The Burke Lab
Ongoing Research Projects
Ongoing projects in the
lab...
Genetics and the Domestication of Sunflower:
Despite being one of the world's most important oilseed crops, we have only a rudimentary understanding of the genetic basis of sunflower domestication. What we've learned thus far is that the genetics underlying sunflower domestication appear to be fundamentally different from the genetics underlying the domestication of other crops. The main objective of this project is to further investigate the genetic basis of trait divergence during the evolution of domesticated sunflower. In other words, the goal is to answer the following questions: How many genes were involved in the evolution of domesticated from wild sunflower? Where in the genome are they located? How large are their effects? Which traits appear to have evolved in response to selection, and which appear to have have evolved as an indirect byproduct of such selection, or even by chance? Taken together, the results of this research will provide a much better understanding of the evolution of domesticated sunflower than is currently available, and the resulting data also has the potential to positively impact ongoing efforts aimed at the continued improvement of sunflower.
Identifying the Targets of Selection During Sunflower Domestication:
The domestication of crop plants from their wild relatives 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.
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 are using a phylogenetic approach to identify the progenitor of safflower, and are also 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.
Genetics and the Domestication of Sunflower:
Despite being one of the world's most important oilseed crops, we have only a rudimentary understanding of the genetic basis of sunflower domestication. What we've learned thus far is that the genetics underlying sunflower domestication appear to be fundamentally different from the genetics underlying the domestication of other crops. The main objective of this project is to further investigate the genetic basis of trait divergence during the evolution of domesticated sunflower. In other words, the goal is to answer the following questions: How many genes were involved in the evolution of domesticated from wild sunflower? Where in the genome are they located? How large are their effects? Which traits appear to have evolved in response to selection, and which appear to have have evolved as an indirect byproduct of such selection, or even by chance? Taken together, the results of this research will provide a much better understanding of the evolution of domesticated sunflower than is currently available, and the resulting data also has the potential to positively impact ongoing efforts aimed at the continued improvement of sunflower.
Identifying the Targets of Selection During Sunflower Domestication:
The domestication of crop plants from their wild relatives 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.
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 are using a phylogenetic approach to identify the progenitor of safflower, and are also 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.