A Lifeboat to the gene pool, PhD defence, Copenhagen Univ (31 March 2011)


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PhD dissertation defence. Utilization of Plant Genetic Resources: A Lifeboat to the Gene Pool. Dag Endresen, 31 March 2011. Academic supervisor: Dvora-Laiô Wulfsohn and Brian Grout. Assessment committee: Theo van Hintum, Nigel Maxted and Åsmund Rinnan.

See also: "http://dagendresen.wordpress.com/2011/04/01/phd-defence/".

Endresen, D.T.F. (2011). Utilization of Plant Genetic Resources: A Lifeboat to the Gene Pool [PhD Thesis]. Copenhagen University, Faculty for Life Sciences, Department of Agriculture and Ecology. Printed at Media-Tryck, Lund University Press, April 2011. Available at: http://goo.gl/pYa9x (PDF 37 MB). ISBN: 978-91-628-8268-6.

Endresen, D.T.F. (2010). Predictive association between trait data and ecogeographic data for Nordic barley landraces. Crop Sci. 50(6):2418-2430. doi: 10.2135/cropsci2010.03.0174

Endresen, D.T.F., K. Street, M. Mackay, A. Bari, and E. De Pauw (2011). Predictive Association between Biotic Stress Traits and Eco-Geographic Data for Wheat and Barley Landraces. Crop Science 51 (5): 2036-2055. doi: 10.2135/cropsci2010.12.0717

Endresen, D.T.F., K. Street, M. Mackay, A. Bari, A. Amri, E. De Pauw, K. Nazari, and A. Yahyaoui (2012). Sources of Resistance to Stem Rust (Ug99) in Bread Wheat and Durum Wheat Identified Using Focused Identification of Germplasm Strategy (FIGS). Crop Science 52, in press. doi: 10.2135/cropsci2011.08.0427

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  • PhD dissertation, 31 March 2011: Endresen, Dag TerjeFilip. Utilization of Plant Genetic Resources: A Lifeboat to the gene Pool. Copenhagen University. ISBN: 978-91-628-8268-6. Photo: Wheat landrace at Alnarp in southern Sweden, August 2010, by Dag Endresen. URL: http://www.flickr.com/photos/dag_endresen/4998314457/
  • Photo: Wheat, TriticumaestivumL., atNöbbelöv in Lund Sweden, June 2010 by Dag Endresen. URL: http://www.flickr.com/photos/dag_endresen/4826175873/, https://picasaweb.google.com/dag.endresen/GermplasmCrops#5497796034327520578
  • Genetic resources from the wild relatives of the cultivated plants contributes the raw material required for domesticated forms and the furtherdevelopment of these food crops. Genebanks preserve and provides plant genetic resources for utilization by plant breeders and other bona fide use.
  • More than 7.4 million genebank accessions; andmore than 1400 genebanks - including approximately 140 large genebanks each holding more than 10.000 accessions: Second Report on the State of the World’s Plant Genetic Resources for Food and Agriculture (2010) Food and Agriculture Organization of the United Nations (FAO).
  • Genebankseedstore documentation system, http://sesto.nordgen.org/sesto/
  • NOTE that the countries are colored by the distribution of accessions:: while the red dots are the georeferenced collecting places.Dynamic maps live to SESTO, created with UMN Mapserver (Dag Endresen, 2009)
  • Demonstration project with implementation of the BioCASE web service software supported by IPGRI/Bioversity International was carried out during 2005/2006. See also http://chm.grinfo.net
  • Demo project in Europe in the context of the EURISCO platform for the implementation of data sharing with web services using the GBIF Integrated Publishing Toolkit, http://ipt.gbif.org, carried out during 2010/2011 with support from GBIF.
  • The purpose of Darwin Core is to facilitate data sharing, http://rs.tdwg.org/dwc/. A requirement for the use of the GBIF IPT is the extension of the Darwin Core to include the additional terms required to describe genetic resources.
  • The ultimate goal is full interoperability and readily access to all sources of information relevant and useful for analysis of genebank datasets – and other biodiversity studies.
  • NordGen study in June 2010, Sea kale (CrambemaritimaL.). Integration of GBIF-mediated occurrence data with other applications like the openModeller generates a probability distribution using the Envelope Score Algorithm. Online analysis at the GBIF data portal, http://data.gbif.org
  • NordGen study in June 2010, Wormwood (Artemisia absinthiumL.). Species distribution model using the Maxent desktop ecological niche modeling software.
  • For more information on Gap Analysis see: http://gisweb.ciat.cgiar.org/GapAnalysis/Photo: South of Tunisia, http://www.flickr.com/photos/dag_endresen/4221301525/
  • Photo from the USDA Photo archive.
  • Photo: Dag Endresen.Field of sugar beet (Beta vulgaris L.) at Alnarp (June 2005). URL: http://www.flickr.com/photos/dag_endresen/4189812241/
  • Photo: Bread wheat (Triticumaestivum L.) at Nöbbelöv in Lund July 2010 by Dag Endresen. URL: http://www.flickr.com/photos/dag_endresen/4826565058/
  • Illustration of trait mining with ecoclimatic GIS layers. GIS layers included in the illustration are from the ICARDA ecoclimatic database, average: annual temperature (front), annual precipitation (middle), and winter precipitation (back) (De Pauw, 2003)
  • Landrace samples (genebank seed accessions)Trait observations (experimental design) - High cost dataClimate data (for the landrace location of origin) - Low cost dataThe accession identifier (accession number) provides the bridge to the crop trait observations.The longitude, latitude coordinates for the original collecting site of the accessions (landraces) provide the bridge to the environmental data.
  • Modern agriculture uses advanced plant varieties based on the most productive genetics. The original land races and wild forms produce lower yields, but their greater genetic variation contains a higher diversity in e.g. resistance to disease. High-yielding modern crops are therefore vulnerable when a new disease arises.
  • Illustration traditional cattle farming: http://commons.wikimedia.org/wiki/File:Traditional_farming_Guinea.jpg (USAID, Public Domain)
  • The WorldClim dataset is described in: Hijmans, R.J., S.E. Cameron, J.L. Parra, P.G. Jones and A. Jarvis, 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25: 1965-1978NOAA GHCN-Monthly version 2:http://www.ncdc.noaa.gov/oa/climate/ghcn-monthly/index.phpWeather stations, precipitation: 20590;temperature:7280
  • We often divide the data for a simulation model project in three equal parts: one set for initial model calibration or training, one set for further calibration or fine tuning; and one test set for validation on the model.
  • GRIN database (USDA-ARS, National Plant Germplasm System, Germplasm Resources Information Network, online http://www.ars-grin.gov/npgs) USDA GRIN, trait data online: http://www.ars-grin.gov/cgi-bin/npgs/html/desc.pl?65049
  • Left side illustration is modified from Wise et al., 2006:201 (PLS Toolbox software manual). The right side illustration is made by the PLS Toolbox software in MATLAB.
  • Photo: USDA ARS Image k1192-1, http://www.ars.usda.gov/is/graphics/photos/mar09/k11192-1.htm
  • USDA ARS Image Archive, http://www.ars.usda.gov/is/graphics/photos/
  • GRIN database (USDA-ARS, National Plant Germplasm System, Germplasm Resources Information Network, online http://www.ars-grin.gov/npgs) USDA GRIN, trait data online: http://www.ars-grin.gov/cgi-bin/npgs/html/desc.pl?1041Dr Harold Bockelman extracted the trait data (C&E)
  • Endresen, D.T.F. (2011). Utilization of plant genetic resources: A Lifeboat to the Gene Pool. PhD dissertation, Copenhagen University. ISBN: 978-91-628-8268-6
  • http://www.life.ku.dk/English/Service/~/media/HOME/docs/pdf/LIFEfrbkort_uk_maj2008.ashxhttp://www.life.ku.dk/English/Service/find_us.aspx
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