SummaryPolyploid wheats comprise four species: Triticum turgidum (AABB genomes) and T. aestivum (AABBDD) in the Emmer lineage, and T. timopheevii (AAGG) and T. zhukovskyi (AAGGA m A m ) in the Timopheevi lineage. Genetic relationships between chloroplast genomes were studied to trace the evolutionary history of the species. Twenty-five chloroplast genomes were sequenced, and 1127 plant accessions were genotyped, representing 13 Triticum and Aegilops species.The A. speltoides (SS genome) diverged before the divergence of T. urartu (AA), A. tauschii (DD) and the Aegilops species of the Sitopsis section. Aegilops speltoides forms a monophyletic clade with the polyploid Emmer and Timopheevi wheats, which originated within the last 0.7 and 0.4 Myr, respectively. The geographic distribution of chloroplast haplotypes of the wild tetraploid wheats and A. speltoides illustrates the possible geographic origin of the Emmer lineage in the southern Levant and the Timopheevi lineage in northern Iraq.Aegilops speltoides is the closest relative of the diploid donor of the chloroplast (cytoplasm), as well as the B and G genomes to Timopheevi and Emmer lineages. Chloroplast haplotypes were often shared by species or subspecies within major lineages and between the lineages, indicating the contribution of introgression to the evolution and domestication of polyploid wheats.

The cuticle plays important roles in plant development, growth and defense against biotic and abiotic attacks. Crystallized epicuticular wax, the outermost layer of cuticle, is visible as white-bluish glaucousness. In crops like barley and wheat, glaucousness is trait of adaption to the dry and hot cultivation conditions, and hentriacontane-14,16-dione (β-diketone) and its hydroxy derivatives are the major and unique components of cuticular wax in the upper parts of adult plants. But their biosynthetic pathway and physiological role largely remain unknown. In the present research, we identified a novel wax mutant in wheat cultivar Bobwhite. The mutation is not allelic to the known wax production gene loci W1 and W2, and designated as W3 accordingly. Genetic analysis localized W3 on chromosome arm 2BS. The w3 mutation reduced 99% of β-diketones, which account for 63.3% of the total wax load of the wild-type. W3 is necessary for β-diketone synthesis, but has a different effect on β-diketone hydroxylation because the hydroxy-β-diketones to β-diketone ratio increased 11-fold in the w3 mutant. Loss of β-diketones caused failure to form glaucousness and significant increase of cuticle permeability in terms of water loss and chlorophyll efflux in the w3 mutant. Transcription of 23 cuticle genes from five functional groups was altered in the w3 mutant, 19 down-regulated and four up-regulated, suggesting a possibility that W3 encodes a transcription regulator coordinating expression of cuticle genes. Biosynthesis of β-diketones in wheat and their implications in glaucousness formation and drought and heat tolerance were discussed.Key Message W3 is essential for β-diketone biosynthesis but suppresses its hydroxylation. Loss-of-function mutation w3 significantly increased cuticle permeability in terms of water loss and chlorophyll efflux.

The current review provides an updated, new insights into the regulation of transcription mediated underlying mechanisms of wheat plants to osmotic stress perturbations. Osmotic stress tolerance mechanisms being complex are governed by multiple factors at physiological, biochemical and at the molecular level, hence approaches like "OMICS" that can underpin mechanisms behind osmotic tolerance in wheat is of paramount importance. The transcription factors (TFs) are a class of molecular proteins, which are involved in regulation, modulation and orchestrating the responses of plants to a variety of environmental stresses. Recent reports have provided novel insights on the role of TFs in osmotic stress tolerance via direct molecular links. However, our knowledge on the regulatory role TFs during osmotic stress tolerance in wheat remains limited. The present review in its first part sheds light on the importance of studying the role of osmotic stress tolerance in wheat plants and second aims to decipher molecular mechanisms of TFs belonging to several classes, including DREB, NAC, MYB, WRKY and bHLH, which have been reported to engage in osmotic stress mediated gene expression in wheat and third part covers the systems biology approaches to understand the transcriptional regulation of osmotic stress and the role of long non-coding RNAs in response to osmotic stress with special emphasis on wheat. The current concept may lead to an understanding in molecular regulation and signalling interaction of TFs under osmotic stress to clarify challenges and problems for devising potential strategies to improve complex regulatory events involved in plant tolerance to osmotic stress adaptive pathways in wheat.

Chromosomal rearrangements (CRs) play important roles in karyotype diversity and speciation. While many CR breakpoints have been characterized at the sequence level in yeast, insects, and primates, little is known about the structure of evolutionary CR breakpoints in plant genomes, which are much more dynamic in genome size and sequence organization. Here, we report identification of breakpoints of a translocation between chromosome arms 4L and 5L of Triticeae, which is fixed in several species, including diploid wheat and rye, by comparative mapping and analysis of the draft genome and chromosome survey sequences of the Triticeae species. The wheat translocation joined the ends of breakpoints downstream of a WD40 gene on 4AL and a gene of the PMEI family on 5AL. A basic helix-loop-helix transcription factor gene in 5AL junction was significantly restructured. Rye and wheat share the same position for the 4L breakpoint, but the 5L breakpoint positions are not identical, although very close in these two species, indicating the recurrence of 4L/5L translocations in the Triticeae. Although barley does not carry the translocation, collinearity across the breakpoints was violated by putative inversions and/or transpositions. Alignment with model grass genomes indicated that the translocation breakpoints coincided with ancient inversion junctions in the Triticeae ancestor. Our results show that the 4L/5L translocation breakpoints represent two CR hotspots reused during Triticeae evolution, and support breakpoint reuse as a widespread mechanism in all eukaryotes. The mechanisms of the recurrent translocation and its role in Triticeae evolution are also discussed.

Global population increase coupled with rising urbanization underlies the predicted need for 60% more food by 2050, but produced on the same amount of land as today. Improving photosynthetic efficiency is a largely untapped approach to addressing this problem. Here, we scale modelling processes from gene expression through photosynthetic metabolism to predict leaf physiology in evaluating acclimation of photosynthesis to rising atmospheric concentrations of CO2 ([CO2]). Model integration with the yggdrasil interface enabled asynchronous message passing between models. The multiscale model of soybean (Glycine max) photosynthesis calibrated to physiological measures at ambient [CO2] successfully predicted the acclimatory changes in the photosynthetic apparatus that were observed at 550 ppm [CO2] in the field. We hypothesized that genetic alteration is necessary to achieve optimal photosynthetic efficiency under global change. Flux control analysis in the metabolic system under elevated [CO2] identified enzymes requiring the greatest change to adapt optimally to the new conditions. This predicted that Rubisco was less limiting under elevated [CO2] and should be down-regulated allowing re-allocation of resource to enzymes controlling the rate of regeneration of ribulose-1,5-bisphosphate (RuBP). By linking the Gene Regulatory Network through protein concentration to the metabolic model, it was possible to identify transcription factors (TFs) that matched the up- and down-regulation of genes needed to improve photosynthesis. Most striking was TF Gm-GATA2, which down-regulated genes for Rubisco synthesis while up-regulating key genes controlling RuBP regeneration and starch synthesis. The changes predicted for this TF most closely matched the physiological ideotype that the modelling predicted as optimal for the future elevated [CO2] world.

Non-additive allelic interactions underlie over dominant and under dominant inheritance, which explain positive and negative heterosis. These heteroses are often observed in the aboveground traits, but rarely reported in root. We identified a very short root (VSR) phenotype in the F1 hybrid between the common wheat (Triticum aestivum L.) landrace Chinese Spring and synthetic wheat accession TA4152-71. When germinated in tap water, primary roots of the parental lines reached ~15 cm 10 days after germination, but those of the F1 hybrid were ~3 cm long. Selfing populations segregated at a 1 (long-root) to 1 (short-root) ratio, indicating that VSR is controlled by a non-additive interaction between two alleles in a single gene locus, designated as Vsr1. Genome mapping localized the Vsr1 locus in a 3.8-cM interval delimited by markers XWL954 and XWL2506 on chromosome arm 5DL. When planted in vermiculite with supplemental fertilizer, the F1 hybrid had normal root growth, virtually identical to the parental lines, but the advanced backcrossing populations segregated for VSR, indicating that the F1 VSR expression was suppressed by interactions between other genes in the parental background and the vermiculite conditions. Preliminary physiological analyses showed that the VSR suppression is independent of light status but related to potassium homeostasis. Phenotyping additional hybrids between common wheat and synthetics revealed a high VSR frequency and their segregation data suggested more Vsr loci involved. Because the VSR plants can be regularly maintained and readily phenotyped at the early developmental stage, it provides a model for studies of non-additive interactions in wheat.

2Global population increase coupled with rising urbanization underlies the predicted need for 2 3 60% more food by 2050, but produced on the same amount of land as today. Improving 2 4 photosynthetic efficiency is a largely untapped approach to addressing this problem. Here, we 2 5 scale modeling processes from gene expression through photosynthetic metabolism to predict 2 6 leaf physiology in evaluating acclimation of photosynthesis to rising [CO 2 ]. Model integration 2 7with the yggdrasil interface enabled asynchronous message passing between models. The 2 8 multiscale model of soybean photosynthesis calibrated to physiological measures at ambient 2 9[CO 2 ] successfully predicted the acclimatory changes in the photosynthetic apparatus that 3 0 were observed at 550 ppm [CO 2 ] in the field. We hypothesized that genetic alteration is 3 1 1 necessary to achieve optimal photosynthetic efficiency under global change. Flux control 3 2 analysis in the metabolic system under elevated [CO 2 ] identified enzymes requiring the 3 3 greatest change to adapt optimally to the new conditions. This predicted that Rubisco was less 3 4 limiting under elevated [CO 2 ] and should be down-regulated allowing re-allocation of 3 5 resource to enzymes controlling the rate of regeneration of ribulose-1:5 bisphosphate (RubP). 3 6 By linking the GRN through protein concentration to the metabolic model it was possible to 3 7 identify transcription factors (TF) that matched the up-and down-regulation of genes needed 3 8 to improve photosynthesis. Most striking was TF GmGATA2, which down-regulated genes 3 9 for Rubisco synthesis while up-regulating key genes controlling RubP regeneration and starch 4 0 synthesis. The changes predicted for this TF most closely matched the physiological ideotype 4 1that the modeling predicted as optimal for the future elevated [CO 2 ] world. 4 2 4 3 KEYWORDS: Gene network model, metabolic model, photosynthesis, global change, Soybean, 4 4 transcription factors, multiscale modeling, model integration 4 5 4 6As the world's most important seed legume and most widely grown dicotyledonous crop, 4 7 the future-proofing of photosynthesis in soybean (Glycine max (L.) Merr.) under rising 4 8 atmospheric concentrations of CO 2 ([CO 2 ]) is of importance. Down-regulation of light-saturated 4 9net leaf CO 2 uptake (A sat ) at elevated [CO 2 ] has been reported for many C 3 crops, yet the 5 0 mechanism underlying this response is poorly understood. Under current [CO 2 ], A sat in C 3 crops 5 1 is most commonly limited by the in vivo Rubsico activity (V c,max ) (Long et al., 2004). However, 5 2 as [CO 2 ] continues to rise, it follows from the steady-state biochemical model of photosynthesis 5 3 of (Farquhar et al., 1980) and its subsequent modifications (Von Caemmerer, 2000) that control 5 4 will shift from Rubisco to RubP regeneration (Long et al., 2004), which is represented by the 5 5maximum in vivo rate of whole chain electron transport (J max ). While described by electron 5 6 transport, most evidence now points to t...

Hidden underground, root systems constitute an important part of the plant for its development, nourishment and sensing the soil environment around it, but we know very little about its genetic regulation in crop plants like wheat. In the present study, we de novo assembled the root transcriptomes in reference cultivar Chinese Spring from RNA-seq reads generated by the 454-GS-FLX and HiSeq platforms. The FLX reads were assembled into 24,986 transcripts with completeness of 54.84%, and the HiSeq reads were assembled into 91,543 high-confidence protein-coding transcripts, 2,404 low-confidence protein-coding transcripts, and 13,181 non-coding transcripts with the completeness of >90%. Combining the FLX and HiSeq assemblies, we assembled a root transcriptome of 92,335 ORF-containing transcripts. Approximately 7% of the coding transcripts and ~2% non-coding transcripts are not present in the current wheat genome assembly. Functional annotation of both assemblies showed similar gene ontology patterns and that ~7% coding and >5% non-coding transcripts are root-specific. Transcription quantification identified 1,728 differentially expressed transcripts between root tips and maturation zone, and functional annotation of these transcripts captured a transcriptional signature of longitudinal development of wheat root. With the transcriptomic resources developed, this study provided the first view of wheat root transcriptome under different developmental zones and laid a foundation for molecular studies of wheat root development and growth using a reverse genetic approach.