Molecular Genomics Laboratory
Welcome to the Molecular Genomics Lab
In our laboratory we apply genome-wide associations, functional genomics and systems genetics to dissect the molecular architecture of complex physiological traits important in swine and in human health. The goal of the swine research is to identify genes, genetic variants, and genetic networks that explain phenotypic variation of susceptibility to Porcine Circovirus 2b (funding from Genome Canada, 2011-1014) and sow reproductive logevity (funding from National Pork Board, 2010-2012 and NIFA, 2013-2015). We also use a mouse resource population (BXD family of strains) as a model for human health to uncover natural genetic variants that explain variation in gut microbial composition and also explore its impact on obesity and other metabolic phenotypes that affect health.
Genome-wide QTL mapping of Bacteroides composition in the gut of BXD RI mice (McKnite et al., 2012). The QTL located on mouse Chr 4 has potential effects across phyla. This locus (LRS=17.9, 87.58-95.23 Mb) explains 20% of the observed variation in the abundance of the genus Bacteroides and associated with suggestive effects in Firmicutes (LRS=13.38, P=0.27). C57BL/6J haplotype (red) is associated with a reduced level of Bacteroides while the DBA/2J haplotype (green) is associated with an increased level of Bacteroides. The QTL region is rich in genes from interferon family such as Ifna1, Ifna12 and Ifnab, all expressed in the cecum of BXD.
Daniel Ciobanu, PhD, Principal Investigator Sarah Barnes, Undergraduate Student Justin Bundy, Research Technician BS & MS, Oklahoma State University Emily Davis, Undergraduate Student Taylor Engle, MS Student BS, St. Lawrence University Erin Jobman, UCARE Student Craig Kreikemeier, DVM Student BS, University of Nebraska - Omaha Katie Lucot, MS Student BS, Cal Pomona Kim Smith, Undergraduate Student
Theresa Bohnert, MS (2011) BS, University of Missouri MS, UNL Jessica Qiu, Research Assistant Autumn McKnite, Research Technician BS, University of Minnesota Melissa Steiner, Undergraduate Student BS, UNL Julie Tart, MS (2012) BS, North-Carolina State University MS, UNL
NIFA: “Translational Genomics for Improving Sow Reproductive Longevity”; 01.01.2012 – 12.31.2014.
National Pork Board: “Genome-wide association analyses of sow reproduction and lifetime productivity”; 05.01.2011 – 05.01.2012.
National Pork Board: “Identification of markers associated with sow life time productivity for whole genomic selection”; 05.01.2009 – 05.01.2010.
- Tart J.K., R.K. Johnson, J.W. Bundy, N.N. Ferdinand, A.M. McKnite, J.R. Wood, P.S. Miller, M.F. Rothschild, M.L. Spangler, D.J. Garrick, S.D. Kachman, D.C. Ciobanu (2013) Genome-wide prediction of age at puberty and reproductive longevity in sows (in print, Animal Genetics).
- McKnite A.M, Perez-Munoz M.E., Lu L., Williams E.G., Brewer S., Andreux P., Wang X., Kachman S.D., Auwerx J., Williams R.W., Benson A.K., Peterson D.P., Ciobanu D.C (2012) Murine Gut Microbiota is Defined by Host Genetics and Modulates Variation of Metabolic Traits, PLoS One, 7(6):e39191. Epub 2012 Jun 18.
- Whitney I.E., Raven M.A., Ciobanu D.C., Poché R.A., Ding Q., Elshatory Y., Gan L., Williams R.W., Reese B.E. (2011) Genetic modulation of horizontal cell number in the mouse retina. Proc Natl Acad Sci U S A. 108: 9697-9702.
- Mozhui, K., R.-M. Karlsson, T.L. Kash, J. Ihne, M. Norcross, S. Patel, M. Camp, H.A. Cameron, D.C. Ciobanu, D.G. Winder, R.W. Williams, A. Holmes (2010) Neuronal and molecular correlates of trait and stress-induced variation in anxiety-like behavior between genetic mouse strains, Journal of Neuroscience 30: 5357-67.
- Kinghorn, B.P., J.W.M. Bastiaansen, D.C. Ciobanu, H.A.M. van der Steen (2010) Quantitative genotyping to estimate genetic contributions to pooled samples and genetic merit of the contributing entities. Acta Agriculturae Scandinavica Section A 60: 3-12.
- Ciobanu D.C., L. Lu, K. Mozui, X. Wang, M. Jagalur, J.A. Morris, W.L. Taylor, K. Dietz, P. Simon, R.W. Williams (2010) Dissection of expression variation and downstream analysis of cis-modulation. Genetics 184, 119-28.
- Du Z.-Q., D.C. Ciobanu, S.K. Onteru, D. Gorbach, A.J. Mileham, G. Jaramillo, M.F. Rothschild (2009) A Gene-based SNP Linkage Map for Pacific White Shrimp, Litopenaeus vannamei. Animal Genetics doi: 10.1111/j.1365-2052.2009.02002.x.
- Ciobanu, D.C., J.W.M. Bastiaansen, J. Magrin, J.L. Rocha, D.-H. Jiang, N. Yu, B. Geiger, N. Deeb, D. Rocha, H. Gong, B.P. Kinghorn, G.S. Plastow, H.A.M. van der Steen and A.J. Mileham (2010) A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei). Animal Genetics doi:10.1111/j.1365-2052.
- Mozhui K., Ciobanu D.C., Schikorski T., Wang X., Lu L., Williams R.W., (2008). Dissection of a QTL hotspot on mouse distal chromosome 1 that modulates neurobehavioral phenotypes and gene expression. PLoS Genet. 4: e1000260.
Molecular Genomics Lab Teaching
Instructor: Daniel Ciobanu
The genomes of humans and several livestock and plant species have been sequenced improving our ability to understand the genetic factors that influence variation of complex traits. This knowledge will be an important component of future animal and plant improvement methods and targeted interventions to enhance human health.
This course is designed for graduate and advance undergraduate studdents in all areas of life sciences. Students will be introduced to structure and function of eukaryotic genomes and to strategies used to identify genetic variants responsible for phenotypic differences.
Personalized genomics, social and ethical aspects associated with genomic information will be discussed.