Bailey, Ernest

Ernest Bailey – AG – Veterinary Sciences

Horse Genome Analysis

Perform a training project on whole genome sequence analysis of an Arabian Horse. However, I will be doing the same analyses (variant characterization of the whole genome sequence) on several horses for my PhD dissertation which is advised by Professor Ernest Bailey at the Department of Veterinary Science, Gluck Equine Research Center. These analyses are computationally intensive and personal computers cannot handle them. Moreover, I have prepared a whole bunch of foundation files on my current DLX account for the mentioned analyses during my training project. Hence, it would be appreciated if you kindly extend my access to my current DLX account for the whole period of my PhD project.

My project will focus on the whole genome sequence analysis of several (5-10) Americal Saddlebred horses to identify causative genetic variants associated with swayback disorder (lordosis).

Students

Navid YousefiMashouf, Graduate Student

John E Eberth

My laboratory has conducted investigations related to gene mapping and use of genomic tools to discover genetic variants associated with desirable traits or with diseases of horses.  As the work progresses, more sophisticated bioinformatics approaches are required.

Current research plans involve the following two projects:

Investigation for genes introgressed from non-caballines to cabalines

A gene (CXCL16) was discovered in horses with two alleles, one of which is very similar to the gene found in non-caballine equids.   The similarity is greater than one would expect based on 4.5 million years of divergence between these species.  This gene plays a role in innate immunity for mammals. This observation leads to the hypothesis that genes from non-caballines introgressed into equids in the recent past, perhaps 500,000 years ago.  To investigate this hypothesis we will compare the whole genome sequences of domestic horses to whole genome sequences of zebras and asses, looking for regions of identity.  This project is led by Ernest Bailey (professor) and in collaboration with Ted Kalbfleisch (professor) at the University of Louisville.  Navid Yousefi-Mashouf is a graduate student at the University of Kentucky also working on the project.

Investigation of Evolutionary New Centromeres in Equids

At one time, centromeres were thought to require repetitive DNA sequences for function.  However, chromosome 11 in the horse was found to lack repetitive DNA sequences characteristic of the other centromeres.  Subsequently, studies in the donkey revealed 16 centromeres with a deficit of repetitive DNA sequence.  The hypothesis arising from these observations is that centromeres form based on epigenetic association of the histone CENP-A and that repetitive DNA sequences are subsequently acquired.  The family Equus appears unique among mammals in having a large number of the evolutionary new centromeres. Studies continue using CHiP-Seq to investigate the histones associated with the centromere and by mapping to reference genomes.  This project is led by Elena Giulotto (professor) at the University of Pavia, Italy and includes collaboration by Ernest Bailey (professor) and Navid Yousefi-Mashouf (graduate student) at the University of Kentucky.

Computational Methods

Both projects involve mapping of whole genome sequences or RNA-seq data to reference genomes, followed by identification of target regions and genetic variants using already developed and freely available software.

Software:

This project will primarily rely on open-source software such as BWA, SAMtools, cufflinks and other similar software.

• Cutadapt (https://code.google.com/p/cutadapt/)
• BWA (http://bio-bwa.sourceforge.net/)
• SAMtools (http://samtools.sourceforge.net/)
• Picard(http://picard.sourceforge.net/)
• Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/                                                                                                                                                                                                                                                                                                                                                             

Collaborators:

I am collaborating with Dr. Theodore Kalbfleisch from the University of Louisville, on the project with CXCL16 and with Elena Giulotto, University of Pavia, Italy with whom we are collaborating on investigations of centromeric epigenetics.  Graduate student, Navid YousefiMashouf is also working on these projects.