training faculty

nnf fellows


research program



Michelle Halstead

3rd year PhD student in Integrated Genetics and Genomics
Member of Dr. Pablo Ross’ Lab

B.S., Animal Science, 2014, UC Davis
A.B., French, 2014, UC Davis

Development of a new organism from a single cell involves massive epigenetic reprogramming; however, the specific chromatin remodeling events that underlie embryonic totipotency have remained elusive thus far due to technical constraints. Consequently, my research uses a new technique to profile changes in open chromatin at base-pair resolution during preimplantation embryogenesis. Using bovine embryos as my model system, I aim to discern the relation of chromatin remodeling to 1) embryonic genome activation and 2) the first differentiation into the inner cell mass, which becomes the embryo proper, and the trophectoderm, which leads to extra-embryonic tissues. I am also currently involved in the functional annotation of the cattle, pig, and chicken genomes: a pilot project aimed at setting standards for future studies affiliated with the FAANG consortium (Functional Annotation of ANimal Genomes).

PAG 2016 - Poster: Ab initio identification of transcription start sites in the bovine genome
ISAG 2016 - Presentation: Profiling open chromatin in chicken tissues using ATAC-seq

2015 - Neal Jorgenson Cattle Travel Award to PAG 2016
2015 - Henry A. Jastro Graduate Research Scholarship Award
2014 - USDA National Need Ph.D. Fellowship: Genomics for Improving Animal Production

Mon, K. K., Saelao, P., Halstead, M. M., Chanthavixay, G., Chang, H. C., Garas, L., Maga, E. A., Zhou, H. (2015). Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks. Front Vet Sci, 2, 61.

Tasha Thompson

3rd year Ph.D. student in Integrated Genetics and Genomics
Member of Dr. Michael Miller’s Lab

B.S., Chemistry, 2012, University of Utah
B.S., Anthropology, 2012, University of Utah

I study the genetic basis of life history variation in steelhead trout and Chinook (King) salmon. While many salmon populations have declined in the past century due to habitat degradation and other human actions, some commercially desirable life history phenotypes have suffered disproportionate declines. For example, adult fish that migrate to their natal streams in a sexually immature state have much higher fat content and higher-quality meat than fish that mature in the ocean prior to migration. However, premature-migrating populations have experienced much sharper declines. Similarly, commercial fishing pressure has selected for fish that mature at younger ages, leading to a significant decrease in average fish size over the past century. Understanding the genetic basis of adult migration time and age at maturity is integral both for conserving declining phenotypes in native populations and producing high-quality hatchery-reared or farmed fish for harvest. My lab has identified the genetic basis of premature migration. I’m currently working on a project to characterize the dominance of the premature migration allele and identify novel loci that explain migration time variation within the premature migration phenotype. In addition, I successfully applied for permits to collect samples that will allow me to test for loci that influence age at maturity.

Coastwide Salmonid Genetics Meeting 2016 - Poster: Rapture Sequencing Analysis Identifies Locations where Hybridization Occurs Between Native Winter and Hatchery Summer Steelhead in the Willamette River Basin, Oregon

2016 - Diablo Valley Fly Fishermen Bob Wisecarver Scholarship
2015 - Best First Year Student Abstract, UC Davis Integrative Genetics and Genomics Colloquium
2015 - People’s Choice Award, Panel Discussion, UC Davis Interdisciplinary Graduate and Professional Student Symposium: Beyond GMO: The Genetics of Food
2014 - USDA National Need Ph.D. Fellowship: Genomics for Improving Animal Production

Daniel J. Prince, Sean M. O'Rourke, Tasha Q. Thompson, Omar A. Ali, Martha Arciniega, Hannah S. Lyman, Ismail K. Saglam, Anthony J. Clemento, Scott L. Harris, Thomas J. Hotaling, Andrew P. Kinziger, Adrian P. Spidle, John Carlos Garza, Devon E. Pearse, Michael R. Miller. The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation. In Prep.

Erin Burns

2nd year Ph.D. student in Animal Biology
Member of Dr. Carrie Finno’s Lab

B.S., Biology and Equestrian Studies, 2015, Rocky Mountain College

My current project focuses on performing a genome-wide association study, using a 670,000 single nucleotide polymorphism (SNP) array, to identify a major genetic locus associated with equine Neuroaxonal Dystrophy (NAD). Equine NAD is a neurodegenerative disorder that affects horses during the first year of life, resulting in ataxia (i.e. coordination). Previous studies have demonstrated that NAD-affected horses have an underlying genetic predisposition to develop the disease in addition to an associated temporal vitamin E deficiency. We currently have 128 horses genotyped across 670,000 SNPs and I will be using linear mixed models through the software programs GenABLE (Yurii Aulchenko, et al. 2007, Bioinformatics) and GEMMA (Xiang Zhou & Matthew Stephens. 2012, Nature Genetics) to analyze the data. I am also involved in the functional annotation of the horse genome as part of the FAANG consortium (Functional Annotation of ANimal Genomes). Additionally, I am involved in a second genome-wide association study to identify genetic loci associated with racing durability in Thoroughbred racehorses starting in August. This project is in collaboration with Doctors Sue stover, Cecilia Pendo and Rebecca Bellone.

2015 - USDA National Need Ph.D. Fellowship: Genomics for Improving Animal Production