Animal Genetics and Genomics Laboratory Publications

The FAANG Project (Functional Annotation of Animal Genomes) Related Publications

  • Kingsley NB, Kern C, Creppe C, Hales EN, Zhou H, Kalbfleisch TS, MacLeod JN, Petersen JL, Finno CJ, Bellone RR.  2020.  Functionally annotating regulatory elements in the equine genome using histone mark ChIP-Seq.  Genes. 11:3. doi.org/10.3390/genes11010003.
  • Gurgul A, Szmatoła T, Ocłoń E, Jasielczuk I, Semik-Gurgul E, Finno CJ, Petersen JL, Bellone RR, Hales EN, Ząbek T, Arent Z, Kotula-Balak M, Bugno-Poniewierska M. 2022. Another lesson from unmapped reads – in depth analysis of RNA-Seq reads from various horse tissues.  Journal of Applied Genetics.  doi:10.1007/213353-022-00705-z.
  • Peng S, Petersen JL, Bellone RR, Kalbfleisch T, Kingsley NB, Barber AM, Cappelletti E, Giulotto E, Finno CJ. 2021. Decoding the Equine Genome: Lessons from ENCODE. Genes. 12(11): 1707. doi.org/10.3390.genes12111707.
  • Peng S, Bellone RR, Petersen JL, Kalbfleisch TS, Finno CJ.  Successful ATAC-seq from snap-frozen equine tissues. 2021. Frontiers in Genetics. 12:641788. doi:10.3389/fgene.2021.641788.
  • Kingsley NB, Hamilton N, Lindgren G, Orlando L, Bailey E, Brooks SB, McCue M, Kalbfleisch TS, MacLeod JN, Petersen JL, Finno CJ, Bellone RR. 2021. Adopt-a-tissue initiative advances efforts to identify tissue-specific histone marks in the mare.  Frontiers in Genetics.  12:390. doi:10.3389/fgene.2021.649959.
  • Donnelly CG, Bellone RR, Hales E, Nguyen A, Katzman S, Dujovne G, Knickelbein K, Avila F, Kablfleisch T, Guiulotto E, Kingsley NB, Tanaka J, Esedaile E, Peng S, Dahlgren A, Fuller A, Mienaltowski M, Raudsepp T, Affolter V, Petersen JL, Finno CJ.  2021. Generation of a Biobank From Two Adult Thoroughbred Stallions for the Functional Annotation of Animal Genomes Initiative.  Frontiers in Genetics.  12:301. doi:10.3389/fgene.2021.650305.
  • Kingsley NB, Kern C, Creppe C, Hales EN, Zhou H, Kalbfleisch TS, MacLeod JN, Petersen JL, Finno CJ, Bellone RR.  2020.  Functionally annotating regulatory elements in the equine genome using histone mark ChIP-Seq.  Genes. 11:3. doi.org/10.3390/genes11010003.
  • Burns EN, Bordbari M, Mienaltowski MJ, Affolter VK, Barro MV, Gianino F, Gianino G, Giulotto E, Kalbfleisch TS, Katzman SA, Lassaline M, Leeb T, Mack M, Müller EJ, MacLeod JN, Ming-Whitfield B, Alanis CR, Raudsepp T, Scott E, Vig S, Zhou H, Petersen JL, Bellone RR, Finno CJ.  2018. Generation of an equine functional annotation of animal genomes biobank.  Animal Genetics. 49(6):564-570.  doi: 10.1111/age.12717.

Studies of Population (Breed) Diversity Related Publications

  • Wilson CS, Petersen JL, Blackburn HD, Lewis RM. 2022. Assessing population structure and genetic diversity in the US Suffolk sheep to define a framework for genomic selection.  Journal of Heredity.  113:431-443. doi:10.1093/jhered/esac026.
  • Yousefi Mashouf N, Mehrabani Yeganeh H, Nejati Javaremi A, Bailey E, Petersen JL. 2021. Genomic comparisons of Persian Kurdish, Persian Arabian, and American Thoroughbred horse populations.  PLoS One. 16(2):e0247123. doi:10.1371/journal.pone.0247123.
  • Tozaki T, Kikuchi M, Kakoi H, Hirota K, Nagata S, Yamashita D, Ohnuma T, Takasu M, Kobayashi I, Hobo S, Manglai D, Petersen JL. 2019.  Genetic diversity and relationships among native Japanese horse breeds, the Japanese Thoroughbred, and horses outside of Japan using genome-wide SNP data.  Animal Genetics.  50:449-459. doi.org/10.1111/age.12819.
  • Petersen JL, Mickelson JR, Valberg SJ, McCue ME.  2015.  Genome-wide SNP data shows little differentiation between the Appaloosa and other American stock horse breeds.  Animal Genetics. 46:585-586.
  • Petersen JL, Mickelson JR, Cleary KD, McCue ME.  2014.  The American Quarter Horse: Population structure and relationship to the Thoroughbred.  Journal of Heredity.  105:148-162.
  • Petersen JL, Mickelson JR, Cothran EG, 34 others, McCue ME.  2013.  Genetic diversity in the modern horse illustrated from genome-wide SNP data.  PLoS One 8(1): e54997. doi10.1371/journal.pone.0054997.

Impact of Heat Stress On Animal Welfare and Productivity Related Publications

  • Sieck RL, Treffer LK, Fuller AM, PointeViana M, Khalimonchuk O, Schmidt TB, Yates DT, Petersen JL. 2022. Beta-adrenergic agonists alter oxidative phosphorylation in primary myoblasts.  Journal of Animal Science. 100(8):skac208. doi: 10.1093/jas/skac208
  • Reith RR, Sieck RL, Grijalva PC, Swanson R, Fuller AM, Diaz DE, Schmidt TB, Yates DT, Petersen JL. 2022. Transcriptome analyses indicate that heat stress-induced inflammation in white adipose tissue and oxidative stress in skeletal muscle is partially moderated by zilpaterol supplementation in beef cattle.  Journal of Animal Science. 100(3):skac109. doi.org/10.1093/jas/skac019.
  • Burrack RM, Duffy EM, Yates DT, Schmidt TB, Petersen JL. 2020.  Whole blood transcriptome analysis in feedlot cattle after 35-days of supplementation with a β1-adrenergic agonist.  Journal of Applied Genetics. 61:117-121. do.org/10.1007/s13353-019-00527-6.
  • Barnes TB, Burrack RM, Schmidt TB, Petersen JL, Yates DT. 2021. Sustained heat stress elevated corneal and body surface temperatures and altered circulating leukocytes and metabolic indicators in wether lambs supplemented with ractopamine or zilpaterol. Journal of Animal Science. 99:skab236. doi:10.1093/jas/skab236.
  • Burrack RM, Duffy EM, Yates DT, Schmidt TB, Petersen JL. 2020.  Whole blood transcriptome analysis in feedlot cattle after 35-days of supplementation with a β1-adrenergic agonist.  Journal of Applied Genetics. 61:117-121. do.org/10.1007/s13353-019-00527-6.
  • Barnes TB, Cadaret C, Beede K, Schmidt TB, Petersen JL, Yates DT.  2019.  Hypertrophic muscle growth and metabolic efficiency were impaired by chronic heat stress, improved by zilpaterol supplementation, and not affected by ractopamine supplementation in feedlot lambs.  Journal of Animal Science.  97:4101-4113. doi:10/1093/jas/skz271.
  • Sieck RL, Fuller AM, Bedwell PS, Ward JA, Sanders SK, Xiang S-H, Peng S, Petersen JL, Steffen DJ. 2020. Mandibulofacial dysostosis attributed to a recessive mutation of CYP26C1 in Hereford cattle.  Genes. 11:1246.  doi:10.3390/genes11111246
  • Petersen JL, Tietze SM, Burrack RM, Steffen DJ. 2019. Evidence for a de novo, dominant germ-line mutation causative of osteogenesis imperfecta in two Red Angus calves. Mammalian Genome.  doi:10.1007/s00335-019-09794-4.