Populations Genomics of Grapes and North American Rootstock Species
Grapes (Vitis vinifera) are one of the most important horticultural crops in the world.  Remarkably, their cultivation relies on the use of North American Vitis species as rootstocks, which traces back to the a pylloxera infestation in 19th century France.  In our ongoing work, we are characterizing the genomes and population genomics of Vitis species in the American Southwest, because these species have the potential to contribute important resistance and tolerance factors to viticulture.

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Epigenetics and the Evolution of Plant Genomes
Transposable elements (TEs) constitute the majority of angiosperm genomic DNA, and their presence is counteracted by a host response that includes DNA methylation.  Methylation affects not only the activity of transposable elements but also the function of nearby genes.  But genes are also methylated.  We have been taking an evolutionary approach to study many aspects of methylation and other epigenetic features – i.e., Why are genes methylated?  When did methylation evolve?  Are TEs controlled targeted differentially for silencing by small RNAs (siRNAs)?  How does methylation variation contribute to genome size differentiation and ultimately interspecific divergence?


E.Coli Experimental Evolution
With collaborators at UCI, we have evolved 120 lines of E. coli under high temperature (42 C).  We are currently investigating the genetic and mechanistic underpinnings of adaptation to this stressful environment.  A key feature of our experiment is its size; the number of evolved lines is an order of magnitude higher than previous experiments.  As a result we can ask questions about parallel pathways to adaptation and the number of genetic solutions to the high temperature challenge.


The Genetics of Domestication
Domestication has been a long-running interest of the lab, particularly elucidating the evolutionary processes and mechanisms that shape extant crop diversity.  Historically most work has focused on the population genetics of maize domestication, but the lab has also contributed to studies in olives, grapes, rice, pearl millet and soybean.


Comparative Genomics & Molecular Evolution
The lab has long been interested in comparisons within and between genomes to characterize evolutionary processes.  A primary goal has been to isolate the factors that contribute to evolutionary rates among genes, including gene expression, methylation and psuedogenization.  Previous work in comparative genomics has included study of grass species and members of the Brassicaceae, as well as pox and herpes viruses.  We also have a budding interest in Xylella fastidiosa, a bacterial pathogen of grapes and olives.