Research

We study a broad range of topics in the lab. Here are four of the major research questions that we are currently focused on answering:

How do populations locally adapt to divergent habitats?

The core area of our research is focused on understanding the process of local adaptation, which occurs when organisms adapt to divergent habitats in nature. To understand the genetic and physiological mechanisms of local adaptation, we are studying the yellow monkeyflower, Mimulus guttatus. M. guttatus is a model genomic system for understanding evolutionary adaptations because it has successfully adapted to a wide array of different habitats across western North America, including toxic copper mine tailings, coastal salt spray zones, alpine regions, and even to the geysers of Yellowstone National Park.OLYMPUS DIGITAL CAMERA

One of our major interests in understanding how local adaptation has contributed to the evolution of coastal perennial and inland annual ecotypes. In the process of identifying the causes of local adaptation we are also elucidating the mechanisms of speciation, as ecotypes represent an intermediate state on the path in the formation of new species. Coastal and inland ecotypes of M. guttatus are very divergent in their morphology and physiology, which reflects local adaptation of these plants to different habitats. Inland habitats rapidly dry out during the seasonal summer drought in California. To escape from the summer drought, inland plants have evolved a “live-fast die-young” strategy whereby they rapidly flower and produce offspring before the summer drought kills them. In contrast, coastal plants have evolved to be slow-growing perennials that survive for many years. Coastal plants can persist through the summer drought because of water supplied by summer sea fog. While coastal plants have access to water year-round, they have had to evolve adaptations to cope with oceanic salt spray and high rates of herbivory.

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To understand how coastal and inland ecotypes of M. gutattus evolved, we are using genomic methods to identify the genes and gene networks responsible for adaptive divergence. We recently identified key candidate genes involved in local adaptation by conducting whole genome sequencing of nearly 100 coastal and inland populations. This study revealed that large chromosomal inversions have trapped adaptive genetic difference between the coastal and inland ecotypes. In addition, we identified candidate genes in the gibberellin (GA) growth hormone pathway that could explain adaptive differences in growth and herbivore defense between coastal and inland populations. To follow up this study, we conducted a series of experiments, in which we found we could convert coastal plants partially into inland plants just by spraying them with GA. Further, we found that one of the chromosomal inversions interacts with GA and controls the production of herbivore resistance compounds. This suggests that the inversion is partially responsible for a classic evolutionary trade-offs between allocation to growth, reproduction, and defense. Overall, these results suggest a generalizable physiological mechanism by which plants adapt to wet and dry habitats.

What factors drive the evolution of gene regulation?

Gene regulation plays a key role in developmental processes and the response of organisms to biotic and abiotic stresses. Previous, we showed that genomic features, especially the local rate of recombination, drive cis-regulatory evolution and the response of stress response genes in Arabidopsis thaliana. Recently, our lab sought to understand how gene expression evolves between locally adapted population of Mimulus guttatus. To accomplish this goal, we planted coastal and inland lines, as well as F1 hybrids, at both coastal and inland field sites. This experimental design allowed us to quantify how coastal and inland genetic variants responded to local and foreign environments. The vast majority (79%) of gene expression differences between locally adapted populations in this study were due to DNA sequence changes in the immediate vicinity of the genes themselves (indicating more changes in local than global regulatory mechanisms). Further, this study revealed that two key genes, CBL10 and SOS1, which are responsible for pumping sodium out of cells, were much more highly expressed in coastal plants than inland plants. This suggests a possible new mechanism for plant tolerance to oceanic salt spray. Overall, our study provides new insights into the evolution of local adaptation and will shape the future direction of the field, which will increasingly involve genomic analyses of gene regulation in nature.

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How can we leverage our understanding of local adaptation to facilitate the production of sustainable liquid biofuels?

Global climate change, caused by anthropogenic increases in carbon dioxide and other greenhouse gases, poses enormous challenges for human civilization and the environment. While sustainable sources of energy (wind, solar) have seen remarkable advances recently, there will likely be a continued need for liquid fuels far into the future. Advanced biofuels, derived from plant feedstock, provide one promising avenue for sustainable liquid fuel production. Perennial feedstock, like switchgrass (Panicum virgatum), have only undergone limited breeding in the past and there is great potential to improve crop yields. One of the major aims of our research program is to understand the genetic basis for local adaptation of switchgrass to different climatic conditions. The long-term goal of this research is to breed high-yielding cultivars that are adapted to different geographic regions of the United States. In particular, our research program is focused on the genetic basis of divergence between northern upland and southern lowland ecotypes of switchgrass. Southern lowland cultivars are adapted to lower latitudes and have many desirable traits, including higher yields, drought and heat tolerance, pathogen resistance, and nutrient-use efficiency. However, southern lowland plants are not as freezing tolerant as northern upland plants, and thus, are subject to winter kill when grown in the Midwest. Thus, the ideal cultivar of the future should combine the adaptive traits of both the southern lowland and northern upland cultivars.

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To identify the loci that are responsible for adaptive traits of the two cultivar types, we have developed a set of new genomic resources for switchgrass. These resources include a genetic mapping population that combines northern upland and southern lowland ecotypes into hybrids that can be used for mapping the regions of the genome responsible for divergence between these ecotypes. We also have worked collaboratively with others to develop a genome-wide association mapping (GWAS) population, which will be able to pinpoint genes responsible for adaptation to different geographic regions. To identify the loci responsible for adaptation across the United States, a large collaborative team planted the upland x lowland genetic mapping population at ten field locations over 17 degrees of latitude) from South Texas to Michigan in 2015. In 2018, we planted a GWAS population at 12 locations stretching over 24 degrees of latitude from central Mexico to South Dakota. The results so far are very exciting, as we have identified key genomic regions controlling divergence in flowering time, biomass production, and disease resistance between southern lowland and northern upland ecotypes. Importantly, we are able to use the results from across the field sites to establish the importance of each region of the genome across geographic space. This knowledge will be crucial for breeding cultivars of switchgrass that perform well in different geographic regions and in future environmental conditions arising from climate change.Screen Shot 2019-02-06 at 9.58.49 AM

How can we improve food security by developing crops that are resilient to global climate change?

Increases in global temperatures associated with climate change pose an enormous challenge for global agriculture and plant populations generally. We recently launched an exciting line of research to confront this challenge through a new focus on plant heat tolerance in the common bean, Phaseolus vulgaris. Beans are an important commodity crop in Michigan and a major food staple globally. In Africa and Latin America, beans are the largest source of plant-based protein and are thus, integral to global food security. In the 21st-century, bean production will be greatly challenged by rising temperatures as beans are extremely sensitive to high temperatures. The primary reason that beans crops fail at high heat is due to male pollen sterility. Our lab is now working to identify the causes of male sterility at high heat and determine what other aspects of physiology are affected by high temperature. To accomplish this goal, we are combining our expertise in plant physiology and gene expression analyses to understand why male sterility occurs at high temperatures. Further, we are leveraging previously developed genome-wide association mapping panels for beans to identify genes responsible for heat tolerance. Finally, we are studying the causes of reproductive isolation between common bean and its independently domesticated relative, tepary bean, which is highly drought and heat tolerant. Overall, our hope is for heat tolerance to be incorporated into future bean breeding efforts to expand the locations in which beans can be planted worldwide and make beans more resilient to global climate change.IMG_1512.jpg