Ongoing projects in the lab...

Comparative Genomics of Phenotypic Variation in the Compositae:
The Compositae (a.k.a. Asteraceae) is one of the largest, most diverse, and most economically important plant families. While lettuce, sunflower, and safflower are the three most valuable members of this family, over 40 species have been domesticated for a wide variety of uses. The Compositae also contains some of the world’s most noxious weeds, which cost the United States ca. $35 billion annually. The primary goal of this project is to develop genomic resources for the continued study of this important plant family. This work will include: (i) sequencing the gene-rich regions of the lettuce, sunflower, and safflower genomes; (ii) generation of “gene catalogs” for 25 additional taxa, including six crops, three weeds, the wild progenitors of ten crops and weeds, representatives of five taxonomically important subfamilies within the family, and an outgroup (i.e., a close relative of the family); (iii) analyses of the prevalence of variation in gene copy number vs. vs. nucleotide variation; (iv) analyses of the effects of whole genome duplications on diversification rates within the family; (v) identification of parallel genetic changes across crop/weed lineages; (vi) construction of ultra-high density genetic maps of lettuce, sunflower, and chicory; (vii) development of permanent populations for genetic mapping in key Compositae species; and (viii) the identification and validation of candidates for genes underlying important crop- and weed-related traits. This research will result in the generation of permanent resources for the Compositae research community, and will have a significant economic impact through its contributions to both crop and weed science. This project will also result in the training of students at all levels in genetics, biochemistry, physiology, comparative genomics, and bioinformatics.

Identifying the Targets of Selection During the Evolution of Cultivated Sunflower:
The evolution of crop plants has involved strong selection on traits relating to things such as seed dormancy and dispersal, growth form, flowering time, yield, palatability, and nutritional value. This selection results in a characteristic decrease in genetic variation in and around the genes controlling such traits, thereby providing a means for identifying agronomically important genes based on patterns of population genetic diversity. This project is aimed at identifying and characterizing genes that experienced selection during the domestication and subsequent improvement of sunflower. The primary goal of this research is to identify genes that bear the population genetic 'signature of selection' based on data derived from molecular genetic markers and DNA sequencing. A related goal is to investigate the function of these genes on the basis of their genomic locations relative to traits that have previously been mapped in sunflower as well as through analyses of gene expression. Taken together, the results of this research will provide a much more detailed understanding of the origin and evolution of one of the world's most important oilseed crops than is currently available. This work will also result in the development of permanent genetic resources for the scientific community, including gene-based simple sequence repeat (SSR) markers as well as DNA sequence data derived from both putatively selected genes and candidate genes identified on the basis of their similarity to genes of known function from other taxa.

Association Mapping in Sunflower:
While great strides have been made with regard to the development of genetic and genomic resources for sunflower research, the lack of tools for efficiently associating genes with phenotypes remains a major obstacle for sunflower researchers. This project seeks to address this situation through the production of permanent, publicly available resources for association mapping in sunflower. Given what we know about the structure of linkage disequilibrium in sunflower, this approach promises to provide much greater mapping resolution than is currently available, potentially allowing us to map functional variation to the level of individual genes. The specific objectives of this proposal are to assemble an association mapping population made up of a diverse collection of inbred sunflower lines, characterize the population structure of these lines, investigate the structure of linkage disequilibrium across the sunflower genome, phenotypically characterize the mapping panel for a variety of traits, and test for associations between candidate gene polymorphisms and variation in the traits of interest.

Fitness-Related QTLs and the Mitigation of Crop-Wild Gene Flow in Sunflower:
With the commercial introduction of genetically modified crops, it is feared that genetically engineered genes or “transgenes” might escape into wild relatives through hybridization. Possible consequences of transgene escape include the generation of more invasive weeds or the decline of natural populations of herbivores, pathogens, and competing plant populations. Research indicates that hybridization between crop plants and their wild relatives is widespread and that at least some transgenes increase the seed production of wild relatives and may pose a risk to the environment. Given these concerns, numerous methods have been suggested to minimize transgene spread. One of these is the placement of transgenes on the same chromosomes and in close proximity to genes involved in domestication that are negatively selected in wild plants. Such “linkage” to domestication genes should limit the spread of the transgene. We propose to evaluate this basic strategy by asking whether chromosomal segments surrounding domestication genes in cultivated sunflowers have moved across the crop boundary in the past through hybridization. This will be accomplished by first enhancing the genetic resources in sunflower and determining more precisely the location of domestication genes. We then will assay the frequency of the chromosomal segments carrying domestication genes in wild sunflower populations that are adjacent to cultivated fields. The frequency and distance of spread of such segments in crop x wild sunflower hybrid populations will provide an indicator of the likely efficacy of this strategy.

The Origin and Evolution of Safflower:
In addition to our domestication-related research on sunflower, we are investigating the origin and evolution of safflower (Carthamus tinctorius). Safflower is an annual, herbaceous crop that thrives in hot, dry climates. Although it was originally grown for its flowers, which served as a source of dye (carthamine). Floral extracts were also been used to flavor foods, and have historically been valued for their numerous medicinal properties. More recently, safflower has been grown as an oilseed crop, and has also been targeted for its potential as a large-scale production platform for plant-made pharmaceuticals. Unfortunately, little is know about the origin and evolution of this fascinating plant. It is widely believed to have been domesticated in the Fertile Crescent at least 4,000 years ago, but relationships amongst safflower and its close relatives remain unresolved. We have used a phylogenetic approach to identify the progenitor of safflower, and are developing the resources necessary for an analysis of the genetic architecture of domestication-related traits in safflower.

Stephanomeria, a New Model for Studying the Genetics of Plant Speciation:
The genus Stephanomeria is a member of the Compositae (a.k.a. the Asteraceae), which is one of the largest and most diverse flowering plant families, comprising one-tenth of all known angiosperm species. This genus contains three especially interesting cases of speciation. The first is the derivation of S. malheurensis from S. exigua which, contrary to the classical view of how species form, occurred in sympatry. The second involves S. diegensis, a diploid hybrid species formed following hybridization between S. exigua and S. virgata. Finally, S. elata is an allopolyploid derived from hybridization between these same two species. In the first two cases, speciation has been accompanied by rapid chromosomal evolution. Moreover, reproductive barriers amongst these species are maintained (at least in part) by hybrid sterility, making these species an ideal system for studying the evolution of hybrid sterility. Beyond offering insight into interesting biological questions, of course, the ideal study system must be genetically tractable. Once again, Stephanomeria does not disappoint, as crosses are relatively easy to make and the generation time is short. We are in the process of investigating the origins of these species in a phylogeographic context, as well as developing the tools necessary for detailed analyses of chromosomal evolution within the genus.