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IUFRO Genomics and forest tree genetics

Keynote speaker abstracts & Biographies

OPENING KEYNOTE LECTURE

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Outi Savolainen

Plant population genetics
University of Oulu

Finland

Genomic consequences of phenotypic selection (in Pinus sylvestris and Arabidopsis lyrata)

Outi Savolainen, Jaakko Tyrmi, Tiina Mattila, Sonja Kujala and Katri Kärkkäinen

Abstract: Conifers are known to experience strong selection in different life stages. Extensive provenance trials and other experiments have demonstrated adaptation to local climatic conditions, as seen in patterns of phenotypic variation correlated with climatic conditions. On the other hand, after selfing, there is high mortality at especially early life stages due to the high numbers of lethal equivalents. Current theories make predictions on the expected patterns of variation at loci related to local adaptation. Further, the effects of selection due deleterious recessives on genomic patterns of variation have also been predicted. Initial genetic data from exome capture in Scots pine and whole genome sequences in the outcrossing perennial Arabidopsis lyrata can be contrasted against some of these predictions.

Biography: Outi Savolainen received her Ph.D. at the University of California in Davis. She is now professor of genetics at the University of Oulu, Finland. Her research interests comprise evolution and genetics of local climatic adaptation in trees, and the consequences for adaptation to climate change. The group also studies similar issues in the perennial Arabidopsis lyrata.  The studies  on Arabiopsis lyrata have also lead to examining the genetics and consequences of incipient reproductive isolation between different populations.

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SESSION 1 : GENETIC ARCHITECTURE OF LOCAL ADAPTATION AND SPECIES BOUNDARIES

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Nicolas Bierne

Integrative genomics
ISEM, CNRS

France

Crossing the species barrier: is local interspecies introgression adaptive?

Abstract: Although introgression -the flow of genes between partially isolated genetic backgrounds- is under study for decades, the qualitative and quantitative importance of introgression in evolution is still discussed. The debate has recently been revivified with genomics data that revealed the ubiquity of introgression in many systems including our own species, and many trees. Many open questions persist about introgression: How long species barriers remain permeable? Why are some regions of the genome less resistant to introgression than others? Is adaptive introgression really so widespread? Could it simply be a spectacular manifestation of the general process of adaptation which nonetheless mainly proceeds by intra-specific evolution? Could the pattern of local introgression be attributed to other phenomena than trans-specific positive selection? I will try to offer some elements of answer to these questions in the light of theoretical arguments from the Fisher's geometric model and of experimental works in my study systems, marine invertebrates, which are not trees but share many similarities with trees.

Biography: I am CNRS researcher at the Institute of Evolutionary Sciences of Montpellier. I am working in a small marine lab in Sète, near the Thau lagoon. I am using molecular markers and genomic sequences, together with experiments, field studies and theory, to study adaptation and speciation in marine species. Marine invertebrates often have high fecundities, important dispersal potential via a passive planktonic phase, and large population sizes which impact their evolution (eg mutation and migration load, adaptive rates, speciation clock etc…) and make them suitable study systems.

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AlexBuerkle

Department of Botany
University of Wyoming

United States

Inconsistent reproductive isolation

Abstract: Speciation has commonly been studied as if variable genetics, phenotypes and environments of species were unlikely to affect reproductive isolation between species. Perhaps unsurprisingly, for taxa that are incompletely isolated, this simplification is probably commonly inappropriate and has the potential to mislead us about the nature of barriers to reproduction between species. I will discuss several examples of diversity of reproductive isolation in plants and animals, and the implications these have for thinking about species and boundaries between them.

Biography: Alex Buerkle received his PhD from Indiana University, and is currently a Professor at University of Wyoming. He develops statistical genetic methods and simulation models to analyze population genomics and understand how evolutionary processes shape genomic variation.  Most of his work has been in the areas of the genetics associated with hybridization and speciation.

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SESSION 2 : LINKING PHENOTYPE, GENOTYPE & ENVIRONMENT

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Angela Hancock

Molecular basis of adaptative evolution
Max F. Perutz Laboratories

Austria

Understanding local adaptation using Arabidopsis thaliana as a model

Abstract: Arabidopsis thaliana is a superb model for studying local adaptation because it is geographically widespread and its range encompasses extensive variation in climate and other environmental factors. I will discuss work we are doing to identify loci and pathways involved in local adaptation across the A. thaliana range as well as efforts to comprehensively characterize population history and adaptation in specific cases. Depending on the details of population history, different models of phenotypic variation and adaptation may be most relevant. Moreover, optimal study design for mapping traits and elucidating adaptive responses depends on population history due to its effects on overall levels of genetic and phenotypic variation, genetic and allelic heterogeneity and the extent of linkage disequilibrium. I will discuss the relevance of these factors to different A. thaliana cases and the more general implications.

Biography: Angela Hancock received her PhD at the University of Chicago in Human Genetics and conducted a postdoc there in Ecology and Evolution. She is now an Independent Group Leader at the Max Planck Institute in Cologne. The Hancock Lab focuses on understanding the molecular basis of adaptation using a combination of approaches including population genetic analysis and modeling, GWAS, QTL mapping, molecular genetics and fieldwork in the Cape Verde and Canary Islands.

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MatthewRockman

Department of Biology
New York University

United States

Maternal and zygotic genetic effects in life-history evolution

Abstract: Early stages of organismal development are subject to unique selective pressures that differ from those experienced by mature individuals. Early stages are also disproportionately dependent on maternally provisioned material. I will describe an experimental genetic model for the interplay of maternal and zygotic genetic effects on phenotypic variation and evolution. Females in our study species make either many small offspring or few large offspring, and the offspring develop through different morphologies and dispersal modes to yield indistinguishable adults. These developmental differences are highly heritable via both maternal and zygotic effects, with implications for how selection shapes the distribution of phenotypes in populations.

Biography: Matt Rockman is associate professor in the Department of Biology and Center for Genomics and Systems Biology at New York University. His research focus is the relationship between the mechanisms that shape phenotypes within individuals (development) and those that shape phenotype distributions in populations (evolution). He performed his PhD work with Greg Wray at Duke University and was a postdoctoral researcher with Leonid Kruglyak at Princeton.

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SESSION 3 : ABIOTIC STRESS RESPONSES & BIOTIC INTERACTIONS

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Rishikesh P. Bhalerao

Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre

Sweden

Molecular basis of adaptation to seasonal changes in boreal trees

Abstract: Trees growing in temperate and boreal forest need to modulate their patterns of growth in order to survive the extreme fluctuations in temperature that accompany the change of seasons. Therefore these trees undergo growth cessation and establish dormancy prior to the advent of winter when temperatures can go down to -50°C. The cessation of growth and establishment of dormancy is controlled by photoperiod. Whereas release of dormancy and subsequent bud flush in the spring are temperature regulated. In contrast to photoperiodic control of growth cessation, the molecular basis of bud dormancy establishment, its release and bud flush is poorly understood. We have identified evolutionarily conserved components of Polycomb and plant hormone ABA as key components of SD mediated bud dormancy establishment. I will discuss the how polycomb and ABA mediate in photoperiodic control of bud dormancy establishment. I will describe our recent results that provide insight into the genetic framework underlying temperature controlled break of dormancy and subsequent bud flush.

Biography: Rishikesh Bhalerao received his Ph. D from Umeå University. After a post-doc at the Max-Planck Institute in Köln he returned to Umeå to The Swedish University of Agricultural Sciences (SLU) where he is currently a professor in plant cell and molecular biology. The main focus of Bhalerao lab is understanding how plants adapt their growth patterns to seasonal changes using hybrid aspen as a model.

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Kathleen Donohue

Department of Biology
Duke University

United States

Pleiotropy in the environmental regulation of germination and flowering

Abstract: Pleiotropy occurs when one gene regulates more than one trait, and it can be a strong constraint on the adaptive evolution of trait combinations.  In many organisms, several major developmental transitions between life stages are regulated by seasonal environmental factors, and the appropriate coordination of developmental transitions across the lifecycle is necessary to express adaptive life-history schedules.  Many life stages may be sensitive to the same environmental factors, but they must respond to them differently.  How do multiple life stages use the same environmental inputs to regulate their independent developmental transitions in a manner that results in adaptive life-history expression?  We examined pleiotropy between the environmental regulation of two important life-stage transitions in plants:  seed germination and the transition to reproduction. We tested whether genes known to regulate flowering responses to environmental cues also regulate seed germination in Arabidopsis thaliana. We found extensive pleiotropy between flowering and germination regulation.  First, the major flowering gene Flowering Locus C (FLC) contributes to seed germination, such that increased FLC activity is associated with increased germination.  Regarding the vernalization pathway, both promoters and repressors of FLC expression also contribute to germination, but in ways that are not predicted based on their function in the flowering pathway.  Likewise, genes in the autonomous pathway  and the photoperiod pathway contribute to germination, but in ways that are not always predictable from their function in the flowering pathway.  In sum,  genes in the vernalization flowering pathway, the autonomous flowering pathway, and the photoperiod flowering pathway all contribute to seed germination.  The combined results suggest that, although the same environmental-sensing pathways are used to regulate these two developmental transitions, the function of genes in those pathways is not always concordant across germination and flowering.  Despite pleiotropy, these two developmental transitions appear to be able to be regulated independently to a great degree.

Biography: Kathleen Donohue received her PhD from the University of Chicago, has had faculty appointments at the University of Kentucky, Harvard University, and is currently Professor at Duke University.  She studies the genetic basis of adaptation in natural plant populations, with a focus on the evolution, genetic basis and adaptive significance of phenotypic plasticity and environmental cuing, parental environmental effects, and niche construction.  She was elected as a Fellow of the American Association for the Advancement of Science, received a John Simon Guggenheim Fellowship, and is President Elect of the American Society of Naturalists.

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Joy Bergelson

Ecology & Evolution
University of Chicago

United States

Diffuse interactions shape the dynamics of a plant pathogen interaction

Abstract: Theories of host pathogen interactions explain the maintenance of resistance polymorphisms in terms of frequency dependent selection acting between an obligately associated host and pathogen. However, many host-pathogen interactions are not obligate: pathogens often infect multiple host species and hosts harbor complex microbial communities. In this talk, I will tease apart the ecological interactions underlying an ancient balanced polymorphism that we have identified in Arabidopsis thaliana in nature. We find that this ancient balanced polymorphism at the R gene, Rps5, persists amidst a web of complex interactions involving multiple host species, multiple bacterial species and multiple effectors segregating among strains of single pathogen species. These results challenge us to understand how selection acts on plant resistance, and how pathogens adapt to their numerous secondary hosts. I will assess how P. syringae adapts to one of its secondary hosts, A. thaliana, through an analysis of whole genome sequences and associated experiments.

Biography: Joy Bergelson is the Louis Block Professor at The University of Chicago, where she serves as the Chair of the Department of Ecology and Evolution. She received her PhD from The University of Washington and an MPhil from the University of York as a Marshall Fellow, prior to positions at the University of Oxford, Washington University and The University of Chicago. She studies the interaction between Arabidopsis thaliana and its natural enemies, and is particularly interested in how ecological and evolutionary dynamics shape each other. This involves a combination of field, computational, genetic and chemical/physiological investigations. She is a Fellow of the American Association for the Advancement of Science, a Cheung Kong Scholar Honorary Professor of Nanjing University, a Packard Fellow and serves on the International Advisory Boards of several institutions and programs in plant biology.

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SESSION 4 : PHYLOGENETICS AND GENOMIC EVOLUTION

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Myriam Heuertz

Genetics and Ecology of Populations
INRA

France

Hybridization and the evolution of tropical tree species complexes

Abstract: Tropical rainforest tree genera often comprise high numbers of species, and closely related species commonly occur in sympatry. There is little information on the proximal genetic mechanisms to explain these patterns of species coexistence. Theoretical models predict that inter-specific hybridization could represent a key factor in the maintenance of highly diverse communities, notably by retarding the (local) extinction of rare species and by allowing the sharing of beneficial genetic variants across species borders. Hybridization could be an especially relevant evolutionary process under climate change, where changes in relative species abundance, distribution ranges and/or phenology can affect interspecific gene flow, and where the sharing of adaptive genetic variation could allow a faster response to environmental change.

Biography: Myriam Heuertz received her PhD from the Université Libre de Bruxelles, Belgium. After appointments in Sweden, Spain and Switzerland, she is currently a research scientist at INRA in Bordeaux, France. She is interested in population and ecological genetics of temperate and tropical trees and her recent work focusses on disentangling the evolution of tropical tree species complexes. 

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Paul Manos

Department of Biology
Duke University

United States

Mighty oaks from little acorns grow: phylogenomic data add new branches to the Quercus tree of life

Abstract: With over 430 species, the oak genus Quercus plays a major ecological role in a variety of ecosystems throughout the northern hemisphere. While oak species diversity and ecological function is well described, the impact of hybridization on evolution above the species level is not as clear. A rapidly developing molecular toolkit has advanced the systematics and biogeography of Quercus, increasing our understanding of the biology and relationships of species. A species-level phylogeny using restriction-site associated DNA sequencing (RADseq) confirms a basic geographic split between Nearctic and Palearctic oak clades, providing unprecedented levels of resolution. The RAD data strongly support eight lineages within the genus. In the Americas, combining phylogeny and fossil and modern distributions with other clade-specific data supports diversification scenarios, including two intercontinental disjunctions. The two largest clades in the genus, Quercus (white oaks) and Lobatae (red oaks), share strikingly similar biogeographic histories. The pattern suggests originations and deeper evolutionary splits at higher latitudes, followed by more recent parallel dispersals and diversifications south to Mexico and Central America. Comparing phylogenies to the results of data analyses using subsamples along multiple parameter axes uncovers evidence for hybridization between a few species from distinct clades. Localized hybridization based on morphology and geographic proximity explains some of these cases, but these analyses also point to more cryptic scenarios involving ancient introgressive hybridization among geographically disjunct and distantly related species. These results demonstrate that a combination of divergent and reticulate processes have promoted the diversification and spread of these ecologically and economically important tree species.

Biography: Paul Manos is the Jack H. Neely Professor and associate chair of Biology at Duke University. He studies the molecular phylogenetics and biogeography of flowering plants, with focus on forest trees, in particular the oak and walnut families and their relatives. He received his master's degree from Rutgers University for genetic work on the red oaks of the eastern U.S. and later investigated the molecular systematics of Quercus and Fagaceae for his doctorate at Cornell University.

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SESSION 5 : USING GENOMICS TO MEET THE CONSERVATION AND BREEDING CHALLENGES

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ChristianMaltecca

Department of Animal Science
NC State University

United States

Causes and consequences of inbreeding: a livestock genomic perspective

Abstract: The role of genomic information to constrain inbreeding and monitoring losses of genetic variation has been widely demonstrated. With the correct use of genomic, genetic diversity and inbreeding accumulation can be effectively managed. Management of diversity rests on three pillars. Understanding the basis and consequences of genetic diversity. Managing the population by controlling its effective size. Optimize genetic variability deployed through mating plans. Inbreeding management often rely on the implicit assumption that individuals with the same inbreeding share the same genomic load. Marker information allows instead for regions-specific stretches of homozygosity causing inbreeding depression to be identified. Yet, these regions are expected to be at a low frequency so that traditional association methods based on estimating dominance effects and geared toward common variants lack statistical power. Methods that exploit the fact that longs runs of homozygosity (ROH) are enriched with deleterious variants can have greater power in identifying haplotypes linked to inbreeding depression. Here we present results from multiple livestock species as well as simulated data that show the power of alternative genomic similarity metrics to curtail inbreeding accumulation and identify potential deleterious haplotypes.

Biography: Christian Maltecca is an Associate Professor in Quantitative Genetics and Breeding at the animal science department at North Carolina State University (NCSU). He is also a faculty of the Genetics program at the same institution. He received is bachelor degree at the Universitá degli Studi di Milano, a Ph.D. in Animal Science from the same institution and a Ph.D. in Dairy Science from the University of Wisconsin Madison. His research focuses on the genetic improvement of economically relevant traits in livestock. His main interests are in the area breeding, genomic prediction, and QTL mapping of functional traits in dairy and swine.

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Aaron B.A. Shafer

Department of Evolutionary Biology
Uppsala University

Sweden

Conservation [and] Genomics of Free-Ranging Populations

Abstract: Governments acknowledge the importance in stemming the loss of biodiversity, and conserving genetic diversity is a strategic goal of the UN’s Convention on Biological Diversity. Genomic approaches have been touted as a promising tool to support such aims, with scaling up to genome-wide data thought to improve upon the traditional conservation genetic inferences and provide qualitatively novel insights for management decisions. However, the generation of genomic data, subsequent analyses and interpretations remain challenging, nuanced, and often far-removed from on-the-ground conservation issues. Here I highlight some of the major hurdles limiting the application of genomic data to conservation biology and offer solutions and outlook for the future.

Biography: Dr. Shafer is a member of an IUCN species survival commission sub committee and associate editor at the journal Conservation Genetics. His research is focused on using genetic and genomic data to better manage and conserve wild populations and he has been involved in a broader discussion of the role of genomic data in conservation biology. Currently based out of Uppsala University, Dr. Shafer will be starting up his own research group at Trent University, Canada.

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SESSION 6 : RESOURCES, TOOLS AND METHODS

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Stephen P. DiFazio

Department of Biology
West Virginia University

United States

Genome Dynamics and Sex Determination in the Salicaceae

Abstract: The Salicaceae family, including Populus and Salix, is a powerful model system for studying the influence of genome structure on the evolution of adaptive traits. A comparison of synonymous nucleotide substition rates between Populus and Salix demonstrates that the Salix lineage has accumulated more polymorphisms. This elevated evolutionary rate is recapitulated in higher rates of genome fractionation in Salix following the shared Salicoid genome duplication. The two genera have numerous contrasting phenotypic characterisitics, including growth form, pollination mode, and generation time. Furthermore, although both species are primarily dioecious, they appear to have different sex determination loci. Sex determination in Populus is controlled primarily by loci on chromosome 19 across all species that have been studied thus far. In contrast, it is now clear that sex determination occurs on Chromosome 15 in Salix purpurea, based on mapping in an F2 intraspecific cross as well as in an association population of unrelated individuals,. This is quite surprising, especially given the high collinearity of the vast majority of the Populus and Salix genomes. Furthermore, examination of the genotypes of sex determination loci in male and female trees suggests that Populus trichocarpa has a predominantly XY sex determination system, while Salix purpurea has a ZW system. A comparative analysis of the sex determination regions of the two genera reveals many shared characteristics, including structural complexity, high repeat density, and suppressed recombination. Ongoing questions include whether there are shared mechanisms of sex determination in the two species, the extent of sex dimorphism, the role of pollinator attraction and defense in sex chromosome evolution, and the presence of sexually antagonistic genes in the sex determination regions.

Biography: Steve DiFazio received his MS in Forest Ecology and a PhD in Forest Science from Oregon State University. His thesis research focused on gene flow and reproductive biology of conifers and cottonwoods. He then worked as a staff scientist at Oak Ridge National Laboratory, focusing on a variety of functional and structural genomics projects, most notably the sequencing of the Populus genome. He is currently a Professor of Biology at West Virginia University, where he continues to study plant genomics with a special focus on his model organisms of choice in the Salicaceae family. He also serves as the Director of the West Virginia University Genomics Core Facility, and acts as a scientific advisor on a variety of public and private research efforts.

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John MacKay

Department of Plant Sciences
Genetics and molecular biology of forest trees

United Kingdom

Gene Copy Number Variations in spruce (Picea spp.): detection and potential roles in evolution

Abstract: Gene copy number variations (CNVs) have been linked to many heritable conditions in human and to evolution in model and crop plants but little is known of their frequency and potential contributions to evolution in forest trees.  This knowledge gap is common to most wild species as established CNV detection approaches usually use high quality reference genome assemblies. Here, we developed two robust approaches to overcome this technical barrier and investigate CNVs in spruce trees. We developed comparative genomic hybridization on arrays (aCGH) and implemented an approach to reanalyse data obtained from Illumina SNP genotyping arrays. Each of the methods targeted independent sets of 14,000 genes and were used to analyze full-sib families, with controls for false discovery. We detected both common or inherited CNVs and rare CNVs classified as de novo mutations. Whole genome hybridizations (aCGH) were obtained for 80 individuals of white, black and interior spruce, the latter representing a natural hybrid, and identified hundreds of CNVs in each pedigree. The entire set represented 3,612 distinct CNV genes which were enriched in stress and defense responses functions. The genes were distributed throughout the genome based on their position on a spruce genetic map, suggesting numerous and widespread structural variation events. The hybrid spruce had much fewer CNVs which could mean that the mixture of different genomes within a single species decreases CNVs, potentially reducing the adaptive variability and evolvability of hybrids. In an independent study, we reanalyzed genotyping array data in 55 full-sib families and over 3500 individuals. Nearly 150 CNVs meeting high stringency and repeatability criteria were studied in detail. We found that this approach was particularly effective at detecting gene copy number losses. Many de novo CNVs were detected and these allowed us to estimate mutation rates, which we found to be highly variable between genes and correlated with expression. We also observed that around half of the inherited CNVs were associated with patterns of transmission distortion.
Taken together, our results indicate that CNVs are over represented in gene families of particular relevance for adaptation and are associated with or influenced by evolutionary processes including hybridization, selection and high mutation rates. Future research is needed to directly test whether CNVs are linked to phenotypic variation which may shed new light into the molecular basis of quantitative traits.

Biography: John MacKay obtained a Ph.D. in genetics at North Carolina State University with Ron Sederoff, worked as a research scientist at the Institute of Paper Science and Technology (Atlanta, USA) and continued his academic career at Laval University (Quebec, Canada) and recently at the University of Oxford where he is the Wood Professor of Forest Science. His research interests include forest genetics and genomics and span both basic and applied questions such as wood formation, tree-insect interactions, quantitative genetics and evolution.

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CLOSING KEYNOTE LECTURE

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Antoine Kremer

Population and quantitative genetics

INRA

France

Concluding remarks: "Assisted migration into the wild"

Abstract: Concluding remarks: "Assisted migration into the wild"

Biography: Antoine Kremer is senior scientist at INRA Bordeaux (France).  He received his phD in quantitative genetics and habilitation degree in population genetics at the University of Paris (Orsay). His research deals with the evolution of genetic diversity and differentiation between natural tree populations, at various hierarchical levels where diversity is expressed (from genes to phenotypic traits). Antoine Kremer initiated Europe-wide forestry research as early as the 1980s based on population genetics and evolutionary biology. His research has focused on the evolution of oaks across Europe, investigated by complementary approaches including paleobotany, population genetics and computer simulations. His current interest addresses microevolution in the context of environmental changes linking genetics, genomics and ecology.

Gene Copy Number Variations in spruce (Picea spp.): detection and potential roles in evolution.