Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential.

Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.

Genome-Wide Identification and Characterization of the Wheat Remorin (TaREM) Family during Cold Acclimation.

Remorins (REMs) are plant-specific proteins that play an essential role in plant-microbe interactions. However, their roles in vernalization and abiotic stress responses remain speculative. Most remorins have a variable proline-rich -half and a more conserved -half that is predicted to form coils. A search of the wheat ( L.) database revealed the existence of 20 different genes, which we classified into six groups on the basis of whether they shared a common phylogenetic and structural origin. Analysis of the physical genomic distributions demonstrated that genes are dispersed in the wheat genome and have one to seven introns. Promoter analysis of genes revealed the presence of putative -elements related to diverse functions like development, hormonal regulation, and biotic and abiotic stress responsiveness. Expression levels of genes were measured in plants grown under field and controlled conditions and in response to hormone treatment. Our analyses revealed that 12 members of the REM family are regulated during cold acclimation in wheat in four different tissues (roots, crowns, stems, and leaves), with the highest expression in roots. Differential gene expression was found between wheat cultivars with contrasting degrees of cold tolerance, suggesting the implication of genes in cold response and tolerance. Additionally, eight genes were induced in response to abscisic acid and methyl jasmonate treatment. This genome-wide analysis of genes provides valuable resources for functional analysis aimed at understanding their role in stress adaptation.

Ice segregation in the crown of winter cereals: Evidence for extraorgan and extratissue freezing.

Meaningful improvements in winter cereal cold hardiness requires a complete model of freezing behaviour in the critical crown organ. Magnetic resonance microimaging diffusion-weighted experiments provided evidence that cold acclimation decreased water content and mobility in the vascular transition zone (VTZ) and the intermediate zone in rye (Secale cereale L. Hazlet) compared with wheat (Triticum aestivum L. Norstar). Differential thermal analysis, ice nucleation, and localization studies identified three distinct exothermic events. A high-temperature exotherm (-3°C to -5°C) corresponded with ice formation and high ice-nucleating activity in the leaf sheath encapsulating the crown. A midtemperature exotherm (-6°C and -8°C) corresponded with cavity ice formation in the VTZ but an absence of ice in the shoot apical meristem (SAM). A low-temperature exotherm corresponded with SAM injury and the killing temperature in wheat (-21°C) and rye (-27°C). The SAM had lower ice-nucleating activity and freezing survival compared with the VTZ when frozen in vitro. The intermediate zone was hypothesized to act as a barrier to ice growth into the SAM. Higher cold hardiness of rye compared with wheat was associated with higher VTZ and intermediate zone desiccation resulting in the formation of ice barriers surrounding the SAM.

Tissue-specific changes in apoplastic proteins and cell wall structure during cold acclimation of winter wheat crowns.

The wheat (Triticum aestivum L.) crown is the critical organ of low temperature stress survival over winter. In cold-acclimated crowns, ice formation in the apoplast causes severe tissue disruption as it grows at the expense of intracellular water. While previous crown studies have shown the vascular transition zone (VTZ) to have a higher freezing sensitivity than the shoot apical meristem (SAM), the mechanism behind the differential freezing response is not fully understood. Cooling cold-acclimated crowns to -10 °C resulted in an absence of VTZ tetrazolium chloride staining, whereas the temperatures at which 50% of the SAM stained positive and 50% of plants recovered (LT50) were similar after cold acclimation for 21 (-16 °C) and 42 d (-20 °C) at 4 °C. Proteomic analysis of the apoplastic fluids identified dehydrins, vernalization-responsive proteins, and cold shock proteins preferentially accumulated in the SAM. In contrast, modifications to the VTZ centered on increases in pathogenesis-related proteins, anti-freeze proteins, and sugar hydrolyzing enzymes. Fourier transform infrared spectroscopy focal plane array analysis identified the biochemical modification of the cell wall to enhance methyl-esterified cross-linking of glucuronoarabinoxylans in the VTZ. These findings indicate that the SAM and VTZ express two distinct tissue-specific apoplastic responses during cold acclimation.

Transcriptomic Insights into Phenological Development and Cold Tolerance of Wheat Grown in the Field.

Cold acclimation and winter survival in cereal species is determined by complicated environmentally regulated gene expression. However, studies investigating these complex cold responses are mostly conducted in controlled environments that only consider the responses to single environmental variables. In this study, we have comprehensively profiled global transcriptional responses in crowns of field-grown spring and winter wheat (Triticum aestivum) genotypes and their near-isogenic lines with the VRN-A1 alleles swapped. This in-depth analysis revealed multiple signaling, interactive pathways that influence cold tolerance and phenological development to optimize plant growth and development in preparation for a wide range of over-winter stresses. Investigation of genetic differences at the VRN-A1 locus revealed that a vernalization requirement maintained a higher level of cold response pathways while VRN-A1 genetically promoted floral development. Our results also demonstrated the influence of genetic background on the expression of cold and flowering pathways. The link between delayed shoot apex development and the induction of cold tolerance was reflected by the gradual up-regulation of abscisic acid-dependent and C-REPEAT-BINDING FACTOR pathways. This was accompanied by the down-regulation of key genes involved in meristem development as the autumn progressed. The chromosome location of differentially expressed genes between the winter and spring wheat genetic backgrounds showed a striking pattern of biased gene expression on chromosomes 6A and 6D, indicating a transcriptional regulation at the genome level. This finding adds to the complexity of the genetic cascades and gene interactions that determine the evolutionary patterns of both phenological development and cold tolerance traits in wheat.

Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms.

Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP) markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called 'large p, small n' problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers). While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat) and Norstar × Cappelle Desprez (bread wheat). The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF), we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez). Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase making map expansion unavoidable. Therefore, we suggest developers improve linkage mapping algorithms for efficient analysis of high-throughput data. This study outlines a practical strategy to estimate the IF due to the proportion of co-segregating markers and outlines a method to scale the length of the map accordingly.

Exploring new alleles for frost tolerance in winter rye.

KEY MESSAGE: Rye genetic resources provide a valuable source of new alleles for the improvement of frost tolerance in rye breeding programs. Frost tolerance is a must-have trait for winter cereal production in northern and continental cropping areas. Genetic resources should harbor promising alleles for the improvement of frost tolerance of winter rye elite lines. For frost tolerance breeding, the identification of quantitative trait loci (QTL) and the choice of optimum genome-based selection methods are essential. We identified genomic regions involved in frost tolerance of winter rye by QTL mapping in a biparental population derived from a highly frost tolerant selection from the Canadian cultivar Puma and the European elite line Lo157. Lines per se and their testcrosses were phenotyped in a controlled freeze test and in multi-location field trials in Russia and Canada. Three QTL on chromosomes 4R, 5R, and 7R were consistently detected across environments. The QTL on 5R is congruent with the genomic region harboring the Frost resistance locus 2 (Fr-2) in Triticeae. The Puma allele at the Fr-R2 locus was found to significantly increase frost tolerance. A comparison of predictive ability obtained from the QTL-based model with different whole-genome prediction models revealed that besides a few large, also small QTL effects contribute to the genomic variance of frost tolerance in rye. Genomic prediction models assigning a high weight to the Fr-R2 locus allow increasing the selection intensity for frost tolerance by genome-based pre-selection of promising candidates.

Adjustments of lipid pathways in plant adaptation to temperature stress.

Modulation of membrane lipid composition under varying environmental conditions is an important part of plant stress adaptation. Most notably, proportional changes of lipid composition in response to temperature changes are a major cellular response to requirements of membrane fluidity adjustment. In higher plants, synthesis of glycerolipids is accomplished by 2 major pathways, the prokaryotic and eukaryotic pathway, located in the chloroplast and the endoplasmic reticulum (ER), respectively. Recently, we systematically investigated the re-adjustments of glycerolipid pathways under temperature stress at the metabolite and transcript levels using 3 plant species with distinct lipid profiles. The relative contributions of 2 pathways and lipid channeling from the ER and chloroplast were both observed in plants under temperature stress. Potential factors controlling the lipid flux were identified through transcriptome analysis.

Understanding the biochemical basis of temperature-induced lipid pathway adjustments in plants.

Glycerolipid biosynthesis in plants proceeds through two major pathways compartmentalized in the chloroplast and the endoplasmic reticulum (ER). The involvement of glycerolipid pathway interactions in modulating membrane desaturation under temperature stress has been suggested but not fully explored. We profiled glycerolipid changes as well as transcript dynamics under suboptimal temperature conditions in three plant species that are distinctively different in the mode of lipid pathway interactions. In Arabidopsis thaliana, a 16:3 plant, the chloroplast pathway is upregulated in response to low temperature, whereas high temperature promotes the eukaryotic pathway. Operating under a similar mechanistic framework, Atriplex lentiformis at high temperature drastically increases the contribution of the eukaryotic pathway and correspondingly suppresses the prokaryotic pathway, resulting in the switch of lipid profile from 16:3 to 18:3. In wheat (Triticum aestivum), an 18:3 plant, low temperature also influences the channeling of glycerolipids from the ER to chloroplast. Evidence of differential trafficking of diacylglycerol moieties from the ER to chloroplast was uncovered in three plant species as another layer of metabolic adaptation under temperature stress. We propose a model that highlights the predominance and prevalence of lipid pathway interactions in temperature-induced lipid compositional changes.

Genotype-dependent Burst of Transposable Element Expression in Crowns of Hexaploid Wheat (Triticum aestivum L.) during Cold Acclimation.

The expression of 1,613 transposable elements (TEs) represented in the Affymetrix Wheat Genome Chip was examined during cold treatment in crowns of four hexaploid wheat genotypes that vary in tolerance to cold and in flowering time. The TE expression profiles showed a constant level of expression throughout the experiment in three of the genotypes. In winter Norstar, the most cold-hardy of the four genotypes, a subset of the TEs showed a burst of expression after vernalization saturation was achieved. About 47% of the TEs were expressed, and both Class I (retrotransposons) and Class II (DNA transposons) types were well represented. Gypsy and Copia were the most represented among the retrotransposons while CACTA and Mariner were the most represented DNA transposons. The data suggests that the Vrn-A1 region plays a role in the stage-specific induction of TE expression in this genotype.

Contrasting cDNA-AFLP profiles between crown and leaf tissues of cold-acclimated wheat plants indicate differing regulatory circuitries for low temperature tolerance.

Low-temperature (LT) tolerance in winter wheat (Triticum aestivum L.) is an economically important but complex trait. Four selected wheat genotypes, a winter hardy cultivar, Norstar, a tender spring cultivar, Manitou and two near-isogenic lines with Vrn-A1 (spring Norstar) and vrn-A1 (winter Manitou) alleles of Manitou and Norstar were cold-acclimated at 6°C and crown and leaf tissues were collected at 0, 2, 14, 21, 35, 42, 56 and 70 days of cold acclimation. cDNA-AFLP profiling was used to determine temporal expression profiles of transcripts during cold-acclimation in crown and leaf tissues, separately to determine if LT regulatory circuitries in crown and leaf tissues could be delineated using this approach. Screening 64 primer combinations identified 4,074 and 2,757 differentially expressed transcript-derived fragments (TDFs) out of which 38 and 16% were up-regulated as compared to 3 and 6% that were down-regulated in crown and leaf tissues, respectively. DNA sequencing of TDFs revealed sequences common to both tissues including genes coding for DEAD-box RNA helicase, choline-phosphate cytidylyltransferase and delta-1-pyrroline carboxylate synthetase. TDF specific to crown tissues included genes coding for phospahtidylinositol kinase, auxin response factor protein and brassinosteroid insensitive 1-associated receptor kinase. In leaf, genes such as methylene tetrahydrofolate reductase, NADH-cytochrome b5 reductase and malate dehydrogenase were identified. However, 30 and 14% of the DNA sequences from the crown and leaf tissues, respectively, were hypothetical or unknown proteins. Cluster analysis of up-, down-regulated and unique TDFs, DNA sequence and real-time PCR validation, infer that mechanisms operating in crown and leaf tissue in response to LT are differently regulated and warrant further studies.

Identification of genomic regions determining the phenological development leading to floral transition in wheat (Triticum aestivum L.).

Autumn-seeded winter cereals acquire tolerance to freezing temperatures and become vernalized by exposure to low temperature (LT). The level of accumulated LT tolerance depends on the cold acclimation rate and factors controlling timing of floral transition at the shoot apical meristem. In this study, genomic loci controlling the floral transition time were mapped in a winter wheat (T. aestivum L.) doubled haploid (DH) mapping population segregating for LT tolerance and rate of phenological development. The final leaf number (FLN), days to FLN, and days to anthesis were determined for 142 DH lines grown with and without vernalization in controlled environments. Analysis of trait data by composite interval mapping (CIM) identified 11 genomic regions that carried quantitative trait loci (QTLs) for the developmental traits studied. CIM analysis showed that the time for floral transition in both vernalized and non-vernalized plants was controlled by common QTL regions on chromosomes 1B, 2A, 2B, 6A and 7A. A QTL identified on chromosome 4A influenced floral transition time only in vernalized plants. Alleles of the LT-tolerant parent, Norstar, delayed floral transition at all QTLs except at the 2A locus. Some of the QTL alleles delaying floral transition also increased the length of vegetative growth and delayed flowering time. The genes underlying the QTLs identified in this study encode factors involved in regional adaptation of cold hardy winter wheat.

Comparative expression of Cbf genes in the Triticeae under different acclimation induction temperatures.

In plants, the C-repeat binding factors (Cbfs) are believed to regulate low-temperature (LT) tolerance. However, most functional studies of Cbfs have focused on characterizing expression after an LT shock and have not quantified differences associated with variable temperature induction or the rate of response to LT treatment. In the Triticeae, rye (Secale cereale L.) is one of the most LT-tolerant species, and is an excellent model to study and compare Cbf LT induction and expression profiles. Here, we report the isolation of rye Cbf genes (ScCbfs) and compare their expression levels in spring- and winter-habit rye cultivars and their orthologs in two winter-habit wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) cultivars. Eleven ScCbfs were isolated spanning all four major phylogenetic groups. Nine of the ScCbfs mapped to 5RL and one to chromosome 2R. Cbf expression levels were variable, with stronger expression in winter- versus spring-habit rye cultivars but no clear relationship with cultivar differences in LT, down-stream cold-regulated gene expression and Cbf expression were detected. Some Cbfs were expressed only at warmer acclimation temperatures in all three species and their expression was repressed at the end of an 8-h dark period at warmer temperatures, which may reflect a temperature-dependent, light-regulated diurnal response. Our work indicates that Cbf expression is regulated by complex genotype by time by induction-temperature interactions, emphasizing that sample timing, induction-temperature and light-related factors must receive greater consideration in future studies involving functional characterization of LT-induced genes in cereals.

Quantitative expression analysis of selected COR genes reveals their differential expression in leaf and crown tissues of wheat (Triticum aestivum L.) during an extended low temperature acclimation regimen.

A number of COR genes (COld-Regulated genes) have been implicated in the acquisition of low temperature (LT) tolerance in wheat (Triticum aestivum L.). This study compared the relative expression patterns of selected COR genes in leaf and crown tissues of wheat near-isogenic lines to increase understanding of the molecular mechanisms underlying LT acclimation. Reciprocal near-isogenic lines were generated such that the dominant Vrn-A1 and recessive vrn-A1 loci were interchanged in a spring cv. Manitou and a winter cv. Norstar. Phenological development, acquisition of LT tolerance, and WCS120 polypeptide accumulation in these genotypes proceeded at rates similar to those previously reported for 6 degrees C acclimation from 0 to 98 d. However, a differential accumulation of WCS120 polypeptide and expression of the COR genes Wcs120, Wcor410, and Wcor14 was observed in the leaf and crown tissues. COR gene transcript levels peaked at 2 d of the acclimation period in both tissues and differences among genotypes were most evident at this time. COR gene expression was highest for the LT-tolerant and lowest for the tender genotypes. However, expression rates were divergent enough in genotypes with intermediate hardiness that comparisons among tissues and/or times during acclimation often resulted in variable interpretations of the relative expression of the COR genes in the determination of LT tolerance. These observations emphasize the need to pay close attention to experimental conditions, sampling times, and genotype and tissue selection in experiments designed to identify the critical genetic components that interact to determine LT acclimation.

Low-temperature acclimation of barley cultivars used as parents in mapping populations: response to photoperiod, vernalization and phenological development.

Six barley (Hordeum vulgare L.) accessions, previously used as parents of mapping populations, were evaluated for characters potentially affecting the location of low-temperature (LT) tolerance QTLs. Three were of winter growth habit (Kompolti Korai, Nure, and Strider), one was facultative (Dicktoo) and two were spring (Morex and Tremois). Final leaf number (FLN) and LT(50 )were determined at weekly intervals from 0 to 98 days of LT acclimation/vernalization under both long day (LD) and short day (SD) photoperiods. The point of vegetative/reproductive transition was determined from measurements of double ridge (DR) formation and FLN. With the exception of Nure, SD delayed development by increasing leaf production. Dicktoo was extremely SD sensitive lengthening its vegetative phase by more than 63 days relative to the LD photoperiod. SD had the opposite effect on Nure, causing an accelerating of flowering exhibiting the characteristic of 'short day vernalization'. All accessions except Dicktoo and Kompolti Korai acclimated rapidly in the first 7 days of LT exposure, approaching their maximum LT tolerance in 14-21 days. Dicktoo and Kompolti Korai continued to slowly acclimate until reproductive transition. The results emphasize two important points: (1) the location of QTLs for LT tolerance, and as a consequence the identification of putative candidate genes, will be a function of the genotypes sampled, the experimental conditions used, and the quality of the phenotypic data and (2) the barley LT tolerance pathway reaches an early impediment relative to closely related more hardy members of the Triticeae such as wheat and rye.

Identification of quantitative trait loci and associated candidate genes for low-temperature tolerance in cold-hardy winter wheat.

Low-temperature (LT) tolerance is an important economic trait in winter wheat (Triticum aestivum L.) that determines the plants' ability to cope with below freezing temperatures. Essential elements of the LT tolerance mechanism are associated with the winter growth habit controlled by the vernalization loci (Vrn-1) on the group 5 chromosomes. To identify genomic regions, which in addition to vrn-1 determine the level of LT tolerance in hexaploid wheat, two doubled haploid (DH) mapping populations were produced using parents with winter growth habit (vrn-A1, vrn-B1, and vrn-D1) but showing different LT tolerance levels. A total of 107 DH lines were analyzed by genetic mapping to produce a consensus map of 2,873 cM. The LT tolerance levels for the Norstar (LT(50)=-20.7 degrees C) x Winter Manitou (LT(50)=-14.3 degrees C) mapping population ranged from -12.0 to -22.0 degrees C. Single marker analysis and interval mapping of phenotyped lines revealed a major quantitative trait locus (QTL) on chromosome 5A and a weaker QTL on chromosome 1D. The 5A QTL located 46 cM proximal to the vrn-A1 locus explained 40% of the LT tolerance variance. Two C-repeat Binding Factor (CBF) genes expressed during cold acclimation in Norstar were located at the peak of the 5A QTL.

Low-temperature tolerance and genetic potential in wheat (Triticum aestivum L.): response to photoperiod, vernalization, and plant development.

It is frequently observed that winter habit types are more low-temperature (LT) tolerant than spring habit types. This raises the question of whether this is due to pleiotropic effects of the vernalization loci or to the linkage of LT-tolerance genes to these vernalization loci. Reciprocal near-isogenic lines (NILs) for alleles at the Vrn-A1 locus, Vrn-A1 and vrn-A1, determining spring and winter habit respectively, in two diverse genetic backgrounds of wheat (Triticum aestivum L.) were used to separate the effects of vernalization, photoperiod, and development on identical, or near identical, genetic backgrounds. The vrn-A1 allele in the winter lines allowed full expression of genotype dependent LT tolerance potential. The winter allele (vrn-A1) in a very cold tolerant genetic background resulted in 11 degrees C, or a 2.4-fold, greater LT tolerance compared to the spring allele. Similarly, the delay in development caused by short-day (SD) versus long-day (LD) photoperiod in the identical spring habit NIL resulted in an 8.5 degrees C or 2.1-fold, increase in LT tolerance. The duration of time in early developmental stages was shown to underlie full expression of genetic LT-tolerance potential. Therefore, pleiotropic effects of the vernalization loci can explain the association of LT tolerance and winter habit irrespective of either the proposed closely linked Fr-A1 or the more distant Fr-A2 LT-tolerance QTLs. Plant development progressively reduced LT-acclimation ability, particularly after the main shoot meristem had advanced to the double ridge reproductive growth stage. The Vrn-1 genes, or other members of the flowering induction pathway, are discussed as possible candidates for involvement in LT-tolerance repression.

TaVRT-2, a member of the StMADS-11 clade of flowering repressors, is regulated by vernalization and photoperiod in wheat.

The initiation of the reproductive phase in winter cereals is delayed during winter until favorable growth conditions resume in the spring. This delay is modulated by low temperature through the process of vernalization. The molecular and genetic bases of the interaction between environmental factors and the floral transition in these species are still unknown. However, the recent identification of the wheat (Triticum aestivum L.) TaVRT-1 gene provides an opportunity to decipher the molecular basis of the flowering-time regulation in cereals. Here, we describe the characterization of another gene, named TaVRT-2, possibly involved in the flowering pathway in wheat. Molecular and phylogenetic analyses indicate that the gene encodes a member of the MADS-box transcription factor family that belongs to a clade responsible for flowering repression in several species. Expression profiling of TaVRT-2 in near-isogenic lines and different genotypes with natural variation in their response to vernalization and photoperiod showed a strong relationship with floral transition. Its expression is up-regulated in the winter genotypes during the vegetative phase and in photoperiod-sensitive genotypes during short days, and is repressed by vernalization to a level that allows the transition to the reproductive phase. Protein-protein interaction studies revealed that TaVRT-2 interacts with proteins encoded by two important vernalization genes (TaVRT-1/VRN-1 and VRN-2) in wheat. These results support the hypothesis that TaVRT-2 is a putative repressor of the floral transition in wheat.

TaVRT-1, a putative transcription factor associated with vegetative to reproductive transition in cereals.

The molecular genetics of vernalization, defined as the promotion of flowering by cold treatment, is still poorly understood in cereals. To better understand this mechanism, we cloned and characterized a gene that we named TaVRT-1 (wheat [Triticum aestivum] vegetative to reproductive transition-1). Molecular and sequence analyses indicated that this gene encodes a protein homologous to the MADS-box family of transcription factors that comprises certain flowering control proteins in Arabidopsis. Mapping studies have localized this gene to the Vrn-1 regions on the long arms of homeologous group 5 chromosomes, regions that are associated with vernalization and freezing tolerance (FT) in wheat. The level of expression of TaVRT-1 is positively associated with the vernalization response and transition from vegetative to reproductive phase and is negatively associated with the accumulation of COR genes and degree of FT. Comparisons among different wheat genotypes, near-isogenic lines, and cereal species, which differ in their vernalization response and FT, indicated that the gene is inducible only in those species that require vernalization, whereas it is constitutively expressed in spring habit genotypes. In addition, experiments using both the photoperiod-sensitive barley (Hordeum vulgare cv Dicktoo) and short or long day de-acclimated wheat revealed that the expression of TaVRT-1 is also regulated by photoperiod. These expression studies indicate that photoperiod and vernalization may regulate this gene through separate pathways. We suggest that TaVRT-1 is a key developmental gene in the regulatory pathway that controls the transition from the vegetative to reproductive phase in cereals.