The genetic and physiological basis for stress tolerance in domesticated sunflower, Helianthus annuus
I am investigating the genetic basis for stress tolerance in sunflower in collaboration with members of the Burke and Donovan labs at UGA.
Local adaptation and fitness trade-offs in the CA annual, Leptosiphon parviflorus
The major plant system I used for my dissertation work is Leptosiphon parviflorus, an annual wildflower native to California grasslands. At Jasper Ridge Biological Preserve (JRBP) in San Mateo County CA, I studied two populations of L. parviflorus that grow on adjacent soil types- serpentine and sandstone soil. Serpentine soils are frequently used for the study of adaptation over small spatial scales, due to their often abrupt boundaries and strong selection pressures. These soils, abundant in CA, are characterized by several stressors, including low calcium to magnesium ratios, low water holding capacities, and high concentrations of heavy metals.
The populations I study are located less than 100 meters apart and evidence shows that gene flow is occurring between them (Kay et al. 2011). Despite this short spatial scale, these populations differ in their flower color and flowering time. Serpentine plants have pink flowers and flower earlier than white-flowered sandstone plants. While flowering time has a genetic and environmental component, flower color is a genetically controlled by a single locus.
My first objective was to determine if these populations are locally adapted to their respective soil types. I conducted four years of reciprocal transplant studies in the field as well as several greenhouse studies using field soil and determined that each population performs best on its native soil type. However, the pattern of local adaptation appears to be asymmetrical. Sandstone plants die before flowering when grown on serpentine soil, but survival is relatively high for both populations on sandstone soil. There are differences among fecundity however, with sandstone plants producing a greater number of flowers on sandstone soil than serpentine plants.
I have continued to explore a number of questions in this system:
1.) What traits are under selection and what are the selective agents?
The populations exhibit heritable differentiation in both flower color and flowering time. To measure selection on these traits, I grew advanced-generation hybrids in the field and observed the relationship between the traits and fitness. See my results about flowering time variation in these populations here.
2.) Does adaptation to one soil type cause fitness trade-offs on the other soil type?
I have taken several approaches to understand the mechanisms underlying adaptive trade-offs in this system. In one set of experiments, I performed field manipulations (supplemental watering, weeding) to determine the relative contribution of soil moisture and competition to the selective environments in each habitat. My results showed that serpentine adapted plants are at a competitive disadvantage in non-serpentine habitats, supporting ecological hypotheses about a trade-off between stress tolerance and competitive ability.
3.) What is the role of flower color in soil adaptation?
Flower color is an especially intriguing trait in this system. Pollinator observations have shown that the pollinators (beeflies) do not appear to discriminate between flower colors. I am currently performing experiments to determine the adaptive role of flower color in this system using Near Isogenic Lines (NILs); genotypes that have the pink flower color locus introgressed into the white sandstone genetic background. These genotypes will be used to determine whether this genetic locus has a pleiotropic effect on other traits and to measure the fitness effects of this individual locus on field soil (and whether it contributes to adaptive trade-offs).
Future Directions:
4.) How many genomic regions are associated with local adaptation?
Since the two populations I am studying are adjacent and connected by gene flow, I expect that any genomic regions that are differentiated between them are associated with adaptive loci. I plan to take advantage of Next Generation Sequencing tools to develop a linkage map and markers throughout the genome to determine the number of unlinked genomic regions that are associated with local adaptation.
The populations I study are located less than 100 meters apart and evidence shows that gene flow is occurring between them (Kay et al. 2011). Despite this short spatial scale, these populations differ in their flower color and flowering time. Serpentine plants have pink flowers and flower earlier than white-flowered sandstone plants. While flowering time has a genetic and environmental component, flower color is a genetically controlled by a single locus.
My first objective was to determine if these populations are locally adapted to their respective soil types. I conducted four years of reciprocal transplant studies in the field as well as several greenhouse studies using field soil and determined that each population performs best on its native soil type. However, the pattern of local adaptation appears to be asymmetrical. Sandstone plants die before flowering when grown on serpentine soil, but survival is relatively high for both populations on sandstone soil. There are differences among fecundity however, with sandstone plants producing a greater number of flowers on sandstone soil than serpentine plants.
I have continued to explore a number of questions in this system:
1.) What traits are under selection and what are the selective agents?
The populations exhibit heritable differentiation in both flower color and flowering time. To measure selection on these traits, I grew advanced-generation hybrids in the field and observed the relationship between the traits and fitness. See my results about flowering time variation in these populations here.
2.) Does adaptation to one soil type cause fitness trade-offs on the other soil type?
I have taken several approaches to understand the mechanisms underlying adaptive trade-offs in this system. In one set of experiments, I performed field manipulations (supplemental watering, weeding) to determine the relative contribution of soil moisture and competition to the selective environments in each habitat. My results showed that serpentine adapted plants are at a competitive disadvantage in non-serpentine habitats, supporting ecological hypotheses about a trade-off between stress tolerance and competitive ability.
3.) What is the role of flower color in soil adaptation?
Flower color is an especially intriguing trait in this system. Pollinator observations have shown that the pollinators (beeflies) do not appear to discriminate between flower colors. I am currently performing experiments to determine the adaptive role of flower color in this system using Near Isogenic Lines (NILs); genotypes that have the pink flower color locus introgressed into the white sandstone genetic background. These genotypes will be used to determine whether this genetic locus has a pleiotropic effect on other traits and to measure the fitness effects of this individual locus on field soil (and whether it contributes to adaptive trade-offs).
Future Directions:
4.) How many genomic regions are associated with local adaptation?
Since the two populations I am studying are adjacent and connected by gene flow, I expect that any genomic regions that are differentiated between them are associated with adaptive loci. I plan to take advantage of Next Generation Sequencing tools to develop a linkage map and markers throughout the genome to determine the number of unlinked genomic regions that are associated with local adaptation.
The genetics of flowering time in Arabidopsis thaliana
Arabidopsis thaliana is a model plant system that is commonly used for studies on the genetic basis of phenotypic traits due to its sequenced and extensively annotated genome. However, despite the wealth of genetic information from these studies, it is unclear how many of the genes identified in lab settings and using lab strains are relevant for adaptation in nature.
Our lab aims to take advantage of the genomic resources of Arabidopsis to understand the genetic basis of adaptive traits. To approach this, my advisor Doug Schemske and his collaborators have embarked on a long-term study using natural Arabidopsis populations that are native to Sweden and Italy (the northernmost and southernmost ends of its native range, respectively). A mapping population of genotyped, recombinant inbred lines (RILs) was created from these populations. Phenotypic traits can be measured on these RIL genotypes to determine which genomic regions affect this trait (and thus likely contain the causal genes). Go here for more details: http://www.plantadaptation.org/home.html
Using this mapping population, I studied the genetic basis of flowering time, using specialty growth chambers programmed to mimic the temperature and photoperiod fluctuations of the natural habitats of the two populations. Flowering time is often thought to be adaptive in plants as it dictates the timing of reproduction, and flowering too early or too late can cause mortality or a reduction in reproductive success. There are a wealth of studies on the genetic basis of flowering time in Arabidopsis, yet most of them use lab strains grown in artificial conditions. While these studies have provided a basic understanding of the biochemical pathways involved in flowering time in plants, our lab is specifically interested in how variation in flowering time genes may contribute to adaptation among natural populations. In this system, we found several large-effect genomic regions that affected flowering time in both environmental conditions and which also co-localize to known flowering time genes.
It is possible that flowering time genes contribute to fitness trade-offs between populations, but this can only be determined by using natural populations grown in natural conditions. A study done by Ågren et al. (2013) measured fitness in this mapping population in both field sites over three years. The genetic regions found to be important for flowering time in my study were compared to the genetic regions found to be important for fitness in the field to see if any of them were the same (an indication that they are adaptive).
We were able to identify a.) the number of genomic regions that contribute to flowering time variation between these populations and their approximate effect sizes; b.) which of these genomic regions co-localized with genomic regions that affect fitness in the field; and c.) candidate genes that are strongly implicated in local adaptation.
Check out our paper to learn more: Dittmar, Oakley, Ågren, Schemske. (2014) Molecular Ecology
Our lab aims to take advantage of the genomic resources of Arabidopsis to understand the genetic basis of adaptive traits. To approach this, my advisor Doug Schemske and his collaborators have embarked on a long-term study using natural Arabidopsis populations that are native to Sweden and Italy (the northernmost and southernmost ends of its native range, respectively). A mapping population of genotyped, recombinant inbred lines (RILs) was created from these populations. Phenotypic traits can be measured on these RIL genotypes to determine which genomic regions affect this trait (and thus likely contain the causal genes). Go here for more details: http://www.plantadaptation.org/home.html
Using this mapping population, I studied the genetic basis of flowering time, using specialty growth chambers programmed to mimic the temperature and photoperiod fluctuations of the natural habitats of the two populations. Flowering time is often thought to be adaptive in plants as it dictates the timing of reproduction, and flowering too early or too late can cause mortality or a reduction in reproductive success. There are a wealth of studies on the genetic basis of flowering time in Arabidopsis, yet most of them use lab strains grown in artificial conditions. While these studies have provided a basic understanding of the biochemical pathways involved in flowering time in plants, our lab is specifically interested in how variation in flowering time genes may contribute to adaptation among natural populations. In this system, we found several large-effect genomic regions that affected flowering time in both environmental conditions and which also co-localize to known flowering time genes.
It is possible that flowering time genes contribute to fitness trade-offs between populations, but this can only be determined by using natural populations grown in natural conditions. A study done by Ågren et al. (2013) measured fitness in this mapping population in both field sites over three years. The genetic regions found to be important for flowering time in my study were compared to the genetic regions found to be important for fitness in the field to see if any of them were the same (an indication that they are adaptive).
We were able to identify a.) the number of genomic regions that contribute to flowering time variation between these populations and their approximate effect sizes; b.) which of these genomic regions co-localized with genomic regions that affect fitness in the field; and c.) candidate genes that are strongly implicated in local adaptation.
Check out our paper to learn more: Dittmar, Oakley, Ågren, Schemske. (2014) Molecular Ecology