Temperate Cereals Research Articles

Virtual water content of temperate cereals and maize: Present and potential future patterns

Knowledge of the virtual water content (VWC) of crops and especially its possible future developments is helpful for improvements in water productivity and water management, which are necessary at global scale due to rising demand for food, the necessity to ease present and future water scarcity, and the reduction of poverty. Using a dynamic global vegetation and water balance model (LPJmL), this study quantifies the VWC of two of the most important crop types worldwide, temperate cereals and maize, at high spatial resolution (0.5°). We analyzed present conditions (1999–2003) and also for the first time also for scenarios of future climate and increasing atmospheric CO2 concentrations (2041–2070; HadCM3, ECHAM5 and CCSM3 climate models, A2 emissions scenario). VWC presently differs significantly among regions: highest values are common in large parts of Africa (>2 m3 kg−1), and lowest values were found e.g. for Central Europe (<0.5 m3 kg−1), indicating that water-use efficiency of crops is much higher in the latter region. The regional patterns of VWC result from complex and interactive processes; the dominant factor is the crop yield level (high VWC values occur most frequently in regions with low yields). Climate change and rising atmospheric CO2 concentration will have non-uniform effects on crop yields and evapotranspiration. Worldwide VWC patterns will change significantly, with a pronounced regional pattern that reflects primarily the changes in yields as driven mainly by regionally decreasing precipitation, increasing temperature and increasing atmospheric CO2 concentration. Although globally the water-use efficiency is projected to increase, many regions—including parts of the US, East and Mediterranean Europe, South Africa, Argentina, Australia and South East Asia—are projected to become less water efficient (higher VWC) for at least one of the crop types. CO2 fertilisation was simulated to generally reduce VWC, though realisation of this effect in the field will depend, for example, on the intensity of nutrient management in the future. The potentially adverse future changes in VWC found here pose a challenge to water management efforts and eventually global trade policies.

Sensitivity of yield and grain nitrogen concentration of wheat, lupin and pea to source reduction during grain filling. A comparative survey under high yielding conditions

Several studies have been conducted to evaluate the response of crops, especially temperate cereals, to different source–sink ratios during grain filling. However, there is much less information about temperate legumes and even less work comparing the two. The objective of this study was to evaluate the response of both grain yield and grain nitrogen concentration of wheat ( Triticum aestivum L.), narrow-leafed lupin ( Lupinus angustifolius L.) and pea ( Pisum sativum L.) to similar source reduction during grain filling. Two field experiments were conducted in a high yielding environment of Southern Chile. In experiment 1 wheat and narrow-leafed lupin were grown for two consecutive years. Experiment 2 evaluated wheat and pea on two sowing dates. In both experiments a reduction in the source–sink ratio was imposed by using black nets that intercepted 90% of the incident solar radiation from the commencement of the linear dry matter accumulation to physiological maturity. Grain yield was differentially ( p < 0.01) decreased by the source reduction in lupin (98%), wheat (63%) and pea (26%). Given that these experiments were carried out in a high yielding environment, the higher response of wheat relative to previous studies supports the hypothesis that the higher the yield potential, the higher the source sensitivity of this crops during the grain filling period. On the other hand, source reduction positively affected ( p < 0.05) grain nitrogen concentration in wheat (66%) and pea (18%) but negatively affected lupin (40%). The higher sensitivity of grain yield compared to that of grain nitrogen yield was the cause of the positive effect of the lower source–sink ratio recorded in wheat and pea. In contrast, source shortage in lupin decreased grain nitrogen concentration probably as result of the quick response of grain growth to source limitation. The contrasting sensitivities of lupin, wheat and pea to source reduction during grain filling prevent us to see grain yield and quality response of these crops as separate groups, i.e. temperate cereals vs. temperate legumes.

Regions associated with repression of the barley (Hordeum vulgare) VERNALIZATION1 gene are not required for cold induction

Activity of the VERNALIZATION1 (VRN1) gene is required for flowering in temperate cereals such as wheat and barley. In varieties that require prolonged exposure to cold to flower (vernalization), VRN1 is expressed at low levels and is induced by vernalization to trigger flowering. In other varieties, deletions or insertions in the first intron of the VRN1 gene are associated with increased VRN1 expression in the absence of cold treatment, reducing or eliminating the requirement for vernalization. To characterize natural variation in VRN1, the first intron of the barley (Hordeum vulgare) VRN1 gene (HvVRN1) was assayed for deletions or insertions in a collection of 1,000 barleys from diverse geographical regions. Ten alleles of HvVRN1 containing deletions or insertions in the first intron were identified, including three alleles that have not been described previously. Different HvVRN1 alleles were associated with differing levels of HvVRN1 expression in non-vernalized plants and with different flowering behaviour. Using overlapping deletions, we delineated regions in the HvVRN1 first intron that are associated with low levels of HvVRN1 expression in non-vernalized plants. Deletion of these intronic regions does not prevent induction of HvVRN1 by cold or the maintenance of increased HvVRN1 expression following cold treatment. We suggest that regions within the first intron of HvVRN1 are required to maintain low levels of HvVRN1 expression prior to winter but act independently of the regulatory mechanisms that mediate induction of HvVRN1 by cold during winter.

Natural variation at the DEP1 locus enhances grain yield in rice

Grain yield is controlled by quantitative trait loci (QTLs) derived from natural variations in many crop plants. Here we report the molecular characterization of a major rice grain yield QTL that acts through the determination of panicle architecture. The dominant allele at the DEP1 locus is a gain-of-function mutation causing truncation of a phosphatidylethanolamine-binding protein-like domain protein. The effect of this allele is to enhance meristematic activity, resulting in a reduced length of the inflorescence internode, an increased number of grains per panicle and a consequent increase in grain yield. This allele is common to many Chinese high-yielding rice varieties and likely represents a relatively recent introduction into the cultivated rice gene pool. We also show that a functionally equivalent allele is present in the temperate cereals and seems to have arisen before the divergence of the wheat and barley lineages.

The molecular biology of seasonal flowering-responses in Arabidopsis and the cereals

In arabidopsis (Arabidopsis thaliana), FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC) play key roles in regulating seasonal flowering-responses to synchronize flowering with optimal conditions. FT is a promoter of flowering activated by long days and by warm conditions. FLC represses FT to delay flowering until plants experience winter. The identification of genes controlling flowering in cereals allows comparison of the molecular pathways controlling seasonal flowering-responses in cereals with those of arabidopsis. The role of FT has been conserved between arabidopsis and cereals; FT-like genes trigger flowering in response to short days in rice or long days in temperate cereals, such as wheat (Triticum aestivum) and barley (Hordeum vulgare). Many varieties of wheat and barley require vernalization to flower but FLC-like genes have not been identified in cereals. Instead, VERNALIZATION2 (VRN2) inhibits long-day induction of FT-like1 (FT1) prior to winter. VERNALIZATION1 (VRN1) is activated by low-temperatures during winter to repress VRN2 and to allow the long-day response to occur in spring. In rice (Oryza sativa) a VRN2-like gene Ghd7, which influences grain number, plant height and heading date, represses the FT-like gene Heading date 3a (Hd3a) in long days, suggesting a broader role for VRN2-like genes in regulating day-length responses in cereals. Other genes, including Early heading date (Ehd1), Oryza sativa MADS51 (OsMADS51) and INDETERMINATE1 (OsID1) up-regulate Hd3a in short days. These genes might account for the different day-length response of rice compared with the temperate cereals. No genes homologous to VRN2, Ehd1, Ehd2 or OsMADS51 occur in arabidopsis. It seems that different genes regulate FT orthologues to elicit seasonal flowering-responses in arabidopsis and the cereals. This highlights the need for more detailed study into the molecular basis of seasonal flowering-responses in cereal crops or in closely related model plants such as Brachypodium distachyon.

Functional Plant Genomics

Functional Plant Genomics

Regulation of flowering in temperate cereals

Long exposure to cold (vernalization) accelerates flowering in winter cereals, a process regulated by the VRN1 (approximately AP1), VRN2, and VRN3 (approximately FT) vernalization genes. Flowering during the fall is prevented by the VRN2 downregulation of VRN3 and low VRN1 transcription. Vernalization induces VRN1, which is followed by the downregulation of VRN2, thereby releasing VRN3. In the longer days of spring, photoperiod genes PPD1 and CO upregulate VRN3, which induces VRN1 above the threshold levels required for flowering initiation. VRN3 transcription is modulated through interactions involving CCT-domain proteins and HAP2/HAP3/HAP5 complexes coded by multiple genes. The vast number of HAP-CCT combinations can provide the flexibility required for integrating seasonal cues and different stress signals in the regulation of the transition to flowering.

Turning a Wild Plant into a Model A Dvu Story

In the past two decades we have witnessed how a useless wild weed has been transformed from an anonymous into a model plant, probably the most widely cultivated plant species. The process has been rather slowly in the beginning, very laborious on the way, extremely expensive and time consuming, but the outcome is priceless the knowledge that is most likely to frame and fill the blueprint of the first artificial plant, as system biology promises. The plant species is Arabidopsis thaliana and the growers are highly qualified researchers worldwide. This review introduces a new anonymous Brachypodium distachyon that raised big hopes for addressing specific problems of fundamental and practical biology in temperate cereals and forage grasses, and is rapidly becoming a sweetheart for the researchers working with these crops, and not only.

Orthology between genomes of Brachypodium, wheat and rice.

BackgroundIn the past, rice genome served as a good model for studies involving comparative genomics of grass species. More recently, however, Brachypodium distachyon genome has emerged as a better model system for genomes of temperate cereals including wheat. During the present study, Brachypodium EST contigs were utilized to resolve orthologous relationships among the genomes of Brachypodium, wheat and rice.FindingsComparative sequence analysis of 3,818 Brachypodium EST (bEST) contigs and 3,792 physically mapped wheat EST (wEST) contigs revealed that as many as 449 bEST contigs were orthologous to 1,154 wEST loci that were bin-mapped on all the 21 wheat chromosomes. Similarly 743 bEST contigs were orthologous to specific rice genome sequences distributed on all the 12 rice chromosomes. As many as 183 bEST contigs were orthologous to both wheat and rice genome sequences, which harbored as many as 17 SSRs conserved across the three species. Primers developed for 12 of these 17 conserved SSRs were used for a wet-lab experiment, which resolved relatively high level of conservation among the genomes of Brachypodium, wheat and rice.ConclusionThe present study confirmed that Brachypodium is a better model than rice for analysis of the genomes of temperate cereals like wheat and barley. The whole genome sequence of Brachypodium, which should become available in the near future, will further facilitate greatly the studies involving comparative genomics of cereals.

Flux Balance Analysis of Barley Seeds: A Computational Approach to Study Systemic Properties of Central Metabolism

The accumulation of storage compounds is an important aspect of cereal seed metabolism. Due to the agronomical importance of the storage reserves of starch, protein, and oil, the understanding of storage metabolism is of scientific interest, with practical applications in agronomy and plant breeding. To get insight into storage patterning in developing cereal seed in response to environmental and genetic perturbation, a computational analysis of seed metabolism was performed. A metabolic network of primary metabolism in the developing endosperm of barley (Hordeum vulgare), a model plant for temperate cereals, was constructed that includes 257 biochemical and transport reactions across four different compartments. The model was subjected to flux balance analysis to study grain yield and metabolic flux distributions in response to oxygen depletion and enzyme deletion. In general, the simulation results were found to be in good agreement with the main biochemical properties of barley seed storage metabolism. The predicted growth rate and the active metabolic pathway patterns under anoxic, hypoxic, and aerobic conditions predicted by the model were in accordance with published experimental results. In addition, the model predictions gave insight into the potential role of inorganic pyrophosphate metabolism to maintain seed metabolism under oxygen deprivation.

Integration of seasonal flowering time responses in temperate cereals

Our paper describes how the genetic pathways which regulate vernalization and long-day flowering responses are integrated to promote spring flowering in cereals. This process is mediated by the VERNALIZATION1 (VRN1) and VRN2 genes. VRN2 encodes a CONSTANS-like protein that represses FLOWERING LOCUS T (FT1) to block the long-day flowering response until plants are vernalized. When plants are vernalized VRN1, a FRUITFUL-like MADS box transcription factor, is induced. This down-regulates VRN2, allowing long-day induction of FT1 to occur post-vernalization. A comparison of the pathways regulating seasonal induction of flowering in cereals with those of Arabidopsis shows the vernalization response pathway has evolved convergently to regulate the activity of a conserved daylength response pathway in these divergent plant lineages.Addendum to: Hemming M.N, Peacock W.J, Dennis E.S, Trevaskis B. Low temperature and daylength cues are integrated to regulate FLOWERING LOCUS T in barley. Plant Physiol 2008; 147:355-66.

Wheat FT protein regulates VRN1 transcription through interactions with FDL2.

A precise regulation of flowering time is central to plant species survival. Therefore, mechanisms have evolved in plants to integrate various environmental cues to optimize flowering time. In this study, we show that the product of the wheat gene TaFT, which integrates photoperiod and vernalization signals promoting flowering, interacts with bZIP proteins TaFDL2 and TaFDL6. We also show that TaFDL2 can interact in vitro with five ACGT elements in the promoter of the meristem identity gene VRN1, suggesting that TaFDL2 is a functional homologue of Arabidopsis FD. No direct interactions between the TaFT protein and the VRN1 promoter were detected. Transgenic wheat plants over-expressing TaFT showed parallel increases in VRN1 transcripts, suggesting that TaFT provides transcriptional activation of VRN1, possibly through interactions with the TaFDL2 protein. The same transgenic plants also showed increased transcript levels of TaFT2 (a TaFT paralogue), indicating that TaFT2 acts downstream of TaFT. The fact that TaFT2 interacts with another bZIP protein TaFDL13, which lacks the ability to interact with the VRN1 promoter, suggests that TaFT and TaFT2 have different gene targets. This observation agrees with the functional divergence observed for the TaFT and TaFT2 orthologous genes in rice. The temperate cereals analyzed so far show VRN1 transcripts in the leaves, a characteristic not observed in Arabidopsis or rice. The high levels of TaFDL2 transcripts observed in wheat leaves provide a simple explanation for this difference. We present a hypothesis to explain the conservation of VRN1 expression in the leaves of temperate cereals.

Globulins are the main seed storage proteins in Brachypodium distachyon

Brachypodium distachyon is being developed as a model system to study temperate cereals and forage grasses. We have begun to investigate its utility to understand seed development and grain filling by identifying the major seed storage proteins in a diploid accession Bd21. With the use of ID SDS-PAGE and mass spectrometry we detected seven major storage protein bands, six of which were identified as globulins. A subset of the major seed proteins isolated from three hexaploid accessions, Bd4, Bd14 and Bd17 were also identified as globulins. Several Brachypodium cDNAs clones encoding globulin were completely sequenced. Two types of globulin genes were identified, Bd.glo1 and Bd.glo2, which are similar to maize 7S and oat 12S globulins, respectively. The derived polypeptide sequences of the globulins contain a typical signal peptide sequence in their polypeptide N-termini and two cupin domains. Bd.glo1 is encoded by a single copy gene, whereas, Bd.glo2 belongs to a gene family.

Genetic resources in the Triticeae

To man Triticeae is one of the most important tribes in the plant kingdom, comprising the temperate cereals wheat, barley, rye, triticale and several important forages. All ca. 350 wild taxa of the tribe thus constitute a gigantic gene pool to the crops. By necessity the primary gene pools have received the highest priority in collecting, evaluation and utilization. However, the wild and weedy taxa have in recent years received an increased attention, but the basic botanical and genetical knowledge is in many groups fragmentary. Even though collecting has been accomplished in many areas, there are still areas which have not been visited. Very limited knowledge is present on seed physiology, seed handling techniques, sampling strategies, and genetic diversity concerning wild species. Most Triticeae species are common over vast areas, but quite a few need special attention, being rare, or threatened by extinction.

A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R

BackgroundRye (Secale cereale L.) belongs to tribe Triticeae and is an important temperate cereal. It is one of the parents of man-made species Triticale and has been used as a source of agronomically important genes for wheat improvement. The short arm of rye chromosome 1 (1RS), in particular is rich in useful genes, and as it may increase yield, protein content and resistance to biotic and abiotic stress, it has been introgressed into wheat as the 1BL.1RS translocation. A better knowledge of the rye genome could facilitate rye improvement and increase the efficiency of utilizing rye genes in wheat breeding.ResultsHere, we report on BAC end sequencing of 1,536 clones from two 1RS-specific BAC libraries. We obtained 2,778 (90.4%) useful sequences with a cumulative length of 2,032,538 bp and an average read length of 732 bp. These sequences represent 0.5% of 1RS arm. The GC content of the sequenced fraction of 1RS is 45.9%, and at least 84% of the 1RS arm consists of repetitive DNA. We identified transposable element junctions in BESs and developed insertion site based polymorphism markers (ISBP). Out of the 64 primer pairs tested, 17 (26.6%) were specific for 1RS. We also identified BESs carrying microsatellites suitable for development of 1RS-specific SSR markers.ConclusionThis work demonstrates the utility of chromosome arm-specific BAC libraries for targeted analysis of large Triticeae genomes and provides new sequence data from the rye genome and molecular markers for the short arm of rye chromosome 1.

A high-throughput Agrobacterium-mediated transformation system for the grass model species Brachypodium distachyon L.

In the ongoing process of developing Brachypodium distachyon as a model plant for temperate cereals and forage grasses, we have developed a high-throughput Agrobacterium-mediated transformation system for a diploid accession. Embryogenic callus, derived from immature embryos of the accession BDR018, were transformed with Agrobacterium tumefaciens strain AGL1 carrying two T-DNA plasmids, pDM805 and pWBV-Ds-Ubi-bar-Ds. Transient and stable transformation efficiencies were optimised by varying the pre-cultivation period, which had a strong effect on stable transformation efficiency. On average 55% of 17-day-old calli co-inoculated with Agrobacterium regenerated stable transgenic plants. Stable transformation frequencies of up to 80%, which to our knowledge is the highest transformation efficiency reported in graminaceous species, were observed. In a study of 177 transgenic lines transformed with pDM805, all of the regenerated transgenic lines were resistant to BASTA, while the gusA gene was expressed in 88% of the transgenic lines. Southern blot analysis revealed that 35% of the tested plants had a single T-DNA integration. Segregation analysis performed on progenies of ten selected T(0) plants indicated simple Mendelian inheritance of the two transgenes. Furthermore, the presence of two selection marker genes, bar and hpt, on the T-DNA of pWBV-Ds-Ubi-bar-Ds allowed us to characterize the developed transformation protocol with respect to full-length integration rate. Even when not selected for, full-length integration occurred in 97% of the transformants when using bialaphos as selection agent.

Control of flowering time in temperate cereals: genes, domestication, and sustainable productivity

The control of flowering is central to reproductive success in plants, and has a major impact on grain yield in crop species. The global importance of temperate cereal crops such as wheat and barley has meant emphasis has long been placed on understanding the genetics of flowering in order to enhance yield. Leads gained from the dissection of the molecular genetics of model species have combined with comparative genetic approaches, recently resulting in the isolation of the first flowering time genes in wheat and barley. This paper reviews the genetics and genes involved in cereal flowering pathways and the current understanding of how two of the principal genes, Vrn and Ppd, have been involved in domestication and adaptation to local environments, and the implications for future breeding programmes are discussed.

BAC 'landing' on chromosomes of Brachypodium distachyon for comparative genome alignment

Fluorescence in situ hybridization (FISH) using bacterial artificial chromosomes (BACs) with large genomic DNA inserts as probes (BAC 'landing') is a powerful means by which eukaryotic genomes can be physically mapped and compared. Here we report a BAC landing protocol that has been developed specifically for the weedy grass species Brachypodium distachyon, which has been adopted recently by the scientific community as an alternative model for the temperate cereals and grasses. The protocol describes the preparation of somatic and meiotic chromosome substrates for FISH, the labeling of BACs, a chromosome mapping strategy, empirical conditions for optimal in situ hybridization and stringency washing, the detection of probes and the capturing and processing of images. The expected outcome of the protocol is the specific assignment of BACs containing single-copy inserts to one of the five linkage groups of the genome of this species. Once somatic or meiotic material is available, the entire protocol can be completed in about 3 d. The protocol has been customized empirically for B. distachyon and its near relatives, but it can be adapted with minor modifications to diverse plant species.

Modelling the role of agriculture for the 20th century global terrestrial carbon balance

AbstractIn order to better assess the role of agriculture within the global climate‐vegetation system, we present a model of the managed planetary land surface, Lund–Potsdam–Jena managed Land (LPJmL), which simulates biophysical and biogeochemical processes as well as productivity and yield of the most important crops worldwide, using a concept of crop functional types (CFTs). Based on the LPJ‐Dynamic Global Vegetation Model, LPJmL simulates the transient changes in carbon and water cycles due to land use, the specific phenology and seasonal CO2 fluxes of agricultural‐dominated areas, and the production of crops and grazing land. It uses 13 CFTs (11 arable crops and two managed grass types), with specific parameterizations of phenology connected to leaf area development. Carbon is allocated daily towards four carbon pools, one being the yield‐bearing storage organs. Management (irrigation, treatment of residues, intercropping) can be considered in order to capture their effect on productivity, on soil organic carbon and on carbon extracted from the ecosystem. For transient simulations for the 20th century, a global historical land use data set was developed, providing the annual cover fraction of the 13 CFTs, rain‐fed and/or irrigated, within 0.5° grid cells for the period 1901–2000, using published data on land use, crop distributions and irrigated areas. Several key results are compared with observations. The simulated spatial distribution of sowing dates for temperate cereals is comparable with the reported crop calendars. The simulated seasonal canopy development agrees better with satellite observations when actual cropland distribution is taken into account. Simulated yields for temperate cereals and maize compare well with FAO statistics. Monthly carbon fluxes measured at three agricultural sites also compare well with simulations. Global simulations indicate a ∼24% (respectively ∼10%) reduction in global vegetation (respectively soil) carbon due to agriculture, and 6–9 Pg C of yearly harvested biomass in the 1990s. In contrast to simulations of the potential natural vegetation showing the land biosphere to be an increasing carbon sink during the 20th century, LPJmL simulates a net carbon source until the 1970s (due to land use), and a small sink (mostly due to changing climate and CO2) after 1970. This is comparable with earlier LPJ simulations using a more simple land use scheme, and within the uncertainty range of estimates in the 1980s and 1990s. The fluxes attributed to land use change compare well with Houghton's estimates on the land use related fluxes until the 1970s, but then they begin to diverge, probably due to the different rates of deforestation considered. The simulated impacts of agriculture on the global water cycle for the 1990s are∼5% (respectively∼20%) reduction in transpiration (respectively interception), and∼44% increase in evaporation. Global runoff, which includes a simple irrigation scheme, is practically not affected.

Duration of vegetative and generative development phases in oat cultivars released since 1921

Genetic yield improvements in oat ( Avena sativa L.) cultivars grown at high latitudes have resulted from marked changes in harvest index and yield components. This study was designed to investigate whether such changes have entailed alterations in duration of different developmental phases: vegetative, generative and grain filling phases and pre-anthesis generative sub-phases such as pre-fertile, pre-abortion, fertile pre-abortion, fertile and abortion sub-phases. We tested 14 oat cultivars released between 1921 and 1988 and 6 breeding lines. Ten randomly sampled plants of each oat entry were collected every 3–4 d (18 times) from seedling emergence until pollination, and apical developmental stages were determined on the most advanced spikelet. Cumulated degree-days (Cdd) for each critical developmental stage and component phases were determined (5 °C as a base temperature). At each measurement the number of leaves, green leaves and tillers on main shoot, apex length (mm) and height to the uppermost node, and stipule (cm) were recorded. Phyllochron (°C d leaf −1) and relative elongation rates (RER) for height characterising traits were calculated. Grain filling was the only period altered by breeding, while no consistent effects on duration of vegetative and generative pre-anthesis phases and sub-phases were detected. Different developmental phases were interrelated: in some cases cultivars with similar duration of pre-anthesis phase, however, differed in duration of some pre-anthesis sub-phases. Their duration was not, however, consistently associated with measured growth and yield parameters. Likely long days that make the northern growing conditions exceptional and unique, substantially narrowed the differences among oat entries in duration of different developmental phases, thereby making their role also less critical in yield determination contrary to the situation in the main global temperate cereal production regions.