Organizers: Om Rajora (University of New Brunswick, Canada) & Wickneswari Ratnam (Universiti Kebangsaan Malaysia)
Assessing the adaptive portfolio of reforestation stocks for future climates. Aitken, S., Yeaman, S., Hodgins, K. (University of British Columbia, Canada; Sally.Aitken@ubc.ca; yeaman@zoology.ubc.ca; hodgins@zoology.ubc.ca), Hamann, A. (University of Alberta, Canada; andreas.hamann@ualberta.ca), Whitlock, M. (University of British Columbia, Canada; whitlock@zoology.ubc.
ca), Liepe, K. (University of Alberta, Canada; liepe@ualberta.ca), Rieseberg, L., Nurkowski, K., MacLachlan, I., Mellway, R., Smets, P. (University of British Columbia, Canada; lriesebe@interchange.ubc.ca; kristin.nurkowski@gmail.com;
ianrmaclachlan@gmail.com; rmellway@mail.ubc.ca; pia.smets@ubc.ca).
Climate change is creating a mismatch between tree populations and the climates they inhabit. Assisted gene fl ow between populations has the potential to mitigate this maladaptation. To better plan for reforestation for new climates, the AdapTree project is characterizing the extent of local adaptation in two widespread conifers in western Canada, lodgepole pine (Pinus contorta) and the interior spruce species complex (Picea engelmannii, P. glauca, and their hybrids). Seedlings from more than 250 populations per species have been phenotyped for climate-related traits including growth, bud phenology, cold hardiness, and heat and drought stress responses under a range of simulated climatic conditions. These individuals have also been genotyped either through resequencing more than 28 000 genes in lodgepole pine and more than 35 000 genes in interior spruce, or through genotyping using a 50 000 single nucleotide polymorphism (SNP) array. Relationships between provenance climate and both phenotypes and SNP genotypes are being used to characterize the extent of, and climatic drivers of, local adaptation in both species. Results will be used to design climate-based seed transfer policies for future climates, and to evaluate the capacity of natural populations to rapidly adapt to new climatic conditions.
Using case studies for enhancing capacity for managing forest genetic resources. Boshier, D. (Bioversity International, UK;
david.boshier@plants.ox.ac.uk), Bozzano, M., Loo, J., Rudebjer, P. (Bioversity International, Italy; m.bozzano@cgiar.org;
j.loo@cgiar.org; p.rudebjer@cgiar.org).
Forest trees are long-lived species with high genetic diversity that is central to their survival, regeneration, and adaptation to climate change. However, forest managers and conservationists are often not well informed about genetic aspects of population viability. Lack of understanding of forest genetic resources (FGR), therefore, constrains sustainable forest management and adaptation to climate change. Tertiary education curricula cover FGR issues poorly or not at all. A vicious cycle is looming in which teaching and understanding of FGR and its importance to sustainable forest management becomes increasingly marginal-ized. We describe a case-study-based approach to teaching and learning about FGR use and conservation. Designed to promote FGR-friendly decision-making, the Training Guide covers practical issues in forest and tree management of both global and local relevance. Each case study provides genetic, ecological, and socioeconomic information as a basis for students’ analysis. Teach-er’s notes, PowerPoint presentations, and videos give background information for each case. The guide targets both tertiary education and on-the-job training. It is or will soon be available in English, Spanish, French, Russian, and Chinese. The material has proved popular with trainees and is fl exible and easy to use in a range of formal and informal learning situations.
Bioprospecting for novel genes through characterization of leaf transcriptome of Withania somnifera, a valued medicinal plant. Dasgupta, M., George, B. (Institute of Forest Genetics and Tree Breeding, India; modhumitaghosh@hotmail.com; blessan.
orion@gmail.com).
In the present era of “-omics,” rapid sequencing and analysis of genomes of non-model species is constantly increasing. Studies have revealed that these uncharacterized genomes are hidden treasures of gene clusters potentially coding for biologically active peptide/compounds. The present study was undertaken to identify novel pathogenesis-related (PR) genes from Withania somnifera, a valued medicinal plant with pharmaceutical and nutraceutical applications. The global transcriptome of salicylic acid treated leaves was sequenced using an Illumina Genome Analyzer IIx sequencer. The de novo assembly, gene ontology (GO) mapping, functional annotation, and pathway analysis of transcript contigs were conducted using different computational pipelines. The assembly generated 73 523 transcript contigs and 71 062 were annotated using BLASTx against the non-redundant (nr) database for Viridiplantae. The annotated transcript contigs were mapped on GO database and 53 424 sequences were assigned GO terms.
The metabolic process and the cellular process constituted the main biological processes and 182 functional pathways were identifi ed from the sequence data. Further, the transcriptome data was mined for PR genes and 18 genes from 12 families were identifi ed and their expression during signal amplifi cation was analyzed using quantitative real time polymerase chain reaction (qRT-PCR) technology. This study provides a repertoire of functional PR gene pools for future transformation programs in diverse genotypes.
Range-wide geographic variation in Prunus africana at the molecular and chemical level. Geburek, T., Schueler, S., Konrad, H., Kadu, C. (Federal Research Centre for Forests, Austria; thomas.geburek@bfw.gv.at; silvio.schuler@bfw.gv.at; heino.konrad@
bfw.gv.at; cheledikadu@gmail.com), Vinceti, B. (Bioversity International, Italy; b.vinceti@cgiar.org), Miretie, Z. (Federal Research Centre for Forests, Austria; ziyinm@yahoo.com).
This paper describes the molecular and chemical variation of Prunus africana, an important Afromontane medicinal tree species.
Genetic variation and differentiation at both chloroplast and nuclear DNA microsatellites were high. The highest molecular richness was detected in the northern distribution area, especially in Ethiopia. Genetic variants detected in the far north were only shared in the southeastern, but not in the western lineage, questioning the immigration routes accepted so far. For both marker types a distinct phylogeographic pattern was detected. Eventually six main regions were differentiated: 1) Ethiopia, 2) West Africa, 3) East Africa west of the Eastern Rift Valley (ERV), 4) East Africa east of the ERV, 5) southern Africa, and
6) Madagascar. The strongest divergence was evident between Madagascar and continental Africa both for chloroplast as well as nuclear microsatellites. Estimates of gene fl ow based on chloroplast and nuclear markers were slightly different indicating a shift of gene fl ow barrier in the ERV over time. Bark extracts were analyzed by gas chromatography. Variation among populations was high. However, contrasting to the DNA data, the populations were only weakly differentiated on a geographic level. The results will be discussed in view of the biography and conservation of this species.
Population and landscape genomics to study local adaptation in loblolly pine (Pinus taeda) populations and to breed more climate change resilient trees. Krutovsky, K. (University of Göttingen, Germany; kkrutov@gwdg.de), Chhatre, V. (U.S. Forest Service, USA; crypticlineage@gmail.com), Lu, M., Byram, T. (Texas A&M University, USA; mira0501@tamu.edu; tbyram@tfs.
tamu.edu), Wegrzyn, J., Neale, D. (University of California at Davis, USA; jlwegrzyn@ucdavis.edu; dbneale@ucdavis.edu), Loopstra, C. (Texas A&M University, USA; c-loopstra@tamu.edu).
Population and landscape genomics help us better understand local adaptation and develop sustainable management of forests to mitigate climate change and to breed more drought and disease resilient trees. Loblolly pine (Pinus taeda L.) has great economic importance and also a wide geographic distribution occupying a variety of environmental conditions, which makes it a good system to address these issues. We used genotypic data based on a genome-wide set of 4 264 single nucleotide polymorphisms (SNPs) representing expressed loci to study association of SNPs with adaptive and breeding value related traits and environmental variables in more than 1 450 loblolly pine trees from the Western Gulf Forest Tree Improvement Program. Numerous signifi cant associations were found between various phenotypic traits, environmental variables and SNPs. We also tested the genome target sequencing techniques for re-sequencing exome regions and for high-throughput SNP discovery and genotyping by sequencing (GBS). More than 6.5 million SNPs were detected that we plan to use for genotyping the entire exome in more than 400 individual trees to link allelic variation with phenotypic variation in important economic, adaptive, and breeding traits.
Implications of our results for breeding, genomic selection, genetic conservation and towards understanding local adaptation will be discussed.
Development of a DNA-based timber-tracking system for Koompassia malaccensis in Malaysia. Lee, C., Tnah, L., Lee, S., Ng, K., Ng, C. (Forest Research Institute Malaysia; leechait@frim.gov.my; leehong@frim.gov.my; leesl@frim.gov.my; kevin@frim.
gov.my; chinhong@frim.gov.my), Diway, B. (Sarawak Forestry Corporation, Malaysia; bibian@sarawakforestry.com), Eyen, K.
(Sabah Forestry Department, Malaysia; eyen.khoo@sabah.gov.my).
Illegal logging jeopardizes sustainable forest management. It is a global issue that needs to be addressed urgently. This project aimed to establish an individual and population database for Koompassia malaccensis in Malaysia, in order to develop a DNA-based timber-tracking system for this widespread and commonly traded timber species. A total of 1 467 K. malaccensis samples collected from 56 locations throughout Malaysia were genotyped using nine short tandem repeat (STR) loci. Forensic parameters and allele frequencies for each locus were estimated, with the minimum allele frequency adjusted to 5/2n. Assuming indepen-dence between alleles and loci, the theoretical 9-locus STR profi le estimates can range from 7.8631 × 10–9 to 7.5240 × 10–48, implying that individual identifi cation is feasible in forensic casework. Results also showed that the individual identifi cation database could be further divided into three subgroups (East Malaysia, West Malaysia, and Peat Swamp Ecotype). From the assignment tests, the mean proportion of baseline individuals correctly assigned to the respective subgroups was 99.2%. The chloroplast DNA analysis was carried out using 395 samples to establish a population identifi cation database, yielding a region specifi c haplotype distribution map. In the case when DNA extraction is feasible, the combined usage of STR and chloroplast markers will enable geographic traceability K. malaccensis timber in Malaysia.
Genetic diversity of central and peripheral populations of Toona ciliata var. pubescens, an endangered tree species endemic to China. Liu, J., Jiang, J. (Chinese Academy of Forestry, China; ywliu2005@163.com; jiang_jingmin@163.com).
Our objective was to examine the genetic diversity of central and peripheral populations of Toona ciliata var. pubescens, to elucidate whether the central-peripheral hypothesis applies to these populations. We analyzed 384 individuals from nine natural populations using eight pairs of polymorphic simple-sequence-repeat (SSR) primers. The results showed that the mean numbers of observed and expected alleles in peripheral populations were higher than in central populations. Both the observed and expected heterozygosities were higher in peripheral populations compared with the central populations. The coeffi cient of gene differentiation of the peripheral populations was 0.3045, which was signifi cantly higher than that of the central populations.
The gene fl ow between central populations was greater than one, but less than one between peripheral populations. This indicates that frequent gene fl ow exists between central populations, while terrain and habitat fragmentation prevent gene fl ow among peripheral populations. A Mantel test indicated there is no relationship between genetic and geographical distance of T. ciliata var. pubescens.
Identifying site characteristics that explain variation in Douglas-fi r productivity, stem form, and adaptability. Magalska, L., Howe, G., Maguire, D., Jayawickrama, K. (Oregon State University, USA; lauren.magalska@oregonstate.edu; glenn.howe@
oregonstate.edu; doug.maguire@oregonstate.edu; keith.jayawickrama@oregonstate.edu).
The ability to project the value of Douglas-fi r plantations is limited by 1) how stand growth, stem quality, and adaptability (e.g., cold hardiness, budburst, survival) are infl uenced by site characteristics; 2) the effects of seed source and genotype transfer among sites; and 3) the effects of near-term climate change. Our objectives were to understand how plantation site characteristics are related to growth, stem form, and adaptability. Differences in productivity among sites result from genetic and environmental variation. To separate these effects, we used progeny tests in which the same genetic materials were planted on multiple sites.
The site characteristics that we focused on included climate, soils, and topography. Measures of site productivity, stem form, and adaptability were explained using correlation, random forest, and linear regression analyses. These analyses identifi ed important site characteristics related to summer drought, cold season temperatures, and precipitation interactions with soil properties. These results will form the foundation of future studies to understand how parental site characteristics are related to the performance of their progeny at each test location, the extent to which seed sources and families can be successfully moved among sites, and the near-term effects of climate change.
Visualising the environmental responses of forest tree populations. Meder, A., Brawner, J. (Commonwealth Scientifi c and Industrial Research Organisation, Australia; roger.meder@csiro.au; jeremy.brawner@csiro.au), Dvorak, W., Hodge, G. (North Carolina State University, USA; dvorak@ncsu.edu; grh@ncsu.edu).
A novel methodology for describing genotype by environment interactions estimated from multi-environment fi eld trials is described and empirical examples using trial networks of pines and eucalypts is presented. The network of experiments consists of replicated fi eld trials of eucalypts across the subtropics of eastern Australia, or across the southern hemisphere in the case of pines. To apply the results across broad landscapes rather than a specifi c environment, species’ productivity is classifi ed simulta-neously by the differential in species’ productivity across a range of sites and the differential in site environmental variables, and their effect on productivity, by site. An important feature of the method is that it abstracts performance away from the specifi c trials that have sampled the target planting environment so that changes in productivity are associated with the environmental variables classifying the trials. This facilitates the visualisation of changes in productivity (GxE) across the climatic variables that classify the landscape rather than changes in productivity among specifi c sets of trials and facilitates an alternative display of GxE which obviates reference back to the trials used to evaluate sets of germplasm.
Genetic structuring and triploidy in North American aspen (Populus tremuloides). Mock, K. (Utah State University, USA;
karen.mock@usu.edu).
Trembling aspen (Populus tremuloides) is the most broadly distributed native tree species in North America, and the species is known for its ability to form large clones through root suckering. Rangewide genetic patterns indicate that there are two major genetic groups of aspen: one in the western United States and one across Canada, Alaska, and parts of the northern United States.
This structure, along with rangewide patterns of genetic diversity, suggests that aspen in the western United States are a distinct lineage and did not participate in the post-glacial expansion across Canada. Aspen populations in the western United States are more distinct from each other, but within-population diversity is lower, compared to aspen in the rest of the species range. This pattern is likely a result of topography and isolation among western United States populations. Furthermore, western North American aspen populations have higher rates of triploidy than in the rest of the range and the proportion of triploidy correlates roughly with drier climates. The data underlying these patterns, and corresponding ecological and management implications, will be discussed.
Karyological studies on Picea spp. Muratova, E. (Sukachev Institute of Forest, Russia; elena-muratova@ksc.krasn.ru).
Species from the genera Picea are stable diploids and contain 24 A-chromosomes (2n=24). In the morphological type Picea, eight pairs are long metacentrics and four pairs are short meta- or submetacentrics. In P. schrenkiana, P. jezoensis, P. pungens, P. x fennica, and P. breweriana, one B-chromosome occurs (2n=24+1B); P. koyamae, and P. engelmannii have one to two (2n=24+1-2B), P. ajanensis and P. meyeri have one to three (2n=24+1-3B) P. obovata has one to four (2n=24+1-4B), and P. glehnii has one to fi ve B-chromosomes (2n=24+1-5B). This is the fi rst study case occurrence of B-chromosomes in four species: P. breweriana, P. pungens, P. koyamae, and P. schrenkiana. At present, B-chromosomes are found in 19 Picea species including interspecies hybrid P. x fennica. Sizes of A-chromosomes Picea are from 9 to 15 mm. Lengths of B-chromosomes of these species compose 25–30% of the A-chromosomes (4–6 mm). In their morphology, B-chromosomes can be metacentric (B1 type) and submetacentric B2 type. It is supposed that submetacentric B-chromosomes originated as the result of pericentric inversion of metacentric ones. The number of B-chromosomes in conifers varies from one to six. The highest number (six) was registered in Picea glauca and P. albertiana; P. glehnii and P. sitchensis had fi ve, and P. obovata had four. Other researchers found that the presence of B-chromosomes can be connected with unfavourable ecological factors. Effects of B-chromosomes can have adaptive characteristics. The results obtained allow us to consider that this system is a general phenomenon and B-chromosomes are of importance for populations and species and may possibly play a role in their adaptations.
The evolutionary history and genetic diversity of ponderosa pine: management implications for an important species of western North America. Potter, K. (North Carolina State University, USA; kpotter@ncsu.edu), Means, R. (Bureau of Land Management, USA; rmeans@blm.gov), Hipkins, V., Mahalovich, M. (U.S. Forest Service, USA; vhipkins@fs.fed.us;
mmahalovich@fs.fed.us).
Ponderosa pine (Pinus ponderosa) is the most broadly distributed pine species of the Western Hemisphere, where it has consider-able ecological and economic importance. It exhibits complicated patterns of morphological and genetic variation, suggesting that it may be in the process of differentiating into multiple species. These patterns have created confusion about evolutionary relationships within the ponderosa pine complex, while the near absence of paleoecological data during the Pleistocene ice age obscures phylogeographic processes that infl uenced the evolutionary history of the complex. This study offers some surprising insights into ponderosa pine evolutionary history and phylogeography using three genetic marker systems: a highly polymorphic mitochondrial minisatellite DNA region, nuclear microsatellites, and allozymes. The results from this study, which encompasses 3 100 trees from 104 populations across the species range, should assist in management decision-making and conservation planning relating to ponderosa pine sub-taxa and populations. For example, mtDNA haplotypes may represent evolutionarily distinct units that may respond differently to climate change because of differences in adaptation to climatic conditions. Measures such as seed archiving, silvicultural treatments, and prescribed fi res should consider whether populations possess rare haplotypes and alleles and high haplotypic or allelic diversity.
The role of genomics research in understanding responses and adaptation of forest trees to changing climate and environmental conditions. Rajora, O. (University of New Brunswick, Canada; Om.Rajora@unb.ca).
Recent climate and environment changes are subjecting our forests to signifi cant abiotic stresses, which can negatively impact their adaptation, health, productivity, and fi tness. Therefore, it is essential to understand the genetic/genomic basis of responses and adaptation of forest trees to these changed conditions so that measures to mitigate the negative impacts of climate and environment change can be developed by selecting, creating, conserving, and sustainably managing well-adapted, genetically
diverse, and healthy forest resources. Genomics research and applications provide excellent opportunities to address these crucial research needs. I will discuss how structural, functional, and population genomics and bioinformatics research and applications can contribute to decode responses and adaptation of forest trees to climate and environment change, and will present highlights of our own research on these aspects. We have identifi ed and characterized genes expressed differentially in response to elevated CO2, drought, and co-stressed conditions, their metabolic pathways and relationships with physiological traits in black spruce (Picea mariana), and mapped quantitative trait loci for phenotypic and ecophysiologic traits related to growth and adaptation to climate change. We have also identifi ed genes under natural selection in response to air pollution and involved in adaptation of red spruce (Picea rubens).
Genetic diversity of introduced species facing climate change: Eucalyptus robusta in eastern Madagascar. Ramananantoan-dro, T., Andriambelo R., R. (University of Antananarivo, Madagascar; ramananantoandro@gmail.com; andriambelo.radonirina@
yahoo.fr), Daniel, V. (CIRAD, Madagascar; daniel.verhaegen@cirad.fr), Chaix, G. (CIRAD, France; gilles.chaix@cirad.fr).
Eucalyptus is the most widely planted species in Madagascar. Eucalyptus robusta is the most common species (225 000 ha) because it is well adapted and has multipurpose wood uses (energy, pole, and timber). Although this species has been naturalized for more than a century, little is known about the introduced genetic diversity. Previous research leads us to assume that it has a
Eucalyptus is the most widely planted species in Madagascar. Eucalyptus robusta is the most common species (225 000 ha) because it is well adapted and has multipurpose wood uses (energy, pole, and timber). Although this species has been naturalized for more than a century, little is known about the introduced genetic diversity. Previous research leads us to assume that it has a