Keynote Speakers

Elizabeth Kellogg - Donald Danforth Plant Science Center

Inflorescence diversity in the grass family

Looking in wild places: crop relatives and Pasteur’s quadrant

Study of wild grasses falls firmly in the realm of use-inspired basic research (also known as Pasteur’s quadrant). All crops grown by humans have been selected from wild species, and often bear flowers and fruits that are similar to their wild ancestors. Study of wild species thus provide insights and hypotheses that can be tested in crops. This talk will focus on recent work on the wild relatives of sorghum and Miscanthus, including the plants of the tallgrass prairie and the great grasslands of Africa. All these plants bear their flowers in tiny clusters (spikelets); the spikelets themselves are borne in sets of two but only one of the pair makes a seed. The production of sterile flowers is paradoxical because it would seem to be a waste of resources. Most species also have an extension of the floral bract (awn). Investigating how the spikelets and awns function in wild species, we have found that that they have novel roles in growth and seed set (yield). These results then inspired experiments and new results in cultivated sorghum.

Robert Hasterok – University of Silesia

Inferring on karyotype structure and evolution in Brachypodium using cross-species chromosome barcoding

Recent synteny-based paleogenomic analyses have identified polyploidisation and dysploidy as the prime mechanisms that are responsible for the diversity in plant karyotypes and indicated that nested chromosome fusions (NCF) are crucial for shaping the chromosome structure in grasses. Although it provided insight into the putative numbers of protochromosomes in the monocot progenitors and permitted the karyotypes of some present-day grasses, including B. distachyon, to be connected with their hypothetical ancestral karyotypes, these studies did not involve other Brachypodium representatives. We present comparative characteristics of various Brachypodium karyotypes using multicolour FISH with chromosome-specific probes. In order to gain the detailed insight into the structure and evolution of individual chromosomes at the cytomolecular level, we conducted cross-species FISH mapping with series of BAC clones that were derived from chromosomes Bd1-Bd5 of B. distachyon and ordered on its physical map. Using this approach, we demonstrated the presence of NCFs and other chromosome rearrangements, such as Robertsonian rearrangements, translocations and inversions that are responsible for diverse karyotypes structure across the genus; some of them were strictly genome-specific. This provides new data regarding karyotype evolution in several Brachypodium species that have various basic chromosome numbers and different ploidy levels. Good examples are prolonged genome stasis found in B. hybridum after the formation of this annual allotetraploid and chromosome dysploidy with diverse genome organisation observed in some perennials, for example B. pinnatum, B. phoenicoides and B. mexicanum. Such cytomolecular studies, in particular when combined with the findings of the ongoing whole genome sequencing projects and further molecular phylogenetic analyses, should contribute to resolving the still enigmatic phylogenetic relations within the Brachypodium genus.

Robin Buell – Michigan State University

Life with 1000 genomes: Defining the pan-genome in maize

One of the major discoveries in plant genomes in the last ten years has been the extent of genome plasticity due to structural variation in the form of copy number variation and presence/absence variation. This genome plasticity leads to the pan-genome which represents all the genes within a species and includes the core genes present in all accessions and dispensable genes that are restricted to a subset of accessions. Large genome resources for maize have been developed including a reference genome with a robust gene atlas, de novo assemblies of multiple inbred genotypes, and seedling transcriptomes for ~1,000 genotypes. These datasets have permitted robust characterization of the maize pan-genome and characterization of core genes present in all genotypes and dispensable genes which are variable among genotypes.

David Des Marais – Massachusetts Institute of Technology

Physiological and developmental control of resource allocation in grasses

All plants must allocate limited resources to survival, growth, and reproduction. Remarkable variation in relative allocation to these three areas is observed within and between species, and in response to environmental factors. Decisions about allocation represent trade-offs between survivorship risk and subsequent fitness benefits. Here, I present results from a combined developmental, physiological, metabolic and transcriptomic study contrasting four Brachypodium species with varying patterns of resource allocation. Two species, B. distachyon and B. stacei, are short-lived species displaying an annual life history pattern. Two species, B. sylvaticum and B. mexicanum, are long-lived species displaying a perennial life history. We specifically test the hypotheses that these two pairs of species differ in their rates of photosynthetic carbon reduction, in their relative growth rates, in their relative allocation to structural, storage and reproductive tissues, and in their capacity to resorb nitrogen from senescing leaves. Our transcriptomic analysis benefits from a new complete genome sequence of B. mexicanum, which I present here for the first time. We further assess genetic correlations among patterns of allocation, primary metabolism, and growth rate among inbred natural accessions of annual B. distachyon and perennial B. sylvaticum.

Eviatar Nevo – University of Haifa

Evolution Canyon: sympatric speciation through niche adaptation across the tree of life

Co-authors: Eviatar Nevo and Kexin Li

"Evolution Canyons" display sharp divergences in microsites (free breeding populations living in contrasting microclimates or edaphic ecologies), and in adaptive evolution and sympatric speciation across the tree of life. Evolution Canyon I (ECI), in Mount Carmel, explored since 1990, consists of two abutting and microclimatically contrasting slopes. Dry-hot tropical savannoid African slope (AS) is at 250 meters distance from the humid-cool temperate forested European slope (ES). In an area of ~7000 m2, representing a transect of increasing aridity from ES to AS, we identified 2500 species from bacteria to mammals. Adaptive evolution was detected in 16 model organisms growing in tropical AS and temperate ES, using allozymes and DNA markers. Among the species that incipiently speciated ecologically and sympatrically are soil bacteria (Bacillus simplex), wild barley (Hordeum spontaneum), wild emmer wheat (Triticum dicoccoides), fruit fly (Drosophila melanogaster), grain beetle (Oryzaephilus surinamensis) and spiny mouse (Acomys cahirinus). At ECI only Brachypodium stacei grows on temperate ES. By contrast, 62 B.hybridum and only 8 B. stacei individuals were recorded on tropical AS. We have sequenced the genomes of two B. stacei ecotypes, one from each slope, and the transcriptomes (from third generation inbred lines) of 6 B. stacei ecotypes from AS and 11 B. stacei ecotypes from ES to explore if this taxon also speciates sympatrically in ECI.

Anne Roulin - University of Zürich

Transposable element evolution in Brachypodium distachyon: what can we learn from population genomics?

Transposable elements (TEs) are mobile DNA sequences which have the capacity to increase their copy number and/or to move from one location to another in their host genome. Because of their dynamics of transposition, TEs constitute the main component of most eukaryotic genomes and the main cause of genome size increase besides whole genome duplication. With the advent of genome sequencing, the last two decades lead to a deeper understanding of the functional role of TEs and it is now well established that TEs can also produce diverse functional changes, from the disruption of coding sequences to the fine-tuning of gene expression through epigenetic mutations. They may therefore constitute a driving force of evolution. However, little is known about their role as source of genetic variation in natural populations, particularly in plants, where research on TEs largely focused on species of agronomical interest.

Brachypodium distachyon has been developed as a powerful model for research on temperate grass species as it is closely related to major crop cereals and to some of the grasses used for biofuel production. In addition, this species is broadly distributed around the Mediterranean rim, providing access to natural populations from contrasting habitats for which a large collection has been collected and sequenced. I will discuss how my group uses these prime resources to investigate the impact of TEs on genetic diversity and evolution in a natural plant system.

Pamela Soltis – University of Florida

"Polyploidy as integrator across levels of biological organization: from cells to ecosystems"

Polyploidy, or whole-genome duplication (WGD), has long been recognized as an important speciation mechanism in plants. However, WGD has biological effects that extend far beyond the generation of new species. WGD is a key integrator across levels of biological organization, with effects that range from the molecular and subcellular levels to those of the ecosystem and Tree of Life. The immediate impact of WGD is duplication of all nuclear genetic material, but over time, the component subgenomes become fractionated to yield a composite of duplicated and unduplicated loci. This loss of duplicate genes can begin to occur surprisingly quickly, in perhaps only a few generations. Through gene loss and shifts in gene expression, polyploid individuals originating from a single polyploidization event may become genetically and phenotypically unique, together forming a morphologically, physiologically, and/or ecologically polymorphic population, in contrast to classical views of allopolyploids as genetically identical and chromosomally fixed F1 hybrids. This array of genetic and phenotypic novelty may provide new variants that can potentially drive evolution in new directions, with consequences for the tempo of diversification at macroevolutionary scales. Case studies in grasses (Poaceae) and Tragopogon (Compositae) will illustrate patterns of duplicate gene loss and shifts in gene expression in synthetic and natural allopolyploids of recent origin. On longer timescales, signatures of ancient WGDs across angiosperms are often associated with accelerated rates of species diversification, suggesting a causal role of WGD in the diversification of these clades. Although statistical support for co-localized WGD events and diversification rate shifts is low across all angiosperms, many individual WGDs appear to be associated with the origins of novel features and increased diversification, suggesting that features that arise via microevolutionary processes may translate into key innovations on macroevolutionary timescales.

David Lowry – Michigan State University

The genetic and physiological basis of local adaptation along environmental gradients

Local adaptation is a fundamental driver of biodiversity on planet Earth. While recent experiments have begun to dissect the genetic basis of local adaptation, we still have a very poor understanding of how individual genetic loci contribute to local adaptation over large-scale environmental gradients. In this presentation, I will report recent results from an unprecedently large local adaptation study, spanning 17 degrees of latitude, in the major bioenergy crop switchgrass (Panicum virgatum). Much of the functional genetic variation in switchgrass is distributed clinally with latitude as well as between upland and lowland ecotypes. Southern lowland populations are generally much more tolerant to heat, drought, and pathogens, while northern upland populations are more freezing tolerant. To understand genetic basis of local adaptation across central North America, we conducted a multi-site quantitative trait locus (QTL) study with a northern upland X southern lowland four-way, pseudo-testcross F2 tetraploid mapping population. The mapping population was planted at 10 field sites stretching from South Texas to South Dakota We have now identified numerous QTLs contributing to variation in biomass, flowering time, plant height, and resistance to pathogens. The vast majority of these QTLs had strong genotype x environment interactions, with additive effects varying greatly among field sites. We are currently conducting follow-up laboratory experiments to further understand the genetic basis of adaptive divergence in pathogen resistance and freezing tolerance between the ecotypes.

Karen-Beth Scholthof – Texas A & M University

Genetics and genomics of Brachypodium-virus interactions

Plant virus infections can be economically devastating to growers, causing annual crop yield losses of 15% or more. In comparison to the advances in understanding virus-host interactions in dicotyledonous plants, studies of virus-grass interactions have been hindered mainly due to the lack of a tractable monocot model system. The recent intensive and thoughtful development of Brachypodium distachyon (Brachypodium) as a model organism in the post-genome era of plant biology, has allowed us to investigate the complex molecular and genetic interactions that occur during virus infections of grasses. Using Panicum mosaic virus (PMV) and its satellites, we have identified mechanisms by which the Brachypodium host machinery subverts the replicative ability of virus infections in grasses. We have characterized genome-wide changes in Brachypodium transcriptome and defense signaling networks, splicing landscapes, as well as virulence determinants critical for PMV infection in grasses. In addition, comparative analyses of Brachypodium and Setaria viridis (a C4 grass) immune responses to eight monocot-infecting viruses made it possible to define conserved and unique defense mechanisms. Our studies underscore the utility of Brachypodium to advance fundamental studies of economically important viruses of grasses. I will discuss key outcomes, the research potential for the system in the coming years, and particular gaps in our understanding of virus-host resistance mechanisms.

Klaus Mayer – Helmholtz Research Center for environmental health

From genome to genomes. Charting the genome landscape(s) of western civilisation

Cereals are the most important crops worldwide. Until recently access to the di-/tetra- and hexaploid cereal genomes was hampered by the enormous size, high repeat content and polyploidy. 17 years after the completion of the human genome these limitations have been circumvented by making use of different complementary approaches. After a decade of technology development and implementation and the decoding of large – in part - polyploid cereal genomes now allow to address genome questions, biological questions and to start to address systems biology and comparative genomic questions. Using the emerging genome sequences as an information backbone, in depth transcriptional profiling of the developing grain in context of a hexaploid genome is undertaken and used to gain insights into the transcriptional coordination among three homeologous subgenomes. Deep profiling of the global transcriptome of single endosperm cell types (starchy endosperm, aleurone and transfer cells, respectively) was performed to test for the effects of polyploidy on gene expression of homeologous, duplicated genes in bread wheat. Expressed genes were subject to network-based co-expression analysis revealing significant cell-type and time point specific gene expression. The presentation will aim to review important steps in the unlocking of large and complex cereal genomes, highlight progress in cereal genome sequencing and a systems biology use case in the multidimensional transcriptional analysis of the developing grain. Also a “sneak preview” of forthcoming data and the analytical challenges and future in cereal genomics will be addressed.

John Vogel - Joint Genome Institution

"More, more, more, the genus Brachypodium as a sequence-enabled functional genomics model"

The development and acceptance of Brachypodium distachyon as a model system was propelled by whole genome sequencing. Since the sequencing of the initial reference genome in 2008 sequencing has continued to push the entire genus into a role as a model for both functional and evolutionary genomics. Functional studies are being enabled by: the sequencing and assembly of over 100 natural accessions, the creation of a pan-genome that showed nearly half of the high-confidence genes are missing from some lines, the creation of reference quality assemblies for three commonly used lines, surveys of the epigenetic landscape, and mutant sequencing that has identified over 1 million mutations. Evolutionary and functional studies have been enabled by the sequencing of three additional species: B. stacei, B. hybridum and B. sylvaticum. The first two together with B. distachyon serve as a tractable model to study polyploid genome evolution and regulation and the latter serves as a model for perenniality. Additional species are being sequenced now that will further serve to understand the evolution of the genus and the molecular basis of perenniality. A brief overview of how various sequencing projects enabled the development of powerful resources with an emphasis on the most recent projects will be presented.