Biodiversity and Risk-Benefit Assessment of Populus, Poplar, Draft Manuscript January 4, 2007
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Biodiversity and risk-benefit assessment of populus, poplar, draft manuscript January 4, 2007 Biodiversity and risk-benefit assessment of populus, poplar, draft manuscript January 4, 2007 .................... 1 1. Some general remarks about regulation............................................................................................................ 2 2. Introduction ...................................................................................................................................................... 3 3. Taxonomy and its relation to biodiversity ........................................................................................................ 3 4. Genomics of poplars......................................................................................................................................... 6 5. Reproduction biology ..................................................................................................................................... 13 6. Risk assessment of transgenic poplars:........................................................................................................... 18 6.1. Long term aspects of tree biology........................................................................................................... 18 6.2. Transgenic poplars in literature, a mini-review ...................................................................................... 19 6.3. Risk assessment: some characteristics for transgenic trees and poplar in particular............................... 22 6.4. Biosafety evaluation of the field release of transgenic poplars according to the Dutch-Swiss-Irish method ........................................................................................................................................................... 26 7. Cited literature................................................................................................................................................ 29 Fig. 1 The single most-parsimonious combined tree found with successive weighting. The tree has 10.271 steps (Fitch length: i.e. equal weights) with CI = 0.16 and RI = 0.38. Numbers avobe the branches are the numbers of estimated changes (ACCTRAN optimization). Underlined numbers below branches are bootstrap values; branches without an underlined number had bootstrap percentages of less than 50%. – A (left). First-branching portion of the tree, arranged with Ceratophyllaceae as the outgroup. Magnoliids form a grade composed of two major subclades (magnolid I and II) with the former sister of the eudicods. Within eudicots, ranunculids and hamamelids form a grade. The caryophyllids are sister to the asterids/rosids (for rosids, see Fig 4B). - B (right). Rosid clade. Note that the glucosinolate and nitrogen-fixing families form clades. Taxa for rbcL sequences were unabailable. + Nitrogen-fixing familiy outside the main nitrogen-fixing clade Fabaceae). ...................................... 5 Fig. 2 Functional Distribution of Genes According to a Modified MIPS (Munich Information Center or Protein Sequences) Classification Scheme of 4842 ESTs from Young Populus Leaves and 5128 ESTs from Leaves Collected in Autumn. Unclassified proteins show similarity to a gene of unknown function, typically an Arabidopsis open reading frame. Data courtesy of Stefan Jansson, from (Wullschleger et al., 2002)................... 6 Fig. 3 Dendrogram of Populus and Salix accessions, constructed from AFLP fragment similarities (Dice coefficient), with the UPGMA clustering method, and based on AFLP markers resolved by five primer combinations (EcoRI+ATA/MseI+ACAA, EcoRI+ ATA/MseI+ACAC, EcoRI+ATA/MseI+ACAG and EcoRI+ ATA/MseI+ACAT, EcoRI+AAA/MseI+ACAT). Accessions marked with an asterisk are potentially mislabeled species or hybrids (see text and Table 2). Species are marked by brackets and arrows, whereas lines group sections. Fig. 1 from (Cervera et al., 2005)............................................................................................................................................. 8 Fig. 4 Phylogenetic analysis of gene families in Populus, Arabidopsis, and Oryza encoding selected lignin biosynthetic and related enzymes. (A) Cinnamate-4-hydroxylase (C4H) gene family. (B) 4-coumaroyl- shikimate/quinate-3-hydroxlase (C3H) gene family. (C) Cinnamyl alcohol dehydrogenase (CAD) and related multifunctional alcohol dehydrogenase gene family. Arabidopsis gene names are the same as those in Ehlting et al. (80). Populus and Oryza gene names were arbitrarily assigned; corresponding gene models are listed in table S13. Genes encoding enzymes for which biochemical data are available are highlighted with a green flash. Yellow circles indicate monospecific clusters of gene family members, from (Tuskan et al., 2006)....................... 9 Fig. 6 (A) The 4DTV metrics for paralogous gene pairs in Populus-Populus and Populus-Arabidopsis. Three separate genome-wide duplications events are detectable, with the most recent event contained within the Salicaceae and the middle event apparently shared among the Eurosids. (B) Percent identity distributions for mutual best EST hit to Populus trichocarpa CDS, from (Tuskan et al., 2006). ........................................................................ 10 2 Fig. 7 Suggested classification, nomenclature and occurrence of Populus species (Eckenwalder 1996), and synonyms given by an earlier classification (Zsuffa 1975) in square brackets...................................................................... 11 Fig. 8 The single most parsimonious bifurcating unrooted tree, based on the Wagner method, representing the phylogeny of Populus. Plain and circled numbers correspond to accession codes (Table 2) and bootstrap values (only those above 50% are shown for main branches, grouping several species), respectively. Fig 2 from (Cervera et al., 2005)........................................................................................................................................... 12 Fig. 9 Crossability of Populus species. Extensive crossability studies have been carried out among species in the Populus (or Leuce), Tacamahaca and Aigeiros sections, while few data are available for those in Turanga and Leucoides (Zsuffa 1975). Interspecific breeding results are summarised. Fig. taken from (OECD, 2001)........... 15 Fig. 10 Natural and introduced Populus hybrids in the environment, modified from (OECD, 2001), from (Hoenicka & Fladung, 2006)..................................................................................................................................................... 16 Fig. 11 Log-likelihoods of microsatellite-based genotype assignments to Populus alba vs. Populus tremula (Fig. 2a) or P. alba vs. P. × canescens hybrids (Fig. 2b). Taxon designations used to perform the analyses were based on leaf morphology and were tested by Bayesian admixture analysis prior to the assignment tests. Open circles, P. alba; filled circles, P. tremula; crosses, P. × canescens hybrids, from (Lexer et al., 2005).................................. 17 Fig. 12 Time-lags between the first introduction of non-native trees to Brandenburg/Germany and the beginning of an invasion process, after (Kowarik, 1992b, 2003a) from (Hoenicka & Fladung, 2006). .......................................... 18 Fig. 13 Problematic exotic tree species (wild or hybrid ones) subject to control in Germany, after (Kowarik, 2003a), adapted, from (Hoenicka & Fladung, 2006) ........................................................................................................ 19 Fig. 14 Transgenic trees in tree physiology and biotechnology from (Herschbach & Kopriva, 2002) ........................... 20 Fig. 15 Tables 1-4: list of transgenic trees for various tansgene traits.......................................................................... 22 Fig. 17 Components of proposed Gene Flow Index (GFI) describing the propensity for successful pollen and/or seed- mediated gene flow through four possible strands: strand CPW for crop pollen-to-wild gene flow, strand CPC for crop pollen-to-crop, strand CSV for crop seed-to-volunteer and strand CSF for crop seed-to-feral, Table 3 from (Flannery et al., 2005).......................................................................................................................................... 27 1. Some general remarks about regulation Public-sector scientists need to play a serious, free role (Strauss et al., 2004) The ‘Monsanto model’ exemplified the first phase of biotechnology development, where the private sector evaluated benefits for transgenic varieties internally, or dictated the terms for evaluation. Moreover, the focus has been on benefits for the company and farmer, rather than broad social and environmental values. Thus, it has been easy to demonize corporate, patent-dominated biotechnology as solely profit-driven. For this to change, much broader public sector participation is needed, both from a technical and ethical viewpoint. As the Nuffield Foundation has shown best, there are strong ethical cases to be made for crop biotechnology http://www.nuffieldbioethics.org/gmcrops/index.asp However, for reasons of credibility, corporations should not be the ones doing it. Because the intellectual property constraints on transgenic products are being relaxed as patents expire, there may be increased public-sector release of regionally valuable transgenic varieties. This would also help to reduce the perception