Research Current Lab Members

Genomics of Plant Domestication


Crops are plant species that have evolved in a cultural context to provide food and other products for human society. Crop species are fascinating subjects for evolutionary study, since they are examples of species that have undergone rapid diversification under intense selective pressures. They also permit us to understand the dynamic interface between genetics, evolution and human culture. We are studying the evolution of genes in Rice (Oryza sativa). By using tools of molecular and evoutionary genomics, these studies provide insights into the processes and mechanisms that accompany cultural selection on plant species during domestication events. Currently we have three active domestication projects in the lab including Asian rice, African rice and date palm (Phoenix dactylifera). For more on our date palm resequencing project visit our 100 Dates! project page.

The Molecular Evolutionary Ecology of Plant Development


Why do different individuals and species look different? How do developmental patterns change as a result of local adaptation? How are environmental signals integrated by organisms to condition an appropriate developmental response? These are some of the questions that we attempt to address by studying the molecular evolution of genes that control inflorescence development in the wild mustard weed Arabidopsis thaliana. We are assessing the evolutionary forces that act in plant developmental pathways at the species level, and in mapping and isolating genes that underlie natural variation in shoot architectures and life histories.

Evolutionary genomic studies of salt stress response in domesticated rice

Both Asian rice (Oryza sativa) and African rice (Oryza glaberrima) are known to be one of the most salt sensitive crops, yet several landraces can grow in mildly saline environments. We are using GWAS and extreme QTL mapping, network reconstruction, and phenomic analysis to explore response and adaptation of rice to saline environments, including the evolution of abiotic stress response mechanisms. The results provide insights into evolution in novel environments and the genetic basis for ecological adaptation.

Environmental Gene Regulatory Interaction Network (EGRINs)


Knowing how genes and functional genetic networks are regulated in response to changing environmental signals, and the variation in the regulatory networks that mediate these responses among natural genotypes, are two main objectives in the study of plant genomics and systems biology. Understanding these key aspects of plant biology is imperative for assessing adaptations to the natural (as well as extreme) range of conditions experienced by plants, as well as to the shifting environmental conditions resulting from global climate change. Cultivated Asian rice,Oryza sativa, is the worlds most widely grown crop species and is a key model system in plant biology. O. sativa ssp. indica and O. sativa ssp. japonica are the two main rice subspecies (or variety groups). The phenotypic diversity found within rice provides an excellent basis for studying local adaptation to various distinct agro-ecological macro-environments and seasons.

A primary aim of EGRINs is to identify rice transcriptional networks associated with fluctuating environmental signals, and examine levels and patterns of global gene expression under different natural agro- ecological macro-environments. The identification of environmental gene regulatory interaction networks and understanding global gene expression patterns in the field will help advance breeding efforts in rice. These results will be especially useful in understanding plant response to climate fluctuations, as well as develop cultivars that can tolerate temperature and water stress.

Evolution of Social Amoeba

The social amoeba Dictyostelium discoideum has emerged as a model system for the study of social ecology and evolution. Upon starvation, individual free-living cells swarm and form a co-operative fruiting body, in which some individuals altruistically provide benefits to the spores than are subsequentially dispersed. We are examining the molecular populationgenetics of Dictyostelium, the relationship of nucleotide variation to kin discrimination and fruiting body formation,and transcriptome changes upon development of interactive structures.