NRSP_old8: National Animal Genome Research Program

(National Research Support Project Summary)

Status: Inactive/Terminating

SAES-422 Reports

06/10/2019

03/16/2020




    1. Liu R, Low WY, Tearle R, Koren S, Ghurye J, Rhie A, Phillippy AM, Rosen BD, Bickhart DM, Smith TPL, Hiendleder S, Williams JL. New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X


    and Y chromosomes. BMC Genomics. 2019 Dec 19;20(1):1000



    1. Fang L, Zhou Y, Liu S, Jiang J, Bickhart DM, Null DJ, Li B, Schroeder SG,


    Rosen BD, Cole JB, Van Tassell CP, Ma L, Liu GE. Comparative analyses of sperm


    DNA methylomes among human, mouse and cattle provide insights into epigenomic


    evolution and complex traits. Epigenetics. 2019 Mar;14(3):260-276.



    1. Liu S, Kang X, Catacchio CR, Liu M, Fang L, Schroeder SG, Li W, Rosen BD,


    Iamartino D, Iannuzzi L, Sonstegard TS, Van Tassell CP, Ventura M, Low WY,


    Williams JL, Bickhart DM, Liu GE. Computational detection and experimental


    validation of segmental duplications and associated copy number variations in


    water buffalo ( Bubalus bubalis ). Funct Integr Genomics. 2019 May;19(3):409-419.



    1. Johnson T, Keehan M, Harland C, Lopdell T, Spelman RJ, Davis SR, Rosen BD,


    Smith TPL, Couldrey C. Short communication: Identification of the pseudoautosomal


    region in the Hereford bovine reference genome assembly ARS-UCD1.2. J Dairy Sci.



    • ;102(4):3254-3258.



    1. Rowan TN, Hoff JL, Crum TE, Taylor JF, Schnabel RD, Decker JE. A multi-breed reference panel and additional rare variants maximize imputation accuracy in cattle. Genet Sel Evol. 2019 Dec 26;51(1):77.

    2. Smith JL, Wilson ML, Nilson SM, Rowan TN, Oldeschulte DL, Schnabel RD, Decker JE, Seabury CM. Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle. BMC Genomics. 2019 Dec 4;20(1):926.

    3. Zwane AA, Schnabel RD, Hoff J, Choudhury A, Makgahlela ML, Maiwashe A, Van Marle-Koster E, Taylor JF. Genome-Wide SNP Discovery in Indigenous Cattle Breeds of South Africa. Front Genet. 2019 Mar 29;10:273.

    4. Hoff JL, Decker JE, Schnabel RD, Seabury CM, Neibergs HL, Taylor JF. QTL-mapping and genomic prediction for bovine respiratory disease in U.S. Holsteins using sequence imputation and feature selection. BMC Genomics. 2019 Jul 5;20(1):555.

    5. Crum TE, Schnabel RD, Decker JE, Regitano LCA, Taylor JF. CRUMBLER: A tool for the prediction of ancestry in cattle. PLoS One. 2019 Aug 26;14(8):e0221471. =

    6. Maldonado MBC, de Rezende Neto NB, Nagamatsu ST, Carazzolle MF, Hoff JL, Whitacre LK, Schnabel RD, Behura SK, McKay SD, Taylor JF, Lopes FL. Identification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation. PLoS One. 2019 Sep 12;14(9):e0222329.

    7. Koltes JE, Cole JB, Serao N, McCue M, Woodward J, Zhang H, McKay S, Lunney J, Kramer L, Schroeder M, Clemmens R, Murdoch B, Rexroad C, Rosa G, Mateescu R, White S, Worku M, Reecy J. A vision for development and utilization of high-throughput phenotyping and big data analytics in livestock. Frontiers in Genetics (2019) Dec 17

    8. Cantrell B, Lachance H, Murdoch B, Sjoquist J, Funston R, Weaber R, McKay S. Global DNA methylation in the limbic system of cattle. Epigenomes – feature cover (2019) 3(2).

    9. Kern C, Wang Y, Chitwood J, Korf I, Delany M, Cheng H, Medrano JF, Van Eenennaam AL, Ernst C, Ross P, Zhou H. Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genomics. 2018 19(1):684.

    10. Mueller, M.L., Cole, J.B., Sonstegard, T.S., Van Eenennaam, A.L. 2019. Comparison of gene editing vs. conventional breeding to introgress the POLLED allele into the U.S. dairy cattle population. Journal of Dairy Science. 102(5): 1-12.

    11. Mueller, M.L., Cole, J.B., Sonstegard, T.S., Van Eenennaam, A.L. Simulation of introgression of the POLLED allele into the Jersey breed via conventional breeding vs. gene editing, Translational Animal Science, Volume 2, Issue suppl_1, September 2018, Pages S57–S60

    12. Van Eenennaam, A.L., Wells, K.D. and Murray, J.D. Proposed U.S. regulation of gene-edited food animals is not fit for purpose. npj Science of Food, 3(3).

    13. Rexroad, C.,Vallet, J., Kumar, L., Reecy, J., Bickhart, D., Blackburn, H., Boggess, M., Cheng, H., Clutter, A., Cockett, N., Ernst, C., Fulton, J., Liu, J., Lunney, J., Neibergs, H., Purcell, C., Smith, T., Sonstegard, T., Taylor, J., Telugu, B., Van Eenennaam, A., Van Tassell, C., and Wells, K. Genome to Phenome: Improving Animal Health, Production and Well-Being A New USDA Blueprint for Animal Genome Research 2018 - 2027. Frontiers in Genetics. 10:327.

    14. Dubrovsky, S., Van Eenennaam, A. L., Karle, B. M., Rossitto, P., Lehenbauer, T. and Aly, S. 2019. Epidemiology of Bovine Respiratory Disease (BRD) in preweaned calves on California dairies: The BRD 10K study. Journal of Dairy Science. 102:7306-7319.

    15. Dubrovsky, S., Van Eenennaam, A. L., Karle, B. M., Rossitto, P., Lehenbauer, T. and Aly, S. 2019. Bovine Respiratory Disease (BRD) cause-specific and overall Mortality in preweaned calves on California dairies: The BRD 10K study. Journal of Dairy Science. 102:7320-7328.

    16. Maier GU, Love WJ, Karle BM, Dubrovsky SA, Williams DR, Champagne JD, Anderson, RJ, Rowe JD, Lehenbauer TW, Van Eenennaam AL, Aly SS. 2019. Management factors associated with bovine respiratory disease in preweaned calves on California dairies: The BRD 100 study. Journal of Dairy Science. 102: 7288-7305

    17. Upperman, L.R., Kinghorn, B.P., MacNeil, M.D., Van Eenennaam, A.L. 2019. Management of lethal recessive alleles in beef cattle through the use of mate allocation software. Genetics, Selection, Evolution. 6;51(1):36.

    18. Van Eenennaam, A.L. 2019. Application of genome editing in farm animals: cattle. Transgenic Research. 28(Suppl 2):93-100.

    19. Young, A.E., T.A. Mansour, B.R. McNabb, J.R. Owen, J.F.Trott, C.T. Brown, and A.L. Van Eenennaam, 2020. Comparative evaluation of the phenotype and genome from offspring of a genome edited, hornless bull and controls. Nature Biotechology. 38:225–232.

    20. Kirkpatrick, B.W., R.M. Thallman and L.A. Kuehn. Validation of SNP associations with bovine ovulation and twinning rate.  Animal Genetics 50(3):259-261. doi: 10.1111/age.12793. Epub 2019 Apr 12.

    21. Lam, P.T., S.L. Padula, T.V. Hoang, J.E. Poth, L. Lin, C. Liang, A.S. LeFever, L.M. Wallace, R. Ashery-Padan, P.K. Riggs, J.E. Shields, O. Shaham, S. Rowan, N.L. Brown, T. Glaser, and M.L. Robinson. Considerations for the use of Cre recombinase for conditional gene deletion in the mouse lens. Human Genomics 10:13. https://doi.org/10.1186/s40246-019-0192-8

    22. Riley, David G., Rhonda K. Miller, K. L. Nicholson, Clare A. Gill, Andy D. Herring, Penny K. Riggs, Jason E. Sawyer, Jeffrey W. Savell, and James O. Sanders. 2019. “Genome Association of Carcass and Palatability Traits from Bos Indicus-Bos Taurus Crossbred Steers within Electrical Stimulation Status and Correspondence with Steer Temperament; 1. Carcass.” Livestock Science 229: 150–58.

    23. Riggs, Penny K., Michael J. Fields, and H. Russell Cross. 2018. “Food and Nutrient Security for a Growing Population Introduction.” ANIMAL FRONTIERS 8 (3): 3–4.

    24. Murano, Elsa A., H. Russell Cross, and Penny K. Riggs. 2018. “The Outbreak That Changed Meat and Poultry Inspection Systems Worldwide.” ANIMAL FRONTIERS 8 (4): 4–8.

    25. Littlejohn, Brittni P., Deborah M. Price, Don A. Neuendorff, Jeffery A. Carroll, Rhonda C. Vann, Penny K. Riggs, David G. Riley, Charles R. Long, Thomas H. Welsh Jr., and Ronald D. Randel. 2018. “Prenatal Transportation Stress Alters Genome-Wide DNA Methylation in Suckling Brahman Bull Calves.”J. Anim. Sci. 96 (12): 5075–99.



  1. Phillips, C.A., Reading, B.J., Livingston, M., Livingston, K. and Ashwell, C.M. Accepted. Evaluation via Supervised Machine Learning of the Broiler Pectoralis Major and Liver Transcriptome in Association with the Muscle Myopathy Wooden Breast. Frontiers in Physiology, in press.

  2. Hornick, K.M. and Plough, L.V., 2019. Tracking genetic diversity in a large-scale oyster restoration program: effects of hatchery propagation and initial characterization of diversity on restored vs. wild reefs. Heredity 123:92-105.

  3. Hughes, A.R., Hanley, T.C., Byers, J.E., Grabowski, J.H., McCrudden, T., Piehler, M.F. and Kimbro, D.L. 2019. Genetic diversity and phenotypic variation within hatchery‐produced oyster cohorts predict size and success in the field. Ecological Applications 29(6): e01940.

  4. Jaris, H., Brown, D.S. and Proestou, D.A. 2019. Assessing the contribution of aquaculture and restoration to wild oyster populations in a Rhode Island coastal lagoon. Conservation Genetics 20(3):503-516.

  5. Proestou, D.A. and Sullivan, M.E. 2020. Variation in global transcriptomic response to Perkinsus marinus infection among eastern oyster families highlights potential mechanisms of disease resistance. Fish and Shellfish Immunology 96:141-151.

  6. Proestou, D.A., Corbett, R.J., Ben‐Horin, T., Small, J.M. and Allen Jr, S.K., 2019. Defining Dermo resistance phenotypes in an eastern oyster breeding population. Aquaculture Research 50:2142-2154.

  7. Ali A., Al-Tobasei R., Lourenco D., Leeds T., Kenney B. & Salem M. (2019) Genome-Wide Association Study Identifies Genomic Loci Affecting Filet Firmness and Protein Content in Rainbow Trout. Frontiers in Genetics 10: 386.

  8. Chapagain P., Arivett B., Cleveland B.M., Walker D.M. & Salem M. (2019) Analysis of the fecal microbiota of fast- and slow-growing rainbow trout (Oncorhynchus mykiss). BMC Genomics 20: 788.

  9. Grummer, J.A., L.B. Behergaray, L. Bernatchez, B.K. Hand, G. Luikart, S.R. Narum, and E.B. Taylor. 2019. Aquatic landscape genomics and environmental effects on genetic variation. Trends in Ecology and Evolution 34:641-654.

  10. Janowitz-Koch, I., C. Rabe, R. Kinzer, D. Nelson, M.A. Hess, and S.R. Narum. 2019. Long-term evaluation of fitness and demographic effects of a Chinook salmon supplementation program. Evolutionary Applications 12:456-469.

  11. Pearse, D.E., Barson, N.J., Nome, T., Gao, G., Campbell, M.A., Abadía-Cardoso, A., Anderson, E.C., Rundio, D.E., Williams, T.H., Naish, K.A., Moen, T., Liu, S., Kent, M., Moser, M., Minkley, D.R., Rondeau, E.B., Brieuc, M.S.O., Sandve, S.R., Miller, M.R., Cedillo, L., Baruch, K., Hernandez, A.G., Ben-Zvi, G., Shem-Tov, D., Barad, O., Kuzishchin, K., Garza, J.C., Lindley, S.T., Koop, B.F., Thorgaard, G.H., Palti, Y., Lien, S. 2019. Sex-dependent dominance maintains migration supergene in rainbow trout. Nature Ecology and Evolution 3: 1731-1742.

  12. Silva, R.M.O., Evenhuis, J.P., Vallejo, R.L., Gao, G., Martin, K.E., Leeds, T.D., Palti, Y., Lourenco, D.a.L. 2019. Whole-genome mapping of quantitative trait loci and accuracy of genomic predictions for resistance to columnaris disease in two rainbow trout breeding populations. Genetics Selection Evolution 51: 42.

  13. Steele, C.A., M.A. Hess, S.R. Narum, M.R. Campbell. 2019. Parentage-based tagging: reviewing the implementation of a new tool for an old problem. Fisheries 44:412-422.

  14. Vallejo, R.L., Cheng, H., Fragomeni, B.O., Shewbridge, K.L., Gao, G., Macmillan, J.R., Towner, R. & Palti, Y. (2019). Genome-wide association analysis and accuracy of genome-enabled breeding value predictions for resistance to infectious hematopoietic necrosis virus in a commercial rainbow trout breeding population. Genetics Selection Evolution 51: 47.

  15. Weigel, D., F. Monzyk, C. Sharpe, S.R. Narum, C.C. Caudill. 2019. Evaluation of a trap-and-transport program for a threatened population of steelhead (Oncorhynchus mykiss). Conservation Genetics 20:1195-1199.

  16. Guillette, T.C., McCord, J., Guillette, M., Polera, M., Rachels, K.T., Morgeson, C., Kotlarz, N., Strynar, M., Knappe, D., Reading, B.J., and Belcher, S.M. 2019. Per and Polyfluoroalkyl Substance Exposure in Striped Bass (Morone saxatilis) of Cape Fear River is Associated with Biomarkers of Altered Immune and Liver Function. Environmental Science and Technology, in press.

  17. Abdelhamed, H., Ozdemir, O., Waldbieser, G., Lawrence, M.L., Karsi, A. 2019. Effects of florfenicol feeding on diversity and composition of the intestinal microbiota of channel catfish (Ictalurus punctatus). Aquaculture Research, in press.

  18. Bosworth, B., Waldbieser, G., Garcia, A., Tsuruta, S., Lourenco, D. 2019. Heritability and response to selection for carcass yield and growth in the Delta Select strain of channel catfish, Ictalurus punctatus. Aquaculture, in press.

  19. Bosworth, B., Waldbieser, G., Garcia, A., Lourenco, D. 2019. Effect of pond- or strip-spawning on growth and carcass yield of channel catfish progeny. Journal of the World Aquaculture Society, in press.

  20. Zhang, Y., Liu, Z.J., and Li, H. 2020. Genomic prediction of columnaris disease resistance in catfish. Marine Biotechnology, in press.

  21. Tan, S., Wang, W., Tian, C., Niu, D., Zhou, T., Yang, Y., Gao, D., and Liu, Z.J. 2019. Post-transcriptional regulation through alternative splicing after infection with Flavobacterium columnare in channel catfish (Ictalurus punctatus). Fish and Shellfish Immunology 91: 188-193.

  22. Rexroad, C., Vallet, J., Matukumalli, L.K., Reecy, J., Bickhart, D., Blackburn, H., Boggess, M., Cheng, H., Clutter, A., Cockett, N., Ernst, C., Fulton, J., Liu, Z.J,, Lunney, J., Neibergs, H., Purcell, C., Smith, T., Sonstegard, T., Taylor, J., Telugu, B., Van Eenennaam, A., Van Tassell, C., and Wells, K. 2019. Genome to phenome: improving animal health, production and well-being: a new USDA blueprint for animal genome research 2018-2027. Frontiers in Genetics 10: 327.

  23. Tan, S., Wang, W., Zhou, T., Yang, Y., Gao, D., and Liu, Z.J. 2019. Polyadenylation sites and their characteristics in the genome of channel catfish (Ictalurus punctatus) as revealed by using RNA-Seq data. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 30: 248-255.

  24. Gao, L., Yuan, Z., Zhou, T., Yang, Y., Gao, D., Dunham, R., and Liu, Z.J. 2019. Foxo genes in channel catfish and their response after bacterial infection. Developmental and Comparative Immunology 97: 38-44.

  25. Wang, W., Tan, S., Luo, J., Shi, H., Jin, Y., Zhou, T., Wang, X., Yang, Y., Niu, D., Yuan, Z., Gao, D., Dunham, R., and Liu, Z.J. 2019. GWAS analysis indicated importance of NF- κB signaling pathway in host resistance against motile Aeromonas septicemia disease in catfish. Marine Biotechnology 21: 335-347.

  26. Bao, L., Tian, C., Liu, S., Zhang, Y., Elaswad, A., Yuan, Z., Khalil, K., Sun, F., Yang, Y., Zhou, T., Ning, L., Tan, S., Zeng, Q., Liu, Y., Li, Y., Li, Y., Gao, D., Dunham, R., Davis, K., Waldbieser, G., and Liu, Z.J. 2019. The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish. BMC Biology 17: 6.

  27. Tan, S., Wang, W., Tian, C., Niu, D., Zhou, T., Jin, Y., Yang, Y., Gao, D., Dunham, R., and Liu, Z.J. 2019. Heat stress induced alternative splicing in catfish as determined by transcriptome analysis. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 29: 166-172.

  28. Zhang, X., Yuan, J., Sun, Y., Li, S., Gao, Y., Yu, Y., Liu, C., Wang, Q., Lv, X., Zhang, X., Ma, K.Y., Wang, X., Lin, W., Wang, L., Zhu, X., Zhang, C., Zhang, J., Jin, S., Yu, K., Kong, J., Xu, P., Chen, N., Zhang, H.-B., Sorgeloos, P., Sagi, A., Warren, A., Liu, Z.J., Wang, L., Ruan, J., Chu, K., Liu, B., Li, F., and Xiang, J. 2019. Penaeid shrimp genome provides insights into benthic adaptation and frequent molting. Nature Communications 10:356.

  29. Li, N., Bao, L., Zhou, T., Yuan, Z., Liu, S., Dunham, R., Li, Y., Wang, K., Xu, X., Jin, Y., Zeng, Q., Gao, S., Fu, Q., Liu, Y., Yang, Y., Li, Q., Meyer, A., Gao, D., and Liu, Z.J. 2019. Genome sequence of walking catfish (Clarias batrachus) provides insight into terrestrial adaptation. BMC Genomics 19: 952.

    1. Greene E., J Flees, A Dhamad, A Alrubaye, S Hennigan, J Pleimann, M Smeltzer, S Murray, J Kugel, J Goodrich, A Robertson, R Wideman, D Rhoads, S Dridi. (2019). Double-stranded RNA is a novel molecular target in osteomyelitis pathogenesis: A translational avian model for human bacterial chondronecrosis with osteomyelitis', The American Journal of Pathology 189(10): 2077-2089. doi.org/10.1016/j.ajpath.2019.06.013

    2. Al-Zahrani K, T Licknack, DL Watson, NB Anthony, DD Rhoads. (2019) Further Investigation of Mitochondrial Biogenesis and Gene Expression of Key Regulators in Ascites- Susceptible and Ascites-Resistant Broiler Research Lines. PLOS One 14: e0205480 doi.org/10.1371/journal.pone.0205480

    3. Tarrant K, JE Fulton, A Lund, DD Rhoads, NB Anthony. 2018. Predicting ascites incidence in a simulated altitude-challenge using single nucleotide polymorphisms identified in multi-generational genome wide association studies. Poultry Science 97(11):3801-3806. org/10.3382/ps/pey273.

    4. Dey S., A. Parveen, K.J. Tarrant, T. Licknack, B.C. Kong, N.B. Anthony, D.D. Rhoads. 2018. Whole Genome Resequencing Identifies the CPQ Gene as a Determinant of Ascites Syndrome in Broilers. PLOS One 13(1): e0189544. doi.org/10.1371/journal.pone.0189544.

    5. Lassiter K, Kong B, Piekarski-Welsher A, Dridi S, and Bottje WG. 2019. Gene expression essential for myostatin signaling and skeletal muscle development is associated with divergent feed efficiency in pedigree male broilers. Frontiers in Physiology. 10:126.

    6. Khatri, B., S. Kang, S. Shouse, N. Anthony, W. Kuenzel and B.C. Kong. 2019. Copy number variation study in Japanese quail associated with stress related traits using whole genome re-sequencing data. PLoS ONE 14(3): e0214543. doi.org/10.1371/journal.pone.0214543.

    7. Kang, S.W., K.D. Christensen, D. Aldridge and W.J. Kuenzel. 2019. Effects of light intensity and dual light intensity choice on plasma corticosterone, central serotonergic and dopaminergic activities in birds, Gallus gallus. Gen. Comp. Endocrinol. doi.org/10.1016/j.ygcen.2019.113289.

    8. Kadhim, H.K., M. Kidd Jr., S.W. Kang and W.J. Kuenzel. 2019. Differential delayed responses of arginine vasotocin and its receptors in septo-hypothalamic brain structures and anterior pituitary that sustain hypothalamic-pituitary-adrenal (HPA) axis functions during acute stress. Gen. Comp. Endocrinol. doi.org/10.1016/j.ygcen.2019.113302.

    9. Kadhim, H.K., S.W. Kang and W.J. Kuenzel. 2019. Differential and temporal expression of corticotropin releasing hormone and its receptors in the nucleus of the hippocampal commissure and paraventricular nucleus during the stress response in chickens (Gallus gallus). Brain Res. 1714:1-7. doi.org/10.1016/j.brainres.2019.02.018.

    10. Saelao, P., Y. Wang, G. Chanthavixay, V. Yu, J. Dekkers, R. Gallardo, T.R. Kelly, S.J. Lamont. Zhou, H. 2018. Integrated proteomic and transcriptomic analysis of differential expression of chicken lung tissue in response to NDV infection during heat stress. Genes 9, 579; doi:10.3390/genes9120579.

    11. Silva APD, Hauck R, Kern C, Wang Y, Zhou H, Gallardo RA. 2019 Effects of Chicken MHC Haplotype on Resistance to Distantly Related Infectious Bronchitis Viruses. Avian Dis. 63(2):310-317. doi: 10.1637/11989-103118-Reg.1

    12. Litvak Y., K.K.Z. Mon, H. Nguyen, G. Chanthavixay, M. Liou, E. M. Velazquez, L. Kutter, M. A. Alcantara, M. X. Byndloss, C.R. Tiffany, G. T. Walker, F. Faber, Y. Zhu, D. N. Bronner, A. J. Byndloss, R. M. Tsolis, H. Zhou. A. J. Baumler. 2019. Commensal Enterobacteriaceae protect against Salmonella colonization by competing for oxygen. Cell Host & Microbe 25, 1-12https://doi.org/10.1016/j.chom.2018.12.003.

    13. Rowland K, Saelao P, Wang Y, Fulton JE, Liebe GN, McCarron AM, Wolc A, Gallardo RA, Kelly T, Zhou H, Dekkers JCM, Lamont SJ. 2018. Association of Candidate Genes with Response to Heat and Newcastle Disease Virus. Genes (Basel). 9(11). pii: E560. doi: 10.3390/genes9110560.

    14. Cadena M, Froenicke L, Britton M, Settles ML, Durbin-Johnson B, Kumimoto E, Gallardo RA, Ferreiro A, Chylkova T, Zhou H, Pitesky M. 2019. Transcriptome analysis of Salmonella Heidelberg after exposure to cetylpyridinium chloride, acidified calcium hypochlorite, and peroxyacetic acid. Journal of Food Protection, Vol. 82, No. 1, 2019, Pages 109–119 doi:10.4315/0362-028X.JFP-18-235.

    15. Saelao, P., Y. Wang, G. Chanthavixay, J. Dekkers, R. Gallardo, A. Wolc. T.R. Kelly, S.J. Lamont. Zhou, H. 2019. Genetics and Genomic Regions Affecting Response to Newcastle Disease Virus Infection under Heat Stress in Layer Chickens. Genes (Basel). 2019 Jan 18;10(1). pii: E61. doi: 10.3390/genes10010061.

    16. Walugembe M, Mushi JR, Amuzu-Aweh EN, Chiwanga GH, Msoffe PL, Wang Y, Saelao P, Kelly T, Gallardo RA, Zhou H, Lamont SJ, Muhairwa AP, Dekkers JCM. 2019. Genetic Analyses of Tanzanian Local Chicken Ecotypes Challenged with Newcastle Disease Virus. Genes (Basel). 2019 Jul 17;10(7). pii: E546. doi: 10.3390/genes10070546.

    17. Egaña-Labrin, S. R. Hauck, A. Figueroa, S. Stoute, H.L. Shivaprasad, M. Crispo, C. Corsiglia, H. Zhou, C. Kern, B. Crossley, R. Gallardo. 2019. Genotypic Characterization of Emerging Avian Reovirus Molecular Variants in California. Sci Rep (9), Article number: 9351 (2019).

    18. Adentunji, M., Lamont, S.J., Abasht, B.A., and Schmidt, C. J. 2019. Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data. PLOS ONE 14(9): e0216838.doi.org/10.1371/journal.pone.0216838

    19. Monson, M.S., Van Goor, A.G., Persia, M.E., Rothschild, M. F., Schmidt, C.J., Lamont, S.J. 2019. Genetic lines respond uniquely within the chicken thymic transcriptome to acute heat stress and low dose lipopolysaccharide. Scientific Reports 9:13649 doi.org/10.1038/s41598-019-50051-0

    20. Barrett, N.W., Schmidt, C.J., Lamont, S.J., Ashwell, C.M., Persia, M.E. 2019. Effects of acute and chronic heat stress on the performance, egg quality, body temperature and blood gas parameters of laying hens. Poultry Science. http://dx.doi.org/10.3382/ps/pez541

    21. Schilling, M., Memari, S., Cavanaugh, M., Katani, R., Deist, M.S., Radzio-Basu, J., Lamont. S.J., Buza, J.J., and Kapur, V. 2019. Conserved, breed-dependent, and subline-dependent innate immune responses of Fayoumi and Leghorn chicken embryos to NDV infection. Scientific Reports 9:7209 doi.org/10.1038/s41598-019-43483-1.

    22. Rowland, K., Ashwell, C.M. Persia, M.P., Rothschild, M.F., Schmidt, C., Lamont, S.J. 2019. Genetic analysis of production, physiologic, and egg quality traits in heat-challenged commercial white egg-laying hens using 600k SNP array data. Genetics Selection Evolution 51:31 doi.org/10.1186/s12711-019-0474-6

    23. Elbeltagy, A.R., Bertolini, F., Fleming, D.S., Van Goor, A., Ashwell, C.M., Schmidt, C.J., Kugonza, D., Lamont, S.J., Rothschild, M.F. 2019. Natural selection footprints among African chicken breeds and village ecotypes. Front. Genet. 10:376. doi: 10.3389/fgene.2019.00376

    24. Rowland, K., Persia, M., Rothschild, M., Schmidt, C., Lamont, S. 2019. Blood gas and chemistry components are moderately heritable in commercial white egg-laying hens under acute or chronic heat exposure. Poultry Science 0:1–5 http://dx.doi.org/10.3382/ps/pez204

    25. Walugembe, M., Bertolini, F., Dematawewa, C.M.B., Reis, M.P., Elbeltagy, A.R., Schmidt, C.J., Lamont, S.J., and Rothschild, M.F. 2019. Detection of selection signatures among Brazilian, Sri Lankan, and Egyptian chicken populations under different environmental conditions. Front. Genet. doi: 10.3389/fgene.2018.00737

    26. Zhuo, Z., Lamont, S., Abasht, B. 2019. RNA-Seq analyses identify additivity as the predominant gene expression pattern in F1 chicken embryonic brain and liver. Genes 10, 27; doi:10.3390/genes10010027

    27. Drobik-Czwarno, W., Wolc, A., Kucharska, K.,Martyniuk. E., Genetic basis of resistance to highly pathogenic avian influenza in chicken. Review article in Polish. Scientific Annals of Polish Society of Animal Production.

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