Unique and conserved MicroRNAs in wheat chromosome 5D revealed by next-generation sequencing

MicroRNAs are a class of short, non-coding, single-stranded RNAs that act as post-transcriptional regulators in gene expression. miRNA analysis of Triticum aestivum chromosome 5D was performed on 454 GS FLX Titanium sequences of flow sorted chromosome 5D with a total of 3,208,630 good quality reads representing 1.34x and 1.61x coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. In silico and structural analyses revealed a total of 55 miRNAs; 48 and 42 miRNAs were found to be present on 5DL and 5DS respectively, of which 35 were common to both chromosome arms, while 13 miRNAs were specific to 5DL and 7 miRNAs were specific to 5DS. In total, 14 of the predicted miRNAs were identified in wheat for the first time. Representation (the copy number of each miRNA) was also found to be higher in 5DL (1,949) compared to 5DS (1,191). Targets were predicted for each miRNA, while expression analysis gave evidence of expression for 6 out of 55 miRNAs. Occurrences of the same miRNAs were also found in Brachypodium distachyon and Oryza sativa genome sequences to identify syntenic miRNA coding sequences. Based on this analysis, two other miRNAs: miR1133 and miR167 were detected in B. distachyon syntenic region of wheat 5DS. Five of the predicted miRNA coding regions (miR6220, miR5070, miR169, miR5085, miR2118) were experimentally verified to be located to the 5D chromosome and three of them : miR2118, miR169 and miR5085, were shown to be 5D specific. Furthermore miR2118 was shown to be expressed in Chinese Spring adult leaves. miRNA genes identified in this study will expand our understanding of gene regulation in bread wheat

Chromosome Bin Map of Expressed Sequence Tags in Homoeologous Group 1 of Hexaploid Wheat and Homoeology With Rice and Arabidopsis

A total of 944 expressed sequence tags (ESTs) generated 2212 EST loci mapped to homoeologous group 1 chromosomes in hexaploid wheat (Triticum aestivum L.). EST deletion maps and the consensus map of group 1 chromosomes were constructed to show EST distribution. EST loci were unevenly distributed among chromosomes 1A, 1B, and 1D with 660, 826, and 726, respectively. The number of EST loci was greater on the long arms than on the short arms for all three chromosomes. The distribution of ESTs along chromosome arms was nonrandom with EST clusters occurring in the distal regions of short arms and middle regions of long arms. Duplications of group 1 ESTs in other homoeologous groups occurred at a rate of 35.5%. Seventy-five percent of wheat chromosome 1 ESTs had significant matches with rice sequences (E ≤ e(−10)), where large regions of conservation occurred between wheat consensus chromosome 1 and rice chromosome 5 and between the proximal portion of the long arm of wheat consensus chromosome 1 and rice chromosome 10. Only 9.5% of group 1 ESTs showed significant matches to Arabidopsis genome sequences. The results presented are useful for gene mapping and evolutionary and comparative genomics of grasses

Control of flowering time and spike development in cereals: the earliness per se Eps-1 region in wheat, rice, and Brachypodium

The earliness per se gene Eps-Am1 from diploid wheat Triticum monococcum affects heading time, spike development, and spikelet number. In this study, the Eps1 orthologous regions from rice, Aegilops tauschii, and Brachypodium distachyon were compared as part of current efforts to clone this gene. A single Brachypodium BAC clone spanned the Eps-Am1 region, but a gap was detected in the A. tauschii physical map. Sequencing of the Brachypodium and A. tauschii BAC clones revealed three genes shared by the three species, which showed higher identity between wheat and Brachypodium than between them and rice. However, most of the structural changes were detected in the wheat lineage. These included an inversion encompassing the wg241-VatpC region and the presence of six unique genes. In contrast, only one unique gene (and one pseudogene) was found in Brachypodium and none in rice. Three genes were present in both Brachypodium and wheat but were absent in rice. Two of these genes, Mot1 and FtsH4, were completely linked to the earliness per se phenotype in the T. monococcum high-density genetic map and are candidates for Eps-Am1. Both genes were expressed in apices and developing spikes, as expected for Eps-Am1 candidates. The predicted MOT1 protein showed amino acid differences between the parental T. monococcum lines, but its effect is difficult to predict. Future steps to clone the Eps-Am1 gene include the generation of mot1 and ftsh4 mutants and the completion of the T. monococcum physical map to test for the presence of additional candidate genes

System of Measuring Projectile's Velocity and Setting Fuse in 35 mm Antiaircraft Ammunition

W artykule omówiono stan zaawansowania prac nad opracowaniem demonstratora technologii systemu programowania pocisku 35x228 mm do przeciwlotniczych zestawów artyleryjskich. Przedstawiono koncepcję, budowę systemu i zasadę działania. Ukazano drogę do wyboru optymalnego rozwiązania. Pokazano przewidywane trudności w realizacji projektu i propozycję ich rozwiązania. W trakcie realizacji projektu rozwojowego pt. "Opracowanie programowalnego naboju kalibru 35x228 do przeciwlotniczego zestawu artyleryjskiego LOARA" nr O R00 0019 08, realizowanego przez Konsorcjum w składzie: PW IMiP, CNPEP RADWAR SA, ZM MESKO SA oraz BUMAR Sp. z o.o., na podstawie umowy z MNiSW, wykonany zostanie demonstrator technologii systemu pomiaru prędkości wylotowej pocisku i programowania zapalnika, który będzie poddany badaniom strzelaniem.The concept of measuring projectile' s velocity and setting time of detonation in Air Bursting Ammunition. Experience in previous works over similar system. Expected difficulties in realization and suggested ways of dealing with them

Genetically modified plants - from the laboratory to practical application in European agriculture. Part II

Wprowadzanie roślin GM do środowiska jest nie tylko przedmiotem regulacji prawnych, ale również istotną kwestią podlegającą dyskusji naukowej i społecznej. W artykule przedstawiono zasady leżące u podstaw oceny ryzyka związanego ze stosowaniem GMO. Przytoczono wyniki licznych badań nad oddziaływaniem odmian GM dopuszczonych do uprawy na gatunki niedocelowe, obejmujące m.in. różne grupy stawonogów żyjących na uprawach GM i w ich otoczeniu. Dokładniej wyjaśniono przypadek oddziaływania kukurydzy GM na motyla monarcha w USA czy też odmian kukurydzy, buraka i rzepaku tolerujących herbicydy na populacje chwastów i żerujących na nich stawonogach i ptakach. Podkreślono konieczność prowadzenia badań opartych o poprawne metodyki. Podano wyniki pierwszych badań polowych prowadzonych w Polsce nad oddziaływaniem kukurydzy MON 810 na środowisko. Przedstawiono działania Europejskiego Urzędu ds. Bezpieczeństwa Żywności (EFSA) obejmujące: (a) budowanie wzajemnego zrozumienia zasad leżących u podstaw przeprowadzania analizy ryzyka dla nowych GMO i (b) zwiększenie przejrzystości w bieżących pracach pomiędzy państwami członkowskimi UE a urzędem i jego komisjami. Powołanie Naukowej Sieci krajowych ekspertów (EFSA Scientific Network) ma tę współpracę zapewnić. Podsumowano podstawy wykrywania i kontroli GMO w laboratoriach referencyjnych w Europie.The release of genetically modified plants into the environment is not only a subject of legal regulations, but also an important subject matter of the scientific and social debate. The article presents rules forming the basis of the risk assessment related to use of GMOs. It quotes the results of numerous studies concerning the impact of GMO varieties approved for cultivation on the nontarget species, including i.a. various groups of arthropods living in the area of GMO crops and in their vicinity. It also offers more precise explanations regarding the cases of the impact of genetically modified corn on the Monarch butterfly in the USA and the impact of herbicide-tolerant varieties of corn, beet and rapeseed on the populations of weeds as well as arthropods and birds feeding on them. Moreover, it underlines the necessity of conducting research based on correct methodologies and provides results of the first farm scale research conducted in Poland regarding the impact of MON 810 corn on the environment. Furthermore, it presents actions of the European Food Safety Authority (EFSA) encompassing: (a) building up mutual understanding of the rules forming the basis of risk assessment for new GMOs and (b) increasing transparency in current works among the EU Member States and EFSA and its committees. Setting up the EFSA Scientific Network is supposed to ensure that cooperation. Finally, the article summarizes the basics of GMO detection and control in the reference laboratories in Europe

Genetically modified plants - from the laboratory to practical use in European agriculture. Part I

Techniki biotechnologiczne umożliwiają hodowcy połączenie korzystnych cech z różnych organizmów. Roślina genetycznie zmodyfikowana zawiera gen lub geny, które zostały zmienione w wyniku działania człowieka metodami inżynierii genetycznej. Od 1996 r. obserwuje się stały wzrost areału upraw roślin zmodyfikowanych genetycznie na świecie, który w 2011 r. osiągnął powierzchnię 160 mln ha. Prawdopodobnie w przyszłości transgeniczność wielokrotna (ang. stacked events) będzie dominowała w nowych odmianach GM, łącząc cechy odporności na szkodniki, tolerancję na herbicydy i niekorzystne warunki środowiska, jak też cechy dotyczące składu związków roślinnych. W Unii Europejskiej i na świecie obowiązują uregulowania prawne kompleksowo obejmujące kwestie GMO. Unia Europejska ma jeden z bardziej restrykcyjnych systemów prawnych dotyczących GMO. Przepisy zapewniają ochronę środowiska, zdrowia zwierząt i człowieka oraz informację dla konsumenta. Wymagają też szczegółowego badania każdego GMO na poszczególnych etapach uzyskiwania zgody na użycie takich organizmów. Współistnienie różnych typów produkcji ma zapewnić rolnikom i konsumentom europejskim możliwość wyboru. Prawo UE stanowi podstawę dla uregulowań prawnych związanych z GMO, obowiązujących w Polsce.Biotechnological techniques enable the breeder to combine a number of favourable properties of different organisms. A genetically modified plant contains gene or genes that have been modified by humans using genetic engineering. Since 1996 a constant expansion of the area of genetically modified crops is observed throughout the world, reaching 160 million has. in 2011. It is likely that in the future stacked events will dominate in new GM varieties, combining properties such as resistance to pests and tolerance to herbicides and adverse environmental conditions, as well as various quality properties. The European Union and other countries have implemented comprehensive legal regulations on matters related to GMO. The EU has one of the more restrictive legal systems on GMO. Those regulations ensure the protection of the environment, human and animal health, and proper information for the consumer. The regulations also stipulate detailed analysis of each GMO at every stage of the process of approval for the use of such organisms. Coexistence of different types of crops is aimed at providing European farmers and consumers with choice options. The EU law is the basis for the legal regulations on GMO applicable in Poland

Gene and repetitive sequence annotation in the Triticeae

The Triticeae tribe contains some of the world’s most important agricultural crops (wheat, barley and rye) and is perhaps, one of the most challenging for genome annotation because Triticeae genomes are primarily composed of repetitive sequences. Further complicating the challenge is the polyploidy found in wheat and particularly in the hexaploid bread wheat genome. Genomic sequence data are available for the Triticeae in the form of large collections of Expressed Sequence Tags (>1.5 million) and an increasing number of bacterial artificial chromosome clone sequences. Given that high repetitive sequence content in the Triticeae confounds annotation of protein-coding genes, repetitive sequences have been identified, annotated, and collated into public databases. Protein coding genes in the Triticeae are structurally annotated using a combination of ab initio gene finders and experimental evidence. Functional annotation of protein coding genes involves assessment of sequence similarity to known proteins, expression evidence, and the presence of domain and motifs. Annotation methods and tools for Triticeae genomic sequences have been adapted from existing plant genome annotation projects and were designed to allow for flexibility of single sequence annotation while allowing a whole community annotation effort to be developed. With the availability of an increasing number of annotated grass genomes, comparative genomics can be exploited to accelerate and enhance the quality of Triticeae sequences annotation. This chapter provides a brief overview of the Triticeae genomes features that are challenging for genome annotation and describes the resources and methods available for sequence annotation with a particular emphasis on problems caused by the repetitive fraction of these genomes

Development of an Expressed Sequence Tag (EST) Resource for Wheat (\u3ci\u3eTriticum aestivum\u3c/i\u3e L.): EST Generation, Unigene Analysis, Probe Selection and Bioinformatics for a 16,000-Locus Bin-Delineated Map

This report describes the rationale, approaches, organization, and resource development leading to a large-scale deletion bin map of the hexaploid (2n = 6x = 42) wheat genome (Triticum aestivum L.). Accompanying reports in this issue detail results from chromosome bin-mapping of expressed sequence tags (ESTs) representing genes onto the seven homoeologous chromosome groups and a global analysis of the entire mapped wheat EST data set. Among the resources developed were the first extensive public wheat EST collection (113,220 ESTs). Described are protocols for sequencing, sequence processing, EST nomenclature, and the assembly of ESTs into contigs. These contigs plus singletons (unassembled ESTs) were used for selection of distinct sequence motif unigenes. Selected ESTs were rearrayed, validated by 5’ and 3’ sequencing, and amplified for probing a series of wheat aneuploid and deletion stocks. Images and data for all Southern hybridizations were deposited in databases and were used by the coordinators for each of the seven homoeologous chromosome groups to validate the mapping results. Results from this project have established the foundation for future developments in wheat genomics