The Burke Lab
Ongoing Research Projects
This page contains an overview
of our major research interests, but first...
A few words about 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.
Ongoing research projects
Comparative genomics of phenotypic variation in the Compositae
One of the main goals of this project is to develop genomic resources for research in the Compositae. 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 crops, weeds, and their wild progenitors, 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. 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 mapping populations for key species within the family; and (viii) the identification and validation of candidates for genes underlying important crop- and weed-related traits.
Sequencing of the sunflower genome
Our lab is involved in a multi-national effort aimed at sequencing the sunflower genome. This project will involve the construction and integration of detailed genetic and physical maps of the sunflower genome, whole genome shotgun sequencing, sequencing of individual BACs and/or BAC pools for finishing, assembly of the resulting data, and annotation of the finished product.
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. In recent years, we've been working to identify and characterize genes that experienced selection during the domestication and subsequent improvement of sunflower. The primary goal of this research has been 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, this work will provide a detailed understanding of the origin and evolution of one of the world's most important oilseed crops.
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. We are addressing 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. This work will involve the assembly of an association mapping population made up of a diverse collection of inbred sunflower lines, characterization of the population and kin structure present within this collection of lines, investigation of the structure of linkage disequilibrium across the sunflower genome, phenotypic characterization of the association population for a variety of agronomically and evolutionary important traits, and tests for associations between candidate gene polymorphisms and variation in traits of interest.
Assessing the fate and impact of crop-wild hybridization 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, possibly generating more invasive weeds and/or causing the decline of herbivore, pathogen, or competing plant populations. In many cases, hybridization between crop plants and their wild relatives is widespread, but our understanding of the factors influencing the movement of crop alleles through wild populations is incomplete. The goals of this project are to identify the types of traits that are likely to provide a selective advantage in the wild, and to develop a better understanding of the factors favoring the establishment of beneficial crop alleles in wild populations.
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.
Hybridization and speciation in Stephanomeria
The genus Stephanomeria (which is likewise a member of the Compositae) contains three particularly 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, is thought to have 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 parental species. We are particularly interested in studying the effects of hybridization and polyploidization on the structure and function of the Stephanomeria genome. We are thus investigating these species in a phylogeographic context, and developing the tools necessary for detailed genomic analyses within the genus.
A few words about 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.
Ongoing research projects
Comparative genomics of phenotypic variation in the Compositae
One of the main goals of this project is to develop genomic resources for research in the Compositae. 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 crops, weeds, and their wild progenitors, 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. 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 mapping populations for key species within the family; and (viii) the identification and validation of candidates for genes underlying important crop- and weed-related traits.
Sequencing of the sunflower genome
Our lab is involved in a multi-national effort aimed at sequencing the sunflower genome. This project will involve the construction and integration of detailed genetic and physical maps of the sunflower genome, whole genome shotgun sequencing, sequencing of individual BACs and/or BAC pools for finishing, assembly of the resulting data, and annotation of the finished product.
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. In recent years, we've been working to identify and characterize genes that experienced selection during the domestication and subsequent improvement of sunflower. The primary goal of this research has been 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, this work will provide a detailed understanding of the origin and evolution of one of the world's most important oilseed crops.
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. We are addressing 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. This work will involve the assembly of an association mapping population made up of a diverse collection of inbred sunflower lines, characterization of the population and kin structure present within this collection of lines, investigation of the structure of linkage disequilibrium across the sunflower genome, phenotypic characterization of the association population for a variety of agronomically and evolutionary important traits, and tests for associations between candidate gene polymorphisms and variation in traits of interest.
Assessing the fate and impact of crop-wild hybridization 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, possibly generating more invasive weeds and/or causing the decline of herbivore, pathogen, or competing plant populations. In many cases, hybridization between crop plants and their wild relatives is widespread, but our understanding of the factors influencing the movement of crop alleles through wild populations is incomplete. The goals of this project are to identify the types of traits that are likely to provide a selective advantage in the wild, and to develop a better understanding of the factors favoring the establishment of beneficial crop alleles in wild populations.
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.
Hybridization and speciation in Stephanomeria
The genus Stephanomeria (which is likewise a member of the Compositae) contains three particularly 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, is thought to have 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 parental species. We are particularly interested in studying the effects of hybridization and polyploidization on the structure and function of the Stephanomeria genome. We are thus investigating these species in a phylogeographic context, and developing the tools necessary for detailed genomic analyses within the genus.
University of Georgia, Department of Plant Biology, Athens, GA 30602