Funded Projects
Genomics of Sunflower (Genome Canada)
Evolutionary Genomics of Plant Adaptation and Speciation (NSERC)
GEPR: Comparative Genomics of Phenotypic Variation in the Compositae (NSF)
Long-term natural selection and adaptive introgression in weed sunflowers (NSF)
Phylogeography and Genomics of Noug, an indigenous oil-seed crop from Ethiopia (NSF, CIDA)
Genomics of Sunflower (Genome Canada)
This project (http://www.sunflowergenome.org) will sequence the genome of the cultivated sunflower, Helianthus annuus, the first genome sequence for the Compositae (Asteraceae), the largest family of flowering plants, whose ~24,000 named species comprise roughly 10% of all flowering plants. Many of these species are economically important crops, medicinal plants or weeds, and this diversity is only beginning to be tapped by modern growers and breeders. The most economically important of these is the sunflower, which is also the most widely studied and genetically well-developed representative of the family. In addition to its importance as an oil seed crop, the sunflower has tremendous potential for cellulosic biomass production, both as a primary source and as a residue of oilseed production.
Because sunflower has a large genome (3,500 Mbp) with abundant repetitive sequences (mainly LTR transposons), a shotgun sequencing approach is unlikely to reliably link, order, and orient sequenced contigs. Therefore, we are proposing a hybrid approach, which incorporates both whole genome shotgun (WGS) sequencing to ~40x with the IlIumina GA platform and sequencing of BAC pools to ~20x with Roche’s GS FLX platform. This strategy will provide sequence equivalent in accuracy to high coverage Sanger sequence, but at a small fraction of the cost. Lastly, we will fill gaps in the assembly by targeted BAC sequencing in a final, finishing stage.
The availability of a full genome sequence will have immediate benefits, allowing several high value projects to move forward at a rapid pace. First, an association-mapping project will characterize genetic and morphological variation among domesticated sunflower lines and the relationship between genetic differences and important crop traits.
A second major focus will be the development of sunflower as a new biofuel source with unique advantages as an annual woody plant. Biofuel development will exploit wood-producing ecotypes of two extremely drought tolerant, wood-forming, desert-dwelling wild species: silverleaf sunflower (H. argophyllus) and Algodones dune sunflower (H. tephrodes). To develop sunflowers as a viable biofuel source, we will first need a better understanding of the genetic basis of wood production in these species. Comparisons of EST sequences from woody and non-woody lines will give us candidate genes to examine. A complementary approach will involve QTL mapping for woody traits and chemical phenotypes in BC1’s and RILs derived from crosses between woody and non-wood lines. QTL-NILs for wood formation will be advanced from these populations and will provide a basis for the development of high-biomass woody cultivars.
Co-PI's: John Burke (University of Georgia), Nolan Kane (UBC), Steve Knapp (University of Georgia), Emily Marden (UBC), Patrick Vincourt (INRA)
Evolutionary Genomics of Plant Adaptation and Speciation (NSERC)
What happens to the boundaries between species following cross-species mating or hybridization? Can hybridization sometimes contribute to the formation of new adaptations or to increase the invasiveness of weedy species? More generally, what makes a plant invasive? These are the basic biological questions we will tackle. The project will focus on the plant family Compositae, which is one of the most important families of flowering plants and includes many important crops and weeds.
We will analyze the effects of hybridization on barriers that prevent the movement of genes between wild sunflower species. Evolutionary biologists once believed that for species to form, barriers to gene flow must be absolute. However, it now appears that some parts of the genome may be protected from interspecific gene flow, while others are not. A fundamental question to be addressed by this proposal concerns the degree of protection provided by individual “speciation” genes.
Hybridization between species is also sometimes viewed as a stimulus for rapid evolutionary change and possibly the evolution of invasiveness. We will identify hybrid combinations of traits and genes that have facilitated range expansion and the evolution of invasiveness of the common sunflower.
Finally, building on a database of genes for the Compositae, we will compare the genomes of invasive and non-invasive populations of Russian knapweed, yellow star-thistle, common sunflower, and blueweed. We will search these genomes for signs of recent strong selection, a “footprint” of the evolution of invasiveness. Genetic changes associated with invasiveness will be characterized and their effects on fitness will be assessed in the field.
http://www3.botany.ubc.ca/rieseberglab/WeedGen/
GEPR: Comparative Genomics of Phenotypic Variation in the Compositae (NSF)
Building on the recent advances of the Compositae Genome Project (CGP; http://compgenomics.ucdavis.edu/), this project will develop extensive resources for functional, comparative, and evolutionary genomics in the Compositae. This work, which will integrate genetic, phenotypic, and molecular evolutionary information, will address several major questions in crop and weed science as well as evolutionary biology. The project addresses multiple recommendations of the recent National Research Council report on the National Plant Genome Initiative including understanding processes of domestication and performance in various environments, developing models for accessing germplasm diversity for crop improvement, and providing multidisciplinary computational and wet lab training.
The specific aims of this project are to:
(i) sequence the gene space of the three most important crops in the Compositae (lettuce, sunflower, and safflower) and Gerbera, a model species for studying plant development, that represent the four major subfamilies within the Compositae;
(ii) greatly increase the taxonomic coverage of the CGP’s EST database using high throughput sequencing of cDNAs from 25 additional taxa, including six crop species, three weed species, the wild progenitors of ten crops and weeds, representatives of five taxonomically important subfamilies of the Compositae, and an outgroup (the Calyceraceae);
(iii) establish the prevalence of copy number variation relative to nucleotide variation and phenotypic diversity using oligonucleotide arrays;
(iv) study the effect of whole genome duplications on diversification rates;
(v) identify genotypic changes driven by parallel selective pressures across crop and weed lineages;
(vi) construct ultra-high density, transcript-based maps using single-feature polymorphisms (SFPs) of lettuce, sunflower and chicory, thereby facilitating detailed comparative analyses of genome evolution;
(vii) develop permanent mapping populations (RILs) of key Compositae species to facilitate generation of similar transcript-based maps in other taxa; and
(viii) use genetic map-based approaches and candidate gene analyses to dissect the genetic changes underlying multiple phenotypic transitions in the Compositae associated with domestication and the evolution of weediness.
CoPIs: Richard Michelmore, University of California (Davis);Rick Kesseli, University of Massachusetts (Boston); John Burke, University of Georgia (Athens); Kent Bradford, University of California (Davis); David Still, California State Polytechnic University (Pomona); Steve Knapp, University of Georgia (Athens); Zhao Lai, Indiana University (Bloomington).
Long-term natural selection and adaptive introgression in weed sunflowers (NSF)
Hybridization is a widespread phenomenon, yet its role in evolution is still under debate. Is it a maladaptive homogenizing force or can it contribute to adaptation and evolutionary diversification? There are many putative examples of adaptive introgression in plants and animals, in which beneficial traits appear to have been transferred from one species into another. However, these cases are not amenable to direct study, because the introgression and putative adaptation have occurred in the past. A novel approach is proposed that compares long-term evolutionary change in experimental hybrid and control (non-hybrid) lines in the field. These lines are modeled on (i.e., derived by crossing the parents of) a well-studied plant hybrid lineage, thus providing a rich context for interpretation.
The proposed project asks: (1) Can introgression increase rates of adaptation?, (2) Can introgression increase rates of phenotypic evolution?, and (3) Are evolutionary trajectories in hybrid populations predictable? These questions will be addressed by tracking fitness, 20 traits, and 20 molecular markers (linked to quantitative trait loci, QTL) in the experimental hybrid and control populations over 5-10 generations. Evolutionary change will be distinguished from phenotypic plasticity by comparing lines in replicated common gardens. Short-term predictability of change in traits will be examined by assessing whether the experimental hybrids converge phenotypically and gentoypically on the natural hybrid upon which they are modeled.
PI: Ken Whitney (Rice University)
Phylogeography and Genomics of Noug, an indigenous oil-seed crop from Ethiopia (NSF, CIDA)
Indigenous crops have the potential to contribute to the food security and income of subsistence farmers because they typically require few agricultural inputs and have significant nutritional value. An example is the indigenous oil-seed crop Noug (Guizotia abyssinica, family: Compositae), which is Ethiopia’s largest oil seed crop and an important agricultural export (as bird feed). Noug has been neglected by the scientific community until very recently and remains semi-domesticated; the crop is self-incompatible, highly-branched, and flowering heads and seeds are less than one-fifth the size of sunflower, its’ most closely related major crop. Here, we propose to develop genomic tools and resources for Noug, with the goal of accelerating ongoing breeding efforts in Ethiopia. PDF
Primary Collaborators: Dr. J. Engels (Bioversity International), E. Bekele (Addis Ababa University), Hannes Dempewolf (UBC)