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227 Abaso, 21 Abies, 4 Abiotic Stress Responses Drought Stress Index A Agrobacterium strains ABA responsive elements (ABRE), 227 biology, pioneering advances in, 5 Abaso, 21 transformation procedures and protocol, Abies, 4 121 Abiotic stress responses Agrobacterium tumefaciens, 120–121 drought stress avoidance strategy, AGL1 strain, 123 232–239 nopaline strains,C58 and LBA4404, hormonal signaling during drought stress, 120–123 model, 239 octopine strains, like EHA105, 123 signaling at cellular and tissue level Aigeiros, 45 cellular defences activation, AINTEGUMENTA (ANT) gene, 179 228–229 Allocation patterns, 46–47 water limitations, 226–228 Allometric relationships, analysis, 47–48 water shortage, cellular consequences, Allozyme 226 diversities, 91 tree-specific adaptation measures markers, 22–26 drought, growth responses, 229–230 Amanita muscaria, 259 hydraulic architecture changes, 1-Aminocyclopropane-1-carboxylate oxidase 230–232 genes (ACO), 236 Abscisic acid (ABA) Angiosperms, 4 as abscission inducing agent, 233 tree model system, 1990s, 68 in Populus wood formation, 220–221 Anthocyanidin reductase (ANR), 291 signaling water limitations, 226–228 Anthocyanidin synthase (ANS), 291 See also Wood Antisense-mediated gene suppression, 117 Abscission Antisense technology, 117 as drought stress avoidance, 232–233 AP/ERF transcription factor families, 85 by seasonal drought stress, 235–239 AP/ERF transcription factors, 85 stress induced, 234–235 APETALA1 (AP1) gene, 159 See also Abiotic stress responses APETALA2 (AP2) gene, 158 Acephala applanata, 255 Aquaporins, 55 Activation tagging effectiveness, Arabidopsis spp. in Populus, 124 A/B/C-function, defined, 164 Adaptive traits, 29–30 FLC gene, 159 Affymetrix platforms, 141, 143 floral signal, 161–162 AFR regulators, 85 LBs in, 189 AGAMOUS (AG) gene, 164 RNA silencing pathways, 157–158 AG co-orthologs, expression, 165 SEP gene, 164 Agilent platforms, 141 temporal signal, 158 Agrobacterium rhizogenes, 121 See also Perennial life S. Jansson et al. (eds.), Genetics and Genomics of Populus, Plant Genetics 369 and Genomics: Crops and Models 8, DOI: 10.1007/978-1-4419-1541-2, C Springer Science+Business Media, LLC 2010 370 Index Arabidopsis thaliana Auxin Response Factor (AFR) transcription as alternative model system, 68 factors, 83 analysis of gene sets from Populus and, AUXIN RESPONSE FACTOR (ARF) gene, 158 81–82 Axillary vegetative meristems, formation, 160 genome comparison, 78 B duplicated, 114 BAC-based physical maps advances and sequence, 5–6 synteny test, 84 as model plant, 3 BAC clones, comparison of sequences, 71 not good for arboreal traits study, 4 BAC end sequences (BES), 72 mutation rate, 92 Bacillus subtilis model, bacterial spore phenylpropanoid enzymes in, 84 formation, 3 in planta methods, 125 BAC minimum tiling path, 11 See also Populus BAC physical map, 69 See also Populus trichocarpa Arabis aplina, 162 genome project Arborea (Laval University, Quebec), 6 Bacterial artificial chromosome (BAC) library, ARBORKNOX1 (ARK1), 213 71 ARBORKNOX2 (ARK2), 213 BARK STORAGE PROTEIN (BSP) gene, 182 ARBORKNOX1 gene, 174 Beauveria bassiana, 264 Arbuscular mycorrhizal (AM) fungi, 248 Beavis effect, 102 and Populus, association, 255–258 Beijing Forestry University’s P. ×tomentosa’s ARF5 (MONOPTOROS) genes, 83 breeding program, 318 ARF5/MP gene, 83 Betula, 4 ARF transcription factor families, 85 Betula papyrifera Marsh., 259 ARK2 overexpression, 213 Biennials, vernalization treatment, 156 ArrayExpress database, 142 Biolistic approaches, 121 Array platforms, 141 Biomass equations, for clones, 48 and cross-species utility, 141 Biomass estimations, 47 Artificial or synthetic miRNAs, role in Biomass yields and growth, 39–44 PTGS, 118 Birch, see Betula Aspens Black cottonwood, see Populus balsamifera L. Arabidopsis AtCBF1, overexpression, 186 BLAST2GO web resource, 142 difference from hybrid poplars, BLASTN hits, 74 204–205 BLASTN searches, 80 gene expression analysis, 178 BLAST search tools, 136 genes in cambial dormancy, 182 BLAT search tools, 136 and hybrid poplars, difference, BpMADS4 gene, 182–183 204–205 Brassica napus, 158 See also perennial life; Populus Breeding and selection for pest resistance, Association mapping (AM), 95, 102–103 328–329 and candidate gene approach, 102 Breeding program and approaches ATP-dependent ATP Binding Cassette (ABC) biomass productivity, 327 class, 85 controlled breeding, 313–322 Autumnal leaf senescence, regulation, F1 inter-specific hybridization, 317, 318 182–183 genecology, 308–313 Autumnal senescence genetic and varietal evaluation, 322–325 ESTs up-regulation/down-regulation, hybrid vigor impact, 318 237–238 intra-specific recurrent breeding program, AUX/IAA interacting proteins, 83 318 AUX/IAA regulators, 85 long-term breeding programs, 318–322 Auxin Efflux Carrier family, 85 Populus cultivars, registered with FAO’s Auxins, in wood formation, 55, 216–218 International Poplar See also Wood Commission, 313 Index 371 specific gravity, evaluated wood quality Cinnmoyl-CoA reductase (CCR), 293 trait, 328 Classifications, Populus, 18, 21–22 testing and selection, 322–329 and inconsistencies, 21–22 translational genomics, 329–336 CLAVATA1-3 (CLV1-3)-WUSCHEL (WUS) See also Reproductive development, in system, 172 Populus Clonal selection, for improvement, 45 Breeding strategies, of Populus, 313, 315–318 Clone number 383-2499, 69 Bud dormancy release, in Populus, 187 Clonostachys rosea, 264 Bud phenology, genetic control, 103–106 CLOVER, 139 Burkholderia cepacia Bu72, 8 CLV3 gene, 174 bZIP transcription factor, (FLOWERING CMap resources, 140 LOCUS D (FD), 159 Coalescent theory, 98 Commercial purposes usage, 40 C Complementation, 113 CACTA elements, 80 Complex traits dissection Caffeic acid O-methyl transferases (COMTs), association mapping and, 102–103 293 incidence of segregation distortion, Caffeoyl CoA O-methyl transferases 101–102 (CCOMTs), 293 linkage mapping and genome dynamics, CALCINEURIN B-LIKE PROTEIN 9 100–102 (AtCBL9), 239 Conifers, 4 Cambium Conservation genomics, 347–349 dormancy, 181–182 genetic diversity conservation, 350–351 features, 202 hybridization and genetic conservation, function, genetic regulation, 212 351–353 global gene expression across, 212–215 population genomics for, 353–357 See also Perennial life Conservation programmes for Populus sp., Canadian forestry, focus on conifers, 6 considerations, 353 Candidate gene approach, 102 CONSTANS (CO) gene, 177 Canopy establishment, influence of CONSTANS/FLOWERING LOCUS T (CO/FT) competition, 45–46 gene, 159 Carbon neutral renewable energy source, 40 Coordinated Agricultural Product (CAP), 330 Cartagena Protocol on Biodiversity, 12 Coppicing, impact on growth, 44 Castanea dentata, 249 Cortinarius sp., 258 CatFisher, 142 Cottonwoods, see Populus angustifolia CBF genes, 187 CTAB-based protocol, 70 CBL-INTERACTING PROTEIN KINASE 10 Cyclin A2 (CYCA2), 214 (CIPK10), 239 Cytokinins, 55, 123 CDNA arrays, 141 in wood formation, 219 Cellular defences, activation, 228–229 See also Wood Cellulose macrofibrils, 208 Cytoskeleton, role, 238 CENTRORADIALIS (CEN) gene, 160 CENTRORADIALIS-LIKE1 (CENL1) gene, D 177–178 DATFAP, annotation-based approach to Chaetomium spirale, 265 identify TFs, 139 Chalcone isomerase (CHI), 291 Defense, in Populus Chalcone synthase (CHS), 291 mutualisms, 250–255 Chilling, 191 endophyte association, 262–263 Chilling-induced removal, of callose, 188 evolutionary history and fossil record, China, controlled breeding techniques of 265–268 Populus, 314 fungal symbionts, 264–265 Cinnamomum zeylanicum, 248 mycorrhizal fungi association, 255–261 Cinnamoyl dehydrogenase (CAD), 293 plant symbiont communities, 261–264 372 Index Defense, in Populus (cont.) E proteins and genomics impact, 288–289 Eco-dormancy, definition, 175 defense-related genes discovery, Ecogenomics model plant, Populus as, 280 285–286 Eco-TILLING approach, 67 gene expression patterns and defense Ectomycorrhizal species, associated with responses, 286–288 Populus, 258 and secondary metabolism, 280–284 Ectomycorrhizal spp. and Populus, application of genomic tools, 285–289 association, 258 biosynthetic pathways, to phenolic Ectomycorrhizal symbiosis, 259–260 compounds, 290 Ectopic approaches, 117 functional analysis of genes, 294–296 Ectopic gene expression, 113 future perspectives, 298–299 Ectopic overexpression, in Populus, 160 importance of variation, 296–298 Effective population size, concept, 92 and phenylpropanoid, genomic analysis, EFP browser, 142–143 289–294 ELEMENT database, 139 variations and secondary metabolite Elite cottonwood hybrids, 157 profiles, 296–298 Endoconidioma populi, 263 Dehydrins, in overwintering, 186 Endo-dormancy, definition, 175 See also Freezing tolerance, in Populus Endophyte and Populus spp., association, DELLA proteins, role, 180 262–263 2,4-Diacetylphloroglucinol (DAPG), 253 Endoplasmic reticulum (ER), role, 189 Dicer, 117 Enhancer and gene traps, 124 Dihydroflavonol reductase (DFR), 291 Enterobacter sp. 638, 8 Diploidization process, 76 Epichloë festucae, 250 Diploid species, nucleotide polymorphism, 92 Epigenetic mechanisms, role, 158 DIURNAL database, 139 Escherichia coli, as model prokaryotic Diurnal project, 139 microbe, 3 DNA-based vectors, microprojectile EST databases, Populus bombardment use, 121 launch, 6 DNA extraction protocol, 70 types, 137–139 Domestication, 46, 307 Ethylene Dominant negative mutations, 117 inhibitory substances, 55 Dormancy in wood formation, 220 in cambium, 181–182 See also Wood cycles, 135, 175 Eucalyptus in Aspen, 176 breeding programs, 307 feature, 176 genome, 68 definition, 174–175 species, 4, 5 genetic control,
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