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Genomics Resources (genomics + resource)
Selected AbstractsBrachypodium: a new monocot model plant system emergesJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 7 2007David F Garvin Abstract The small grass species Brachypodium distachyon (purple false brome) is potentially an ideal model plant system for grass crop research. To realise this potential, a range of genetic and genomic resources have been developed in a very short period of time, and more still are in the pipeline. David Garvin explains how these resources will establish B. distachyon as the newest model plant system and will fill a long-empty void in genomics resources for grass crop improvement. Copyright © 2007 Society of Chemical Industry [source] Characterization of de novo transcriptome for waterhemp (Amaranthus tuberculatus) using GS-FLX 454 pyrosequencing and its application for studies of herbicide target-site genesPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 10 2010Chance W Riggins Abstract BACKGROUND: Waterhemp is a model for weed genomics research in part because it possesses many interesting biological characteristics, rapidly evolves resistance to herbicides and has a solid foundation of previous genetics work. To develop further the genomics resources for waterhemp, the transcriptome was sequenced using Roche GS-FLX 454 pyrosequencing technology. RESULTS: Pyrosequencing produced 483 225 raw reads, which, after quality control and assembly, yielded 44 469 unigenes (contigs + singletons). A total of 49% of these unigenes displayed highly significant similarities to Arabidopsis proteins and were subsequently grouped into gene ontology categories. Blast searches against public and custom databases helped in identifying and obtaining preliminary sequence data for all of the major target-site genes for which waterhemp has documented resistance. Moreover, sequence data for two other herbicide targets [4-hydroxyphenylpyruvate dioxygenase (HPPD) and glutamine synthetase], where resistance has not yet been reported in any plant, were also investigated in waterhemp and six related weedy Amaranthus species. CONCLUSION: These results demonstrate the enormous value of 454 sequencing for gene discovery and polymorphism detection in a major weed species and its relatives. Furthermore, the merging of the 454 transcriptome data with results from a previous whole genome 454 sequencing experiment has made it possible to establish a valuable genomic resource for weed science research. Copyright © 2010 Society of Chemical Industry [source] The control of chlorophyll catabolism and the status of yellowing as a biomarker of leaf senescencePLANT BIOLOGY, Issue 2008H. Ougham Abstract The pathway of chlorophyll catabolism during leaf senescence is known in a fair amount of biochemical and cell biological detail. In the last few years, genes encoding a number of the catabolic enzymes have been characterized, including the key ring-opening activities, phaeophorbide a oxygenase (PaO) and red chlorophyll catabolite reductase (RCCR). Recently, a gene that modulates disassembly of chlorophyll,protein complexes and activation of pigment ring-opening has been isolated by comparative mapping in monocot species, positional cloning exploiting rice genomics resources and functional testing in Arabidopsis. The corresponding gene in pea has been identified as Mendel's I locus (green/yellow cotyledons). Mutations in this and other chlorophyll catabolic genes have significant consequences, both for the course of leaf senescence and senescence-like stress responses, notably hypersensitivity to pathogen challenge. Loss of chlorophyll can occur via routes other than the PaO/RCCR pathway, resulting in changes that superficially resemble senescence. Such ,pseudosenescence' responses tend to be pathological rather than physiological and may differ from senescence in fundamental aspects of biochemistry and regulation. [source] Plant cell wall biosynthesis: genetic, biochemical and functional genomics approaches to the identification of key genesPLANT BIOTECHNOLOGY JOURNAL, Issue 2 2006Naser Farrokhi Summary Cell walls are dynamic structures that represent key determinants of overall plant form, plant growth and development, and the responses of plants to environmental and pathogen-induced stresses. Walls play centrally important roles in the quality and processing of plant-based foods for both human and animal consumption, and in the production of fibres during pulp and paper manufacture. In the future, wall material that constitutes the major proportion of cereal straws and other crop residues will find increasing application as a source of renewable fuel and composite manufacture. Although the chemical structures of most wall constituents have been defined in detail, the enzymes involved in their synthesis and remodelling remain largely undefined, particularly those involved in polysaccharide biosynthesis. There have been real recent advances in our understanding of cellulose biosynthesis in plants, but, with few exceptions, the identities and modes of action of polysaccharide synthases and other glycosyltransferases that mediate the biosynthesis of the major non-cellulosic wall polysaccharides are not known. Nevertheless, emerging functional genomics and molecular genetics technologies are now allowing us to re-examine the central questions related to wall biosynthesis. The availability of the rice, Populus trichocarpa and Arabidopsis genome sequences, a variety of mutant populations, high-density genetic maps for cereals and other industrially important plants, high-throughput genome and transcript analysis systems, extensive publicly available genomics resources and an increasing armoury of analysis systems for the definition of candidate gene function will together allow us to take a systems approach to the description of wall biosynthesis in plants. [source] The molecular analysis of leaf senescence , a genomics approachPLANT BIOTECHNOLOGY JOURNAL, Issue 1 2003Vicky Buchanan-Wollaston Summary Senescence in green plants is a complex and highly regulated process that occurs as part of plant development or can be prematurely induced by stress. In the last decade, the main focus of research has been on the identification of senescence mutants, as well as on genes that show enhanced expression during senescence. Analysis of these is beginning to expand our understanding of the processes by which senescence functions. Recent rapid advances in genomics resources, especially for the model plant species Arabidopsis, are providing scientists with a dazzling array of tools for the identification and functional analysis of the genes and pathways involved in senescence. In this review, we present the current understanding of the mechanisms by which plants control senescence and the processes that are involved. [source] | |||||||||||||