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Molecular Cytogenetics and Genomics Laboratory

Recent Publications


Avila F, Baily MP, Merriwether DA, Trifonov VA, Rubes J, et al. (2015) A cytogenetic and comparative map of camelid chromosome 36 and the minute in alpacas. Chromosome Res 23: 237-251.



Webb SJ, Zychowski GV, Bauman SW, Higgins BM, Raudsepp T, et al. (2014) Establishment, characterization, and toxicological application of loggerhead sea turtle (Caretta caretta) primary skin fibroblast cell cultures. Environ Sci Technol 48: 14728-14737.

Ghosh S, Qu Z, Das PJ, Fang E, Juras R, et al. (2014) Copy number variation in the horse genome. PLoS Genet 10: e1004712.

Fellows E, Kutzler M, Avila F, Das PJ, Raudsepp T (2014) Ovarian dysgenesis in an alpaca with a minute chromosome 36. J Hered 105: 870-874.

Avila F, Das PJ, Kutzler M, Owens E, Perelman P, et al. (2014) Development and application of camelid molecular cytogenetic tools. J Hered 105: 858-869.

Avila F, Baily MP, Perelman P, Das PJ, Pontius J, et al. (2014) A comprehensive whole-genome integrated cytogenetic map for the alpaca (Lama pacos). Cytogenet Genome Res 144: 196-207.



Li G, Davis BW, Raudsepp T, Pearks Wilkerson AJ, Mason VC, et al. (2013) Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution. Genome Res 23: 1486-1495.

Seabury CM, Dowd SE, Seabury PM, Raudsepp T, Brightsmith DJ, et al. (2013) A multi-platform draft de novo genome assembly and comparative analysis for the Scarlet Macaw (Ara macao). PLoS One 8: e62415.

Das PJ, Mishra DK, Ghosh S, Avila F, Johnson GA, et al. (2013) Comparative organization and gene expression profiles of the porcine pseudoautosomal region. Cytogenet Genome Res 141: 26-36.

Das PJ, McCarthy F, Vishnoi M, Paria N, Gresham C, et al. (2013) Stallion sperm transcriptome comprises functionally coherent coding and regulatory RNAs as revealed by microarray analysis and RNA-seq. PLoS One 8: e56535.


Raudsepp T, McCue ME, Das PJ, Dobson L, Vishnoi M, et al. (2012) Genome-wide association study implicates testis-sperm specific FKBP6 as a susceptibility locus for impaired acrosome reaction in stallions. PLoS Genet 8: e1003139.

Avila, F., Das, P.J., Kutzler, M., Owens, E., Perelman, P., Rubes, J., Johnson, W.E. and Raudsepp.T. 2012. Development and application of molecular tools for camelid cytogenetics. The Journal of Heredity (special issue for camelid genetics; accepted for publication).

Avila, F., Das, P.J., Kutzler, M.A., Owens, E., Perelman, P., Raudsepp, T. 2012. Development and application of molecular tools for camelid cytogenetics. Cytogenetics and Genome Research 136:314-359(11).

Das, P.J., Mishra, D. K., Avila, F., Johnson, G., Chowdhary, B. P., Raudsepp, T. 2012. Identification and expression analysis of the pig pseudoautosomal region using molecular cytogenetics approach. Cytogenet Genome Res 136:314-359(13).

Ferrer, M., Anderson, D., Jones, M., Raudsepp, T., Avila, F., Miesner, M., DeBey, B., Kutzler, M. 2012. Segmental aplasia of the right uterine horn with mucometra in an alpaca. JAVMA 241(6):697-700.

Janečka JE, Chowdhary B, Murphy WJ. 2012. Exploring the correlations between sequence evolution rate and phenotypic divergence across the Mammalian tree provides insights into adaptive evolution. Journal of Bioscience 37:1-13.

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

Steelman SM, Chowdhary BP. 2012. Plasma proteomics shows an elevation of the anti-inflammatory protein APOA-IV in chronic equine laminitis. BMC Vet Res. 8(179).

Steelman S, Chowdhary B, Suchodolski J, Dowd S, JanečkaJE. 2012. Pyrosequencing of 16s rRNA Genes in fecal samples reveals high diversity of hindgut microflora in horses and potential links to chronic laminitis. BMC Veterinary Research 8:231. DOI: 10.1186/1746-6148-8-231


Durkin K, Raudsepp T and Chowdhary BP (2011) Cytogenetic Evaluation of the Stallion. In Equine Reproduction. (Eds. A.O. McKinnon, E.L. Squires, W.E. Vaala and D.D. Varner), Wiley Blackwell, Ch. 306.

Kachroo, P., Ivanov, I., Davidson, L.A., Chowdhary, B.P., Lupton, J.R., Chapkin, R.S. 2011. Classification of Diet-Modulated Gene Signatures at the Colon Cancer Initiation and Progression Stages. Digestive Diseases and Sciences. 9:2595-604.

Paria, N.*, Raudsepp, T* ., Wilkerson, A.J., O'Brien, P.C.M., Ferguson-Smith, M.A., Love, C.C., Arnold, C., Rakestraw, P., Murphy, W.J., Chowdhary, B.P. (2011) A gene catalogue of the euchromatic male specific region of the horse Y chromosome: Comparison with human and other mammals. PLoS ONE 6(7):e212374: 1-13. *These authors have equal contribution

Raudsepp, T. and Chowdhary, B.P. 2011. Cytogenetics and physical chromosome maps. Chpt. 7. In: The Genetics of the Pig (Eds. A. Ruvinsky and M. Rothschild), CAB International, pp. 134-78.


Das, P.J., Paria, N., Gustafson-Seabury, A., Vishnoi, M., Chaki, S., Love, C.C., Varner, D.D., Chowdhary, B.P., Raudsepp, T. 2010. Total RNA isolation from stallion sperm and testis biopsies. Theriogenology, 74, 1099-1106

Das, P.J., Vishnoi, M., Kachroo, P., Wang, J., Love, C.C., Varner, D.D., Chowdhary, B.P., Raudsepp, T. 2010. Expression microarray profiling of sperm and testis mRNA of reproductively normal stallions. Animal Reproduction Science, 121S, S175.

Juras R., Raudsepp T., Das P.J., Conant E., Cothran E.G. 2010. XX/XY blood lymphocyte chimerism in heterosexual dizygotic American Bashkir Curly horse twins. J Equine Vet Sci 30, 575-580.

Raudsepp, T. , Durkin, K., Lear, T., Das, P.J., Avila, F. Kachroo, P., Chowdhary, B.P. 2010. Molecular heterogeneity of XY sex reversal in the horse. Animal Genetics 41 (Suppl. 2), 41-52 (Special Issue on Horse Genetics and Genomics).

Sudderth, A.K., Das, P.J., Varner, D.D., T. Raudsepp, T. 2010. Determination of optimal semen processing methods for total RNA isolation and sperm genomic analysis. Animal Reproduction Science, 121S, S149-S150.


Alizadeh, A., Hong, L.Z, Kaelin, C.B, Raudsepp, T, Manuel, H and Barsh, G.S. 2009. Genetics of Sex-linked yellow in the Syrian hamster. Genetics, 181(4):1427-1436.

Brinkmeyer-Langford, CL, Childers C. Fritz K. Gustafson- Seabury A. Cothran M. Raudsepp, T. Womack, JE and Skow, LC. 2009. A High Resolution RH Map of the Bovine Major Histocompatibility Complex. BMC Genomics, 10:182-191.

Bright LA, Burgess SC, Chowdhary BP, Swiderski CE, McCarthy FM. Structural and functional-annotation of an equine whole genome oligoarray. BMC Bioinformatics 2009;10: 1-8.

Das, P.J., Chowdhary, B.P., Raudsepp, T. 2009. Characterization of the bovine pseudoautosomal region (PAR) and comparison with sheep, goat and other mammalian PARs. Cytogenet. Genome Res., 126, 139-147.

Davis BW, Raudsepp T, Pearks Wilkerson AJ, Agarwala R, Schäffer AA, Houck M, Ryder OA, Chowdhdary BP, Murphy WJ. 2009. A high-resolution cat radiation hybrid and integrated FISH mapping resource for phylogenomic studies across Felidae. Genomics, 93:299-304.

Di Meo GP, Perucatti A, Peretti V, Incarnato D, Ciotola F, Liotta L, Raudsepp T, Di Berardino D, Chowdhary B, Iannuzzi L. 2009. The 450-band resolution G- and R-banded standard karyotype of the donkey (Equus asinus, 2n = 62). Cytogenet Genome Res. 125: 266-271.

Liu J, Westhusin M, Johnson G, Raudsepp T, Chowdhary B, Burghardt R, Long C, Kraemer D. 2009. Evaluation of culture systems for attachment and proliferation of the epithelial cells cultured from ovine semen. Anim Reprod Sci. 115: 49-57.

Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A, Tomsho LP, Packard M, Zhang Y, McClellan LR, Qi J, Zhao F, Gilbert MTP, Dalén L, Arsuaga JL, Ericson PGP, Huson DH, Helgen KM, Murphy WJ, Götherström A, Schuster SC (2009) The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Research 19:213-220. Received JOURNAL COVER.

Schneider, D.A, Tibary, A., Raudsepp, T., Das, P.J., O'Rourke, K.I. 2009. Blood chimerism confounds genetic relative susceptibility testing for classical scrapie in sheep. J.Vet. Diagnostic Investigation, 21:295-305.

Shields, J.E., K.J. Kochan, K.J., Jeong, J., Abbey, C.A., Raudsepp, T., Riggs, P.K. 2009. Initial characterization of a gene abundantly expressed in stallion testis. J. Equine Vet. Sci., 29, 324-325

Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR, Blöcker H, Distl O, Edgar RC, Garber M, Leeb T, Mauceli E, MacLeod JN, Penedo MCT, Raison JM, Sharpe T, Vogel J, Andersson L, Antczak DF, Biagi T, Binns MM, Chowdhary BP, Coleman SJ, Della Valle G, Fryc S, Guérin G, Hasegawa T, Hill EW, Jurka J, Kiialainen A, Lindgren G, Liu J, Magnani E, Mickelson JR, Murray J, Nergadze SG, Onofrio R, Pedroni S, Piras MF, Raudsepp T, Rocchi M, Røed KH, Ryder OA, Searle S, Skow L, Swinburne JE, Syvänen AC, Tozaki T, Valberg SJ, Vaudin M, White JR, Zody MC, Broad Institute Genome Sequencing Platfor, Broad Institute Whole Genome Assembly Team, Lander ES, and Lindblad-Toh K. 2009. Genome sequence, comparative analysis and population genetics of the domestic horse (Equus caballus). Science 326 (5954): 865-867.


Brinkmeyer-Langford C, Raudsepp T, Gustafson-Seabury A, Chowdhary BP. 2008. A BAC contig map over the proximal approximately 3.3 Mb region of horse chromosome 21. Cytogenet. Genome Res. 120:164-172.

Chowdhary, B.P., Paria, N.P., Raudsepp, T. 2008. Potential applications of equine genomics in dissecting diseases and fertility. Animal Reproduction Science, 107, 208-218.

Chowdhary BP, Raudsepp T. 2008. The Horse Genome Derby: racing from map to whole genome sequence. Chromosome Res. 16, 109-127.

Pearks-Wilkerson, A.J., Raudsepp, T., Graves, T., Warren, W., Chowdhary, B.P., Skow, L.C., Murphy, W.J. 2008. Physical mapping, gene discovery, and comparative analysis of X-degenerate genes from the domestic cat Y chromosome. Genomics, 92: 329-338.

Raudsepp, T. and Chowdhary, B.P. 2008. FISH for mapping single copy genes. In: Phylogenomics: Methods in Molecular Biology (Ed. W. Murphy), Humana Press, New Jersey, USA, pp.31-49.

Raudsepp, T. and Chowdhary, B. P. 2008. The horse pseudoautosomal region (PAR): characterization and comparison with the human, chimp and mouse PARs. Cytogenet. Genome Res. 121, 102-109.

Raudsepp, T., Gustafson-Seabury, A., Durkin, K., Wagner, M.L., Goh, G., Seabury, C.M., Brinkmeyer-Langford, C., Lee, E.-J., Agarwala, R., Stallknecht Rice, E., Schäffer, A.A., Skow, L.C., Tozaki, T., Yasue, H., M. Penedo, C.M., Lyons, L.A., Khazanehdari, K.A., Binns, M.M., MacLeod, J.N., Distl, O., Guérin, G., Leeb, T., Mickelson, J.R., Chowdhary, B.P. 2008. A 4103 marker integrated physical and comparative map of the horse genome, Cytogenet. Genome Res., 122, 28-36.


Chiang, H.-I., Zhou, H., Raudsepp, T., Jesudhasan, P.R., Zhu, J.J. 2007. Chicken CD69 and CD94/NKG2-like genes in a chromosomal region syntenic to mammalian natural killer gene complex. Immunogenetics 59, 603-611.

Coleman SJ, Gong G, Gaile DP, Chowdhary BP, Bailey E, Liu L, MacLeod JN (2007) Evaluation of Compass as a comparative mapping tool for ESTs using horse radiation hybrid maps. Anim Genet 38:294-302

Goh, G*, Raudsepp, T*, Durkin, K, Wagner, ML, Schäffer, AA, Agarwala, R, Tozaki, T, Mickelson, JR and Chowdhary, BP. 2007. High-resolution gene maps of horse chromosomes 14 and 21: additional insights into evolution and rearrangements of HSA5 homologues in mammals. Genomics 89:89-112. Received JOURNAL COVER, *equal contribution.

Hansen GR, Abbey CA, Gaile DP, Raudsepp T, Chowdhary BP, Womack JE, Gill CA. 2007. Assignment of six genes to bovine chromosomes 5 and 16 by fluorescence in situ hybridization, radiation hybrid mapping and genetic linkage analysis. Cytogenet. Genome Res. 116: 194-197.

Herszberg B, Mata X, Giulotto E, Decaunes P, Piras FM, Chowdhary BP, Chaffaux S, Guerin G (2007) Characterization of the equine glycogen debranching enzyme gene (AGL): Genomic and cDNA structure, localization, polymorphism and expression. Gene 404:1-9

Momozawa, Y., Takeuchi, Y.,Tozaki, T., Kikusui, T.,Hasegawa, T., Raudsepp, T., Chowdhary, B.P., Kusunose, R. and Mori, Y. 2007. SNP detection and radiation hybrid mapping horses of nine candidate genes for temperament. Animal Genetics, 38, 81-91.

Prause A, Guionaud CT, Klukowska-Rotzler J, Giulotto E, Magnani E, Chowdhary BP, Philipp U, Leeb T, Mevissen M (2007) Chromosomal assignment of five equine HTR genes by FISH and RH mapping. Anim Genet 38:83-4.

Stübs D, Kuiper H, Mömke S, Chowdhary BP, Distl O (2007) Assignment of the TYK2 gene to equine chromosome 7q12-q13. Archiv für Tierzucht 50:322-323.