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Invited Speakers
DNA barcoding in land plants: challenges, development and applications
Aron Fazekas
Biodiversity Institute of Ontario (BIO) and Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1
The BIO herbarium has been actively engaged in barcoding research since the initial stages of plant DNA barcoding. The concept of DNA barcoding has been designed as a system to facilitate species identification and recognition through the use of nucleotide sequence data derived from a small portion of the genome. In animals, the mitochondrial cytochrome c oxidase (cox1) gene has demonstrated high levels of species resolution in a diverse array of taxa and has facilitated the discovery of new species, provided insight into ecological process, revealed fraud in the food industry, and been used to track invasive species. The primary challenge in barcoding plants has been to identify a similar genomic region to use as a plant DNA barcode. The focus-to-date has been on regions of the plastid genome, with a consensus recently achieved by the international barcoding community. As in animal systems, plant DNA barcoding has wide-ranging applications. In addition to local and international floristic projects, we have used the barcode method in ecological applications. Two projects currently in progress are examining aspects of below ground diversity. The first project explores patterns of below ground plant diversity and its determinants, through an analysis of roots, and compares this with above ground diversity, revealing contrasting patterns of community structure. A separate project uses DNA barcoding to examine the mutualism between plant species and the AMF fungi that colonize their roots, and suggests that the community structure of AMF fungi varies with host plant species.
Further Information:
www.biodiversity.uoguelph.ca
www.uoguelph.ca/foibis/aron
P.M. Hollingsworth et al. (2009) PNAS 160: 12794-12797
A.J. Fazekas et al. (2009) Mol. Ecol. Resources 9: 130-139
Timing is everything: Circadian clock function in Arabidopsis and Brassica
C. Robertson McClung
Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, 03755, USA.
Circadian rhythms, biological rhythms with a period of approximately one solar day, are widespread in nature and are driven by endogenous, self-sustaining clocks. Evidence is accumulating in many species that circadian clocks allow organisms to coordinate their biology with their temporal environment and thus enhance fitness. Efforts to elucidate the plant circadian clock mechanism have emphasized Arabidopsis thaliana and show the clock to be composed of multiple interlocked negative feedback loops. I will discuss the roles of a family of Pseudo-Response Regulators in clock responses to temperature, an important environmental time cue. To determine the extent to which the Arabidopsis clock serves as a model for other species, we have investigated the crop plant, Brassica rapa. We have identified Quantitative Trait Loci (QTL) for the period of the circadian rhythm in leaf movement, as well as for a number of morphometric parameters, including flowering time, size of floral organs, and hypocotyl length, in a set of Recombinant Inbred Lines derived from two diverse parents, R500 and IMB211. Efforts to identify the gene responsible for a QTL for period length will be presented. One candidate is GIGANTEA (GI), identified as a clock component in Arabidopsis. GI is polymorphic between R500 and IMB211 and the IMB211 GI allele rescues the short period phenotype of the Arabidopsis gi-201 null mutant, whereas the R500 allele further shortens the period, which is consistent with their relative effects on period in B. rapa. Both alleles rescue the late flowering phenotype of gi-201. We have identified several putative null gi alleles in the B. rapa TILLING collection at the John Innes Institute and will use these to test the effects of the two B. rapa GI alleles on period length in a B. rapa tissue culture system that expresses robust circadian rhythms in gene expression.
Further Information:
www.dartmouth.edu/~rmcclung
A genomic systems approach toward identifying regulators of fruit development and ripening in tomato.
J. Giovannoni, J. Vrebalov, R. J. Lee, R. Alba, M. Chung, Z. Fei,
Boyce Thompson Institute for Plant Research and USDA-ARS Robert W. Holley Center, Tower Road, Cornell University campus, Ithaca, NY 14853 USA. jjg33@cornell.edu
The ripening and development of fleshy fruits is regulated by environmental, hormonal and developmental cues and influences the accumulation of important nutritional metabolites. Our laboratory uses tomato as a model system to understand ripening regulation and has identified a number of necessary ripening genes via positional cloning of loci underlying ripening mutations and transcriptional profiling studies of ripening associated gene expression. With the advent of modern genomics approaches and accumulation of genomics-scale date sets we are confronted with challenges in data management, analysis and interpretation and also great opportunities to extract novel meaning from these data if analyzed properly. We have attempted to capture data related to genotype, developmental stage, gene expression and nutritional metabolites and have created a public database to facilitate data management and analysis (Tomato Functional Genomics Database, http://ted.bti.cornell.edu/). Emphasis in our group is on the carotenoid, ascorbate and folate biosynthesis pathways during tomato fruit development and ripening. Our goal is to use correlation analysis of gene expression and metabolite levels to identify novel gene candidates associated with ripening and nutrient content. The database and examples of candidate genes and subsequent functional studies will be presented. To date we have identified six transcription factors that we have shown to be necessary for tomato fruit ripening via transgenic studies including two MADS-box, two NAC domain, an Ethylene Response Factor (ERF) and an APETALA2 gene homolog. One of the MADS-box genes, TAGL1, is especially intriguing in that it suggests a molecular link between fleshy fruit development and eventual ripening via a single gene product.
Further Information:
www.bti.cornell.edu/JimGiovannoni.php
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