The Cornucopia of Small RNAs in Plant Genomes

Regulatory small RNAs (approximately 20 to 24 nt in length) are produced through pathways that involve several key evolutionarily conserved protein families; the variants of these proteins found in plants are encoded by multigene families and are known as Dicer-like, Argonaute, and RNA-dependent RNA polymerase proteins. Small RNAs include the well-known classes of microRNAs (miRNAs, ~21 nt) and the small-interfering RNAs (siRNAs, ~24 nt). Both of these types of molecules are found across a broad set of eukaryotic species, although the siRNAs are a much larger and more diverse class in plants due to the abundance of heterochromatic siRNAs. Well-studied species such as Arabidopsis have provided a foundation for understanding in rice and other species how small RNAs function as key regulators of gene expression. In this paper, we review the current understanding of plant small RNA pathways, including the biogenesis and function of miRNAs, siRNAs, trans-acting siRNAs, and heterochromatic siRNAs. We also examine the evolutionary relationship among plant species of both their miRNAs and the key enzymatic components of the small RNA pathways. Many of the most recent advances in describing small RNAs have resulted from advances in sequencing technologies used for identifying and measuring small RNAs, and these technologies are discussed. Combined with the plethora of genetic tools available to researchers, we expect that the continued elucidation of the identity and functions of plant small RNAs will be both exciting and rewarding.     

Flower Development and Photoperiodic Control of Flowering in Rice

Floral transition,which is referred to as a plant’s transition from vegetative stage to reproductive stage,is considered to be a critical developmental switch in higher plants,for a timely flowering is a major factor of reproductive success.Endogenous and environmental cues,such as photoperiod,light quality,plant hormones concentrations and temperature,provide information to the plants whether the environment is favorable for flowering.These cues promote,or prevent,flowering through a complex genetic network,mediated by a careful orchestration of temporal and spatial gene expression.One of such cues is photoperiod.Rice(Oryza sativa L.) serves as a powerful model species for the understanding of flowering in higher plants,including flower development and photoperiodic control of flowering.In this review,we overviewed and discussed the flower development and its model.We also overviewed the photoperiodic pathways in rice flowering control,and summarized the pathways at molecular level.     

Simulation analysis of relative yield advantage of barley and wheat in an eastern Mediterranean climate

Barley (Hordeum vulgare) and wheat (Triticum aestivum) are similar crops that can be grown in the arid regions of southwestern Asia. Generally, barley is favored over wheat in drier areas. However, the quantitative basis for the relative advantage of each crop under differing growing conditions has not been resolved. This study was undertaken to compare the two crops using the same model structure. A wheat model developed for southwestern Asia was readily adapted to simulate barley. Simulations of barley crops proved to be robust over a range of environments. Comparison of simulated yields in a number of environments showed that the critical difference between species was the cumulative effect of plant development traits that allowed barley to mature much earlier than wheat. Consequently, early maturity of barley in contrast to wheat often allowed barley to complete its growing cycle before water-deficit conditions developed in the spring. There was, however, little or no yield advantage for barley in seasons of high rainfall. Also, rare seasons with significant rainfall after barley matured allowed wheat to actually produce the greater yield. These simulation results indicated that development traits are crucial in the interaction between crop yield and exposure to water deficits at the end of the growing season.     

Phosphomannose isomerase,pmi, as a selectable marker gene for durum wheat transformation

Transgene technology provides a powerful tool for developing traits that are otherwise difficult to achieve through conventional methods. The development of transgenic plants requires the use of selectable marker genes, as the efficiency of plant transformation is less than optimal for many important species, especially for monocots such as durum wheat (Triticum turgidum var. durum). Many concerns have been expressed about the persistence of currently used marker genes in plants used for field cultivation. To sustain further progress in this area, alternative efficient selection methods are desirable. A recent development is the use of selective genes that give transformed cells a metabolic advantage (positive selection) compared to untransformed cells, which are slowly starved with a concomitant reduction in growth and viability. This selection strategy is in contrast to traditional negative selections during which the transgenic cells are able to survive on a selective medium whereas the non-transgenic cells are actively killed by the selective agent. We compared the ‘selection efficiency’ of a commonly used negative selection method that employs the Streptomyces hygroscopicus bar gene to confer resistance to the herbicide bialaphos, to a positive selection employing the Escherichia coli phosphomannose isomerase (pmi) gene as the selectable gene and mannose as the selective agent. Calli derived from immature embryos of the durum wheat cultivar Svevo were bombarded separately with bar and pmi genes using a biolistic system. The integration and expression of the two genes in the T₀ generation were confirmed by PCR analysis with specific primers for each gene and the chlorophenol red assay, respectively. The selection efficiency, calculated as the number of expressing plants divided by the number of total regenerants, was higher when pmi was used as the selectable marker gene (90.1%) than when bar was used (26.4%). Thus, an efficient selection method for durum wheat transformation was established that obviates the use of herbicide résistance genes.     

Wheat transformation: current technology and applications to grain development and composition

Transgenesis is a powerful research tool that can be adapted to investigate many aspects of gene function. It has been used widely in model plants such as Arabidopsis, tobacco and rice but until recently, bottlenecks in DNA-delivery and tissue culture meant that it could not be used routinely for wheat research. However, many aspects of grain development and composition are unique to wheat and cannot be easily investigated in model species. Over the last decade, progress in biolistic- and Agrobacterium-mediated DNA delivery, reduction in genotype-dependency in wheat tissue culture and in the development of a range of supplementary technologies has enabled its application in this traditionally recalcitrant crop. The use of genetic modification has already made a significant impact on our understanding of interactions between high molecular weight glutenin subunits and their individual contribution to dough strength. As candidate genes become available the application of genetic transformation is set to play a major part in the elucidation of their function in determining other important grain traits such as starch and lipid composition, dietary fibre composition and grain texture.     

Enhancing the mineral and vitamin content of wheat and maize through plant breeding

More than half of the world's population suffers micronutrient undernourishment. The main sources of vitamins and minerals (iron, zinc, and vitamin A) for low-income rural and urban populations are staple foods of plant origin that often contain low levels or low bioavailability of these micronutrients. Biofortification aims to develop micronutrient-enhanced crop varieties through conventional plant breeding. HarvestPlus, the CGIAR's biofortification initiative, seeks to breed and disseminate crop varieties with enhanced micronutrient content that can improve the nutrition of the “hard to reach” (by fortification or supplementation programmes) rural and urban poor in targeted countries/regions. In attempting to enhance micronutrient levels in maize and wheat through conventional plant breeding, it is important to identify genetic resources with high levels of the targeted micronutrients, to consider the heritability of the targeted traits, to explore the availability of high throughput screening tools and to gain a better understanding of genotype by environment interactions. Biofortified maize and wheat varieties must have the trait combinations which encourage adoption such as high yield potential, disease resistance, and consumer acceptability. When defining breeding strategies and targeting micronutrient levels, researchers need to consider the desired micronutrient increases, food intake and retention and bioavailability as they relate to food processing, anti-nutritional factors and promoters. Finally, ex ante studies are required to quantify the burden of micronutrient deficiency and the potential of biofortification to achieve a significant improvement in human micronutrient status in the deficient target population in order to determine whether a biofortification program is cost-effective.     

Usefulness of Japanese-radish residue in biological soil disinfestation to suppress spinach wilt disease accompanying with proliferation of soil bacteria in the Firmicutes

Biological soil disinfestation (BSD) is an effective method to suppress soilborne plant diseases by incorporation of plant biomass into soil under reduced, anoxic condition. Usefulness of Japanese-radish (daikon) residue as plant biomass for BSD was investigated by both model and field experiments in comparison with the effects of Brassica juncea plants or wheat bran. Considerable amounts of acetate together with minor amounts of propionate and butyrate were detected from the radish-treated soils at similar levels with those in soils treated with B. juncea plants or wheat bran. BSD treatments with radish residue reduced spinach wilt disease incidence in both model and field experiments. When the BSD-treated soil was treated again with irrigation and covering without biomass before next cropping, however, wilt disease was hardly suppressed. Clone library analysis based on 16S rRNA gene sequences was carried out to determine the changes in the bacterial community compositions in the treated soil samples. The analyses showed that the bacterial communities in the radish-treated soils were dominated by members of the classes Clostridia and Bacilli of the phylum Firmicutes in both experiments. The clostridial groups detected were diverse and the major operational taxonomic units (OTUs) were closely related to Clostridium saccharobutylicum, Clostridium sufflavum, Clostridium xylanovorans, and Oxobacter pfennigii, which had been commonly detected as the dominant groups in BSD-soils treated with B. juncea plants or wheat bran in our previous studies. The dominant clone groups belonging to the Bacilli class were closely related to several species such as Bacillus niacini, Bacillus circulans, and Bacillus pycnus. Dominancy of the Bacilli groups seemed to increase when radish residue was repeatedly applied as BSD material.     

Genomics and the physiologist: bridging the gap between genes and crop response

Plant physiologists have traditionally studied the relationship between crop performance (the phenotype) and the environment. Global change processes present multiple challenges to crop performance that can be met effectively by changing the crop environment through management, and by modifying the crop genome (the genotype) through plant breeding and molecular biology. In order to increase the reliability of crop performance prediction based upon genetic information, new tools are needed to more effectively relate observed phenotypes to genotypes. The emerging discipline of genomics offers promise of providing such tools, and may provide a unique opportunity to enhance genetic gains and stabilize global crop production. Genomics has developed from the confluence of genetics, automated laboratory tools for generating DNA- and RNA-based data, and methods of information management. Functional genomics concentrates on how genes function, alone and in networks, while structural genomics focuses on physical and structural aspects of the genome. The traditional strengths of physiology lie in interpreting whole plant response to environmental signals, dissecting traits into component processes, and predicting correlated responses when genes and pathways are perturbed. These complement information on the genetic control of signal transduction, gene expression, gene networks and candidate genes. Combining physiological and genetic information can provide a more complete model of gene-to-phenotype relationships and genotype-by-environment interactions. Phenotypic screening procedures that more accurately identify underlying genetic variation, and crop models that incorporate Mendelian genetic controls of key processes provide two tangible examples of fruitful collaboration between physiologists and geneticists. These point to a productive complementary relationship between disciplines that will speed progress towards stable and adequate food production, despite challenges posed by global climate change.     

小麦SnRK2家族基因鉴定及进化分析

SnRK2是一种植物特异性的丝氨酸/苏氨酸蛋白激酶，在植物生长发育和胁迫耐受信号传递过程中发挥着至关重要的作用。为探索SnRK2在小麦抗逆中的作用，基于最新的小麦基因组信息，采用blastp和hmmer两种方法在普通小麦中共鉴定到30个SnRK2基因家族成员。系统发育分析表明，SnRK2基因在普通小麦及其祖先物种的进化过程中高度保守。利用RNA seq数据分析小麦SnRK2基因在不同组织以及不同胁迫条件下的表达模式，结果表明，小麦SnRK2基因家族成员在不同组织以及不同胁迫条件下表达量均存在差异，且具有显著的组织特异性。通过qRT PCR进一步验证6个小麦SnRK2基因的表达模式，发现不同基因之间的表达量存在明显差异，推测小麦SnRK2基因家族的部分成员出现功能分化。随后，利用已发表的六倍体小麦重测序数据，分析不同小麦群体中SnRK2基因的核苷酸多样性(P_i)和分化指数(F_st)，并解析单倍型，推测Ta 5B SnRK2.28基因的AA单倍型为优异等位变异。通过同源建模预测小麦SnRK2蛋白的三维结构，发现小麦SnRK2蛋白结构在进化上高度保守。     

Development of analytical systems based on real-time PCR for Triticum species-specific detection and quantitation of bread wheat contamination in semolina and pasta

The cereal composition of specific foods is always a key factor in the quality and safety of the final product. It is important to introduce new control methods for certain special foods, such as those for coeliac consumers, where the contamination of different cereal species must be accurately determined. Moreover, pasta made from durum wheat is considered superior in several qualitative aspects to that manufactured with bread wheat or a mixture of the two species. This work has been directed toward the development of analytical systems for the qualitative and quantitative detection of specific cereals in food. More specifically, the primary aim of this work has been to develop analytical tools based on end-point and real-time PCR to detect the presence of Triticum species in flour and food. Furthermore, qualitative and quantitative PCR-based methods are proposed to detect hexaploid wheat adulteration in pasta.     

小麦抗逆相关转录因子DREB密码子偏好性特征分析

DREB(dehydration responsive element binding)转录因子在植物抵抗干旱、高盐、低温等非生物逆境中发挥着重要作用。为探究普通小麦抗逆相关转录因子DREB密码子的偏好性特征,本研究运用CodonW、CHIPS和CUSP软件程序分析了小麦DREB基因的密码子使用特性,并与13种植物的DREB密码子偏性进行比较。结果表明,小麦DREB基因主要偏好以GC结尾的密码子;根据RSCU值,确定小麦DREB基因的高频密码子有14个;不同作物间DREB基因的密码子选用偏好性存在一定差异;基于DREB编码序列的聚类分析比基于密码子使用偏性聚类分析更能准确地反映物种间的亲缘关系;属于真核生物的酵母菌比属于原核生物的大肠杆菌更适宜作为DREB基因表达的异源受体。小麦DREB与模式植物基因组之间密码子使用偏性差异较小,拟南芥可能比烟草和番茄更适合作为该基因转基因研究的理想受体。小麦DREB密码子偏性分析为该基因的异源表达及分子遗传研究提供了一定的理论依据。     

Spray retention on whole plants: modelling,simulations and experiments

Retention of sprays on plants is a critical component influencing the effectiveness of agrichemical applications. Previous simulations of spray retention by plants gave poor agreement for hard-to-wet species when compared with actual measured retention. A new model is developed here that accounts for: species wettability, impaction angle, droplet bounce, partial retention on shatter, a variable time to shatter, and the number of daughter droplets produced. The aim of this study was to compare predictions from the new model with data obtained by spraying five mixtures via five nozzles onto easy-to-wet cotton (Gossypium hirsutum L.), and hard-to-wet wheat (Triticum aestivum L.) and fat hen (Chenopodium album L.). The new model correctly predicts retention to be highest on cotton and lowest on wheat. The trend in both measured data and the model predictions is for retention to decrease with increasing droplet size, on all three plant species. Formulation is correctly predicted to have little influence on retention by easy-to-wet cotton plants and to enhance retention by the harder-to-wet wheat and fat hen plants. The parameters that describe partial retention on shatter and variable time to shatter have a substantial influence on retention, as they affect primary or secondary droplet capture. A better understanding of the kinetic energy effects and the interactions between the formulation and the leaf surface are needed to refine their input values.     

Molecular Genetics of Rice Root Development

Plant roots have a large range of functions, including acquisition of water and nutrients, as well as structural support. Dissecting the genetic and molecular mechanisms controlling rice root development is critical for the development of new rice ideotypes that are better adapted to adverse conditions and for the production of sustainably achieved rice yield potential. Most knowledge regarding the gene networks involved in root development has been accumulated in the model dicotyledon plant species Arabidopsis thaliana. Rice, the model monocotyledon species, presents several singularities compared to A. thaliana, including a root architecture characterized by a fibrous root system comprising five types of embryonic and postembryonic roots. The anatomy and morphology of the rice root system, which is typical for a cereal, differs from that of A. thaliana, for instance, by the presence of a lysigenous cortex and additional cell layers compared to the dicotyledon model. Moreover, the structure and functions of the root apical meristem (RAM) of rice are distinct from those of A. thaliana. Recently, several rice root mutants have been identified via forward or reverse genetics, and these will aid in forming hypothesis to characterize either the divergence or conservation of genetic pathways relative to A. thaliana. Furthermore, these mutants will help to identify key genes in rice roots that may be missing in A. thaliana. This review summarizes both classical and recent data concerning the molecular genetics of rice root development, including root anatomy and morphology, RAM structure, RAM patterning, and root mutants.     

小麦 TaGF14m基因的克隆及其盐胁迫响应分析

14-3-3蛋白家族在真核生物中广泛存在且高度保守,可结合多种靶蛋白参与植物代谢、发育以及胁迫响应等多种生理过程和信号途径。 TaGF14m基因是14-3-3基因家族成员之一。本研究以中国春为材料,对其进行了克隆和分析,并通过在拟南芥中过表达,分析该基因在盐胁迫下的功能。结果表明, TaGF14m基因含有5个外显子和4个内含子,开放阅读框为789 bp,编码262个氨基酸;小麦幼苗叶片中 TaGF14m基因在盐胁迫下上调表达;与野生型拟南芥相比,过表达 TaGF14m的转基因拟南芥在盐胁迫下生长受到明显抑制,根长也显著变短;SOS途径相关基因表达分析显示, TaGF14m基因可能通过SOS途径负调控盐胁迫耐受性。     

A universal protocol for identification of cereals

Plant fingerprinting and identification has increasingly become a focus in commerce and manufacturing with an emphasis on fast, reliable and cost effective high throughput techniques. GBSS1 is a well conserved single copy nuclear gene in the grass family with potential for generating a universal approach to grass fingerprinting. Alignment of DNA sequences from Poaceae members identified five well conserved regions. PCR primers designed to these regions amplified single DNA fragments on all grasses tested. DNA sequencing revealed polymorphism within these DNA fragments allowing identification at the species level. A universal sequencing primer for Poaceae enabled pyrosequencing through a 28 base pair highly polymorphic region generating unique pyrograms for rice, wheat, barley and maize. Analysis of exon/intron composition including intron length and number, of GBSS1 provided another distinct fingerprinting method for grasses. Phylogenetic utility of these fragments was demonstrated by production of phylograms consistent with previously described taxonomic relationships for the Poaceae family. The sequence polymorphism of the GBSS1 gene provides the basis for universal primer design for identification of members of the Poaceae family. The protocols developed may prove more generally useful in the distinction of plant species in other plant families.     

Fusarium genetic traceability: Role for mycotoxin control in small grain cereals agro-food chains

Risks associated with mycotoxin contamination of cereals, that are included in the ten major staple foods and greatly contribute to the dietary energy intake, are of worldwide relevance. In small grain cereals, mycotoxins are produced by fungi such as Aspergillus, Penicillium, Alternaria and Fusarium that colonize the plant in the field and can grow during the post-harvest period, producing several classes of mycotoxins. The identification of mycotoxigenic fungal species and strains is essential for developing effective strategies for control. For this purpose, genetic traceability has proved to be a valuable tool that can be applied along the whole production chain, starting in the field for early diagnosis of FHB (Fusarium Head Blight) disease to the final processing steps, such as malting or pasta making. In this paper, DNA-based analytical tools that are currently available for the identification and quantification of mycotoxigenic fungal species and strains are reviewed, with particular emphasis on Fusarium, and their possible applications in mycotoxin control in small grain cereal chains are discussed.     

Adapting the CROPGRO perennial forage model to predict growth of Brachiaria brizantha

Warm-season grasses are economically important for cattle production in tropical regions, and tools to aid in management and research of these forages would be highly beneficial. Crop simulation models synthesize numerous physiological processes and are important research tools for evaluating production of warm-season grasses. This research was conducted to adapt the perennial CROPGRO Forage model to simulate growth of the tropical species palisadegrass [Brachiaria brizantha (A. Rich.) Stapf. cv. Xaraes] and to describe model adaptation for this species. In order to develop the CROPGRO parameters for this species, we began with values and relationships reported in the literature. Some parameters and relationships were calibrated by comparison with observed growth, development, dry matter accumulation and partitioning during a 2-year experiment with Xaraes palisadegrass in Piracicaba, SP, Brazil. Starting with parameters for the bahiagrass (Paspalum notatum Flugge) perennial forage model, dormancy effects had to be minimized, and partitioning to storage tissue/root decreased, and partitioning to leaf and stem increased to provide for more leaf and stem growth and less root. Parameters affecting specific leaf area (SLA) and senescence of plant tissues were improved. After these changes were made to the model, biomass accumulation was better simulated, mean predicted herbage yield per cycle was 3573 kg ha⁻¹, with a RMSE of 538 kg DM ha⁻¹ (D-Stat = 0.838, simulated/observed ratio = 1.028). The results of the adaptation suggest that the CROPGRO model is an efficient tool to integrate physiological aspects of palisadegrass and can be used to simulate growth.