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Nolan Kane
Post-Doctoral Fellow
nckane(at)gmail.com
Sequencing the sunflower genome
The Asteraceae (Compositae), with nearly 25,000 named species, is the largest plant family, with numerous important crops (sunflower, safflower, lettuce, artichoke, endive, chicory and many more), noxious weeds (e.g. knapweeds, thistles, dandelions) and ecologically important wild species (silverswords, Artemisia, Senecio), yet has no sequenced genome due to the prohibitively large genome sizes of most Asteraceae species. This lack of genomic information has limited our ability to understand the roles of natural selection, artificial selection and gene flow in shaping both wild and domesticated members of the Asteraceae, and to better characterize the enzymes responsible for the diverse secondary metabolites in medicinally important species.
In collaboration with groups at University of Georgia (http://sunflower.uga.edu/ http://www.theburkelab.org/ ) and INRA (http://cnrgv.toulouse.inra.fr/en/projects/genomics_of_sunflower) in France, I am working on a Genome Canada funded project to sequence the full genome of the common sunflower Helianthus annuus. The sunflower genome is large and complex: at 3.5 Gb it is slightly larger than the human genome. Once completed, the sequenced sunflower genome will dramatically enhance the utility of the EST libraries and other genetic data currently available for sunflower and dozens of economically important relatives because there is no closely-related plant family from which a genome has been sequenced.
Evolution of wood production in Helianthus
Sunflower is currently valued as an economic crop primarily for its seeds, which are used as whole kernels and also are important for high-quality cooking oil. However, H. argophyllus and some other sunflowers also contain woody stems, which could serve as an important secondary product. Together with collaborators at UGA, we are developing crosses between H. annuus and these closely related woody annual and perennial species, in order to improve our understanding of the genes underlying this trait and to begin the process of introducing genes for wood production into domesticated sunflower lineages. By converting the stem tissue of domesticated sunflowers from porous “pith” to solid wood that may be valuable for paper production or energy production, and could be burned directly or fermented into ethanol or other biofuels.
Genetics of sunflower domestication
The Common Sunflower is the most well-documented example of a crop domesticated by Native Americans in the southeastern US, providing evidence for a sixth independent center of domestication. I have sequenced transcriptomes from across the ranges of wild Helianthus annuus as well as numerous accessions of domesticated H. annuus, to identify regions of the genome under selection during domestication. This genetic work is complemented by association mapping in wild and domesticated sunflowers, allowing us to examine the phenotypes associated with some of these genes.
Weedy and invasive species cause billions of dollars per year in damage and control costs. Yet we know little about the genetic origins of most weedy populations. In a study of weedy and invasive varieties of H. annuus inhabiting cultivated corn fields, I found that that weedy varieties have evolved multiple times from nearby wild populations. Despite these multiple, independent origins, a handful of gene expression changes were shared between many or all of these weedy genotypes, representing interesting candidate genes potentially underlying adaptation of these weeds to agricultural environments. Following up on these findings, I am currently looking at sequence and expression variation associated with high performance in conditions mimicking agricultural and natural habitats, and examining the role of hybridization between wild and domesticated sunflowers in the evolution of weedy and invasive sunflower populations.
Role of selection and gene flow in population homogenization and differentiation
Many plant and animal taxa experience occasional hybridization, with the potential for gene flow across even widely divergent groups. Simultaneously, some widely-distributed species experience too little intraspecific gene flow to prevent divergence due to drift. These two phenomena add up to a classic conundrum for speciation biologists: how can an individual species evolve as a cohesive unit, distinct from other species when some some divergent taxa appear to have too much gene flow and in other apparently good species there is too little?
In my dissertation work, I found selection can homogenize variation within species, and that selection enables divergent taxa to retain important genetically-based differences despite gene flow. For example, in drought- and salt-tolerant populations of H. annuus a surprisingly large fraction of the genome (1-5%) shows some evidence of recent selective sweeps, which may contribute to local or regional adaptations. These sweeps altered genetic variation in striking ways, effectively homogenizing populations under similar selection while enhancing divergence between populations experiencing different selective regimes. At a higher taxonomic scale, I found that H. annuus and a distantly related species H. argophyllus have exchanged genes across much of the genome, but remain remaining morphologically and ecologically distinct due to selective sweeps. Currently, I am using next-generation technology to sequence dozens of individuals' transcriptomes from across the ranges of five wild Helianthus species (including the three used in my dissertation work) as well as numerous accessions of domesticated H. annuus. The resulting transcriptome sequence data will enable me to characterize the fixed genetic differences between species and subspecies in this group, and to identify regions of the genome that have experienced recent selective sweeps.
Selected publications:
Dempewolfe, H., Kane N. C. Ostvik K. L. et al. 2010. Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass. – the development of a library of expressed sequence tags, microsatellite loci and the sequencing of its chloroplast genome. Molecular Ecology Resources 10:1048-1058.
Barker, M. S., Dlugosch, K. M., Dinh, L., Challa, S., Kane, N. C., King, M. G. and Rieseberg, L. H. 2010. EvoPipes.net: Bioinformatic pipelines and forums for ecological and evolutionary genomics. Evolutionary Bioinformatics 6:143-149.
Kane, N. C., King, M., Barker, M. S., Raduski, A., Karrenberg, S., Yatabe, Y, Knapp, S. J. and Rieseberg, L. H. 2009. Comparative genomic and population genetic analyses indicate highly porous genomes and high levels of gene flow between divergent Helianthus species. Evolution. 63: 2061-2075.
Barker, M. S., Kane, N. C., Kozik, A. Michelmore, R. W., Knapp, S. J., Kesseli, R. K. Still, D. W., Bradford, K. J. and Rieseberg, L. H. 2008. Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Molecular Biology and Evolution. 25:2445-2455.
Lai, Z. Kane, N. C., and Rieseberg, L. H. 2008. Natural variation in gene expression between wild and weedy populations of Helianthus annuus. Genetics. 179: 1881-1890.
Kane, N. C. and Rieseberg, L. H. 2008. Genetics and the evolution of weediness in Helianthus annuus. Molecular Ecology 17: 384-394.
Yatabe, Y., Kane, N. C. Scotti-Saintagne, C. and Rieseberg, L. H. 2007. Rampant gene exchange across a strong reproductive barrier between the annual sunflowers, Helianthus annuus and H. petiolaris. Genetics 175: 1883-1893.
Kane, N. C. and Rieseberg, L. H. 2007. Selective sweeps reveal candidate genes for adaptation to drought and salt tolerance in common sunflower, Helianthus annuus. Genetics 175: 1823-1824.
Current work aims to identify genes underlying the major morphological differences between domesticated (large heads) and wild (small heads) Common sunflowers (H. annuus).