Molecular Cytogenetics and Genomics Laboratory

RESEARCH

Recent Publications:

Raudsepp T, McCue ME, Das PJ, Dobson L, Vishnoi M, Fritz KL, Schaefer R, Rendahl AK, Derr JN, Love CC, Varner DD, Chowdhary BP. Genome-Wide Association Study Implicates Testis-Sperm Specific FKBP6 as a Susceptibility Locus for Impaired Acrosome Reaction in Stallions. PLoS Genet. 2012 Dec;8(12):e1003139.
PubMed PMID: 23284302

Steelman SM, Chowdhary BP, Dowd S, Suchodolski J, Janečka JE. Pyrosequencing of 16S rRNA genes in fecal samples reveals high diversity of hindgut microflora in horses and potential links to chronic laminitis. BMC Vet Res. 2012 Nov 27;8:231. PubMed PMID: 23186268

Steelman SM, Chowdhary BP. Plasma proteomics shows an elevation of the anti-inflammatory protein APOA-IV in chronic equine laminitis. BMC Vet Res. 2012 Sep 27;8:179. PubMed PMID: 23016951

Das PJ, Lyle SK, Beehan D, Chowdhary BP, Raudsepp T. Cytogenetic and molecular characterization of Y isochromosome in a 63XO/64Xi(Yq) mosaic karyotype of an intersex horse. Sex Dev. 2012;6(1-3):117-27. PubMed PMID: 22005008

Raudsepp T, Das PJ, Avila F, Chowdhary BP. The pseudoautosomal region and sex chromosome aneuploidies in domestic species. Sex Dev. 2012;6(1-3):72-83. PubMed PMID: 21876343

Avila F, Das PJ, Kutzler M, Owens E, Perelman P, Rubes J, Hornak M, Johnson WE, Raudsepp T. Development and Application of Camelid Molecular Cytogenetic Tools. J Hered. 2012 Oct 29. [Epub ahead of print] PubMed PMID: 23109720

Fellows E, Kutzler M, Avila F, Das PJ, Raudsepp T. Ovarian Dysgenesis in an Alpaca with a Minute Chromosome 36. J Hered. 2012 Sep 24. [Epub ahead of print] PubMed PMID: 23008444

Janecka J, Chowdhary B, Murphy W. Exploring the correlations between sequence evolution rate and phenotypic divergence across the Mammalian tree provides insights into adaptive evolution. J Biosci. 2012 Nov;37(5):897-909. PubMed PMID: 23107925

Genome Structure and Evolution

We are studying the structure and evolution of genomes using both traditional approaches, such as karyotyping, fluorescent in situ hybridization (FISH), construction of contigs of overlapping of BACs, development of gene maps, and Sanger sequencing, and combine them with the latest technological advancements, including whole genome tiling arrays and next-generation 454 sequencing. We previously developed a physical map of the equine genome that was critical during the annotation of the equine genome sequence assembly. Our studies compare chromosome structure and gene content between and within species, and also examine various rearrangements that affect the phenotype of individuals and cause major physical abnormalities, such as XY sex reversal. Recently, we have characterized the equine Pseudoautosomal Region (PAR) and created a physical ordered map of the male-specific region of the Y chromosome (MSY) that we are using to sequence and assemble the MSY. The evolutionary dynamics of this region are very different from that of autosomes and the X. We are currently identifying MSY genes that are important for male fertility, sex development, and other traits.

Genetic Basis of Equine Disease

In parallel with our investigation of the equine genome, we are also leveraging the resources that we have developed to study the genetic basis of several equine diseases such as Recurrent Airway Obstruction, Contracted Foal Syndrome, and infertility. Our approaches include Genome Wide Association studies using the Affymetrix equine SNP chip, gene expression microarrays, candidate gene mapping, microsatellite linkage studies, and proteomics. Under collaboration with Dr. Adelson (University of Adelaide), we recently developed a whole genome tiling array for horses so that we can also examine the contribution of copy number variation.

We are currently examining the role of major chromosomal rearrangements in equine reproductive disorders. Recently we have determined there is heterogeneity in the mutations responsible for XY sex reversal in horses. The MSY portion of the Y chromosome harbors testis-specific genes that have been tied to fertility disorders in humans and mice. Yet, the role they play in other species remains to be discovered. Interestingly, many important gene families present on the Y are lineage specific, for example, some the ones present in humans are not found in chimpanzees. We are therefore focusing on identifying and characterizing comparable MSY male-specific genes and gene families in horses, and examining their role in stallion fertility.

Equine Laminitis

Laminitis is one of the most significant equine diseases facing the horse industry today. The acute form may be brought on by overconsumption of grain or lush pasture, severe illness or infection, prolonged weight bearing, or even metabolic syndrome. We are using a combination of functional genomics techniques, including transcriptomics, 16S pyrosequencing, proteomics, and metabolomics to create a detailed picture of the complex events that precipitate acute laminitis. Our research has led to the identification of several genes that are differentially expressed in all models of laminitis, suggesting that these genes are integral to disease pathogenesis. In addition, we are currently exploring the potential use of a metabolic biomarker to identify horses at risk of developing laminitis after colic.

Although most researchers focus exclusively on acute laminitis, many horses live for years with chronic laminitis. In addition to chronic foot pain and lameness, this disease can also cause poor body condition and changes in systemic immunity. In collaboration with Dr. David Hood of The Hoof Project, we have recently described how chronic laminitis affects the way that the horse's immune system responds to challenges. We have also discovered several molecular pathways underlying the poor hoof growth that is characteristic of this disease. We are currently exploring the use of neutraceuticals to address both problems in foundered horses.

The laminitis projects are led by Dr. Samantha Steelman along with Daisy Johnson (M.S. student) and Amy Jackson (B.S. student).

Alpaca Genomics

In 2005, the alpaca became the first camelid species to have its genome sequenced, in an effort led by Dr. Warren Johnson at the National Cancer Institute. The Alpaca Genome Project, which also includes the generation of a medium-density Radiation Hybrid (RH) map for the alpaca, set the foundation for genomic studies in camelids. Such studies are critical for the development of molecular tools for reliable disease diagnostics and treatment in alpacas that will improve the health and welfare of these animals. In order to develop such useful tools detailed knowledge of the alpaca genome is needed. Therefore, our lab is currently developing a comprehensive cytogenetic map using Fluorescence in situ Hybridization (FISH). This cytogenetic map aims to efficiently integrate the genome sequence, RH map, and physical chromosome structure, as well as map candidate genes for traits of economic and biological importance in alpacas. Such genes include candidates for disease resistance, congenital disorders, reproduction, fiber color and texture. We are also interested in comparing the genome organization of alpacas and dromedary camels by constructing an alpaca/camel comparative chromosome map, in order to further understand camelid chromosome evolution. Finally, we are using the molecular markers generated by the alpaca cytogenetic map to study chromosomal abnormalities that affect the health of different camelid species.

Conservation Genetics

We are studying the population structure and genomic diversity of endangered species using microsatellite genotyping and sequence analysis of mtDNA and nuclear genomes. Some of our work includes studies on ocelots and bobcats in Texas. However, our main focus is on the snow leopard; a species for which very little information is available. We are conducting noninvasive genetic surveys of snow leopards in Mongolia in partnership with Dr. Munkhtsog (Irbis Mongolia and Mongolian Academy of Sciences) and Dr. Rodney Jackson (Snow Leopard Conservancy), and are also working with researchers in other countries including Bhutan, Nepal, India, China, Tajikistan, and Kyrgyzstan. This approach has yielded some of the first quantitative estimates of abundance derived from genetic analysis of snow leopard scats. Landscape connectivity is one of the most important parameters in conservation because it influences population persistence and the response of species to disturbance. Therefore, we are also currently examining phylogeography and landscape genetics of snow leopards. This information will be used to prioritize areas for conservation and to aid in the development of effective conservation initiatives in Mongolia, and other range countries. You can learn more about applications of genetics to snow leopard conservation and wildlife monitoring by listening to a radio interview of Dr. Janecka by Dibesh Karmachayra (Center for Molecular Dynamics-Nepal) on KEEPS FM98.3 Kathmandu (March 2010), when Janecka went there to train technicians in nonivasive methodogy: March 2010 Interview Part 1 & Part 2. Janecka's look back on 2010 in the Snow Leopard Conservancy Live Journal.

Emilee Larkin, who worked in the lab for two years as an undergraduate thesis researcher and is now in vet school, has been studying the genetic basis of the white coat color in tigers. Click here to read more about her project.

Adaptation to Environmental Stressors

We are studying how species adapt to environmental stressors with a focus on the snow leopard in partnership with Dr. Munkhtsog (Irbis Mongolia and Mongolian Academy of Sciences), Dr. Rodney Jackson (Snow Leopard Conservancy), and Drs. Satish Kumar and Ajay Gaur (Center for Cellular and Molecular Biology, India). The snow leopard shares its most recent common ancestor with the tiger; they diverged about 2 million years ago. Despite their close relationship they have evolved remarkably different ecology and behavior. The snow leopard is a species found in rugged, mountainous areas and occurs at very high-altitudes (above 12,000 feet) in Central Asia, yet in places like Mongolia it is found at lower elevations (below 7,000 feet). The high altitude populations are subject to great environmental stressors including low levels of oxygen, cold temperatures, and low moisture availability. We are studying how molecular adaptations have enabled snow leopards to thrive in this challenging environment. Initially, the project is focusing on globins because they influence the amount of oxygen carried in blood, however, we will also expand this to other genes that likely play a role.