Research in the lab revolves around plant evolutionary genetics, with particular focus on the population genetics of maize. Below are excerpts of some ongoing work in the lab. For a more detailed look at work in the lab, please browse our publications.
Genomics of adaptation in maize
After it's domestication 9,000 years ago in southwest Mexico, maize spread rapidly, adapting to a number of different environments across the Americas and, in more recent times, much of the rest of the world. Using genotyping and next-generation sequencing, we are working to identify loci responsible for some of these adaptations.
Projects underway include single nucleotide polymorphism genotyping of a large chronologically-stratified sample of modern maize lines to identify loci that have been selected during recent breeding in the U.S. and a combination of quantitative trait locus mapping and genome resequencing to investigate parallel evolution in the adaptation of maize to high-altitude environments in both Mexico and South America.
A collaboration with the Maize Diversity Project has also recently allowed us to take a population genomic approach to the study of maize domestication. Work is under way analyzing full-genome resequencing data from 75 maize and teosinte plants.
Projects underway include single nucleotide polymorphism genotyping of a large chronologically-stratified sample of modern maize lines to identify loci that have been selected during recent breeding in the U.S. and a combination of quantitative trait locus mapping and genome resequencing to investigate parallel evolution in the adaptation of maize to high-altitude environments in both Mexico and South America.
A collaboration with the Maize Diversity Project has also recently allowed us to take a population genomic approach to the study of maize domestication. Work is under way analyzing full-genome resequencing data from 75 maize and teosinte plants.
Centromere Evolution in Zea
The genus Zea is an excellent study system for investigating what is known as the “Centromere Paradox.” The paradox lies in centromeres serving an essential and conserved function while showing evidence of rapid evolution across taxa. We have developed a hierarchical panel including tropical and temperate inbred maize lines, maize landraces, wild subspecies, and sister species to explore the role of centromeres in Zea diversification. This panel is being used in several projects in our lab including population genetic analysis of centromeric and non-centromeric single nucleotide polymorphisms, sequence evolution of foundation kinetochore proteins, and cross-taxa characterization of centromeric repeats and retroelements. Collectively these studies will test hypotheses of transposon activity, meiotic drive, and speciation.
Ecological Genetics of Teosinte
Wild relatives of maize, teosintes, grow naturally in central and southwestern Mexico. Zea mays ssp. parviglumis and ssp. mexicana populations grow in varied environments from hot, mid-elevation (600 m) areas to cooler higher altitudes (>2500 m). Populations also differ in terms of phenology and morphology. We have sampled populations that represent both the genetic and environmental diversity of the two subspecies. We want to understand the genetic basis of adaptation to local conditions. Genome wide diversity and genetic differentiation among populations is used to identify the genomic regions and genes contributing to local adaptation. Further, the contribution of hybridization between teosinte and maize and its role on highland adaptation is inspected by studying sympatric and allopatric populations. Other work underway includes study of the evolutionary dynamics of a domestication gene in natural populations and the adaptive role of a large inversion polymorphism in teosinte.
Fruit & Nut Tree Genetics
Work in the lab includes collaboration on several projects involving fruit and nut tree genomics.
Working with the Walnut Genome Analysis group, we are creating a genetic map from a segregating population of 352 F1s using industry standard ‘Chandler’ as the maternal parent, and performing association mapping for several agronomic traits with a diverse walnut germplasm collection.
Almond production in California is limited by soilborne pests and diseases. To aid in the development of rootstocks with combined resistance, we are harnessing genomic resources of for almond, peach, and their wild relatives to identify SNPs that may associate with disease resistance.
Diospyros is pantropical genus best known for the persimmon and its ebony wood. We are working with both Sanger and next-generation sequencing of a number of Mexican taxa of Diospyros in order to better understand its phylogeny and genomics.
Working with the Walnut Genome Analysis group, we are creating a genetic map from a segregating population of 352 F1s using industry standard ‘Chandler’ as the maternal parent, and performing association mapping for several agronomic traits with a diverse walnut germplasm collection.
Almond production in California is limited by soilborne pests and diseases. To aid in the development of rootstocks with combined resistance, we are harnessing genomic resources of for almond, peach, and their wild relatives to identify SNPs that may associate with disease resistance.
Diospyros is pantropical genus best known for the persimmon and its ebony wood. We are working with both Sanger and next-generation sequencing of a number of Mexican taxa of Diospyros in order to better understand its phylogeny and genomics.