CArG-box at the NtBPL promoter, the direct binding of NtSVP to the NtBPL promoter was demonstrated by yeast one-hybrid assay, electrophoretic mobility shift assay, and dual-luciferase assay, in which NtSVP may act as a repressor of NtBPL. Microarray analysis showed that down-regulation of NtBPL resulted in differential expression of genes associated with a number of hormone biogenesis and signalling genes such as those for auxin and gibberellin. These findings together suggest the function of a MADS-box transcription factor in plant pedicel development, probably via negative regulation of a BP-like class I KNOX gene. The present work thus postulates the conservation and divergence of the molecular regulatory pathways underlying the development of plant inflorescence architecture.