Selected Publications | Douglas Rhoads

Selected Publications from the Research of Douglas Rhoads

Rhoads, D.D., Pummill, J. and Alrubaye, A.A.K. (2024) Molecular Genomic Analyses of Enterococcus cecorum from Sepsis Outbreaks in Broilers. Microorganisms Vol. 12 Issue 2 Pages 250 https://doi.org/10.3390/microorganisms12020250
Shwani, A.; Zuo, B.; Alrubaye, A.; Zhao, J.; Rhoads, D.D. (2024) A Simple, Inexpensive Alkaline Method for Bacterial DNA Extraction from Environmental Samples for PCR Surveillance and Microbiome Analyses. Applied Sciences, 14, 141. https://doi.org/10.3390/app14010141
Rhoads, D.D., N.S. Ekesi, A.A.K. Alrubaye, J. Pummill (2023) Horizontal transfer of a probable chicken-pathogenicity mobile genetic element from Staphylococcus aureus to Staphylococcus agnetis. PLoS One 18: e0283914. org/10.1371/journal.pone.0283914
Foley, SL, S Algarni, J Han, DD Gudeta, BK Khajanchi, SC Ricke, YM Kwon and DD Rhoads (2023) In silico analyses of diversity, and dissemination of antimicrobial resistance genes and mobile genetics elements, for plasmids of enteric pathogens. Frontiers in Microbiology 13:2022. doi.org/10.3389/fmicb.2022.1095128
Lee K, Anthony N, Orlowski S, Rhoads D. 2022. SNP-based breeding for broiler resistance to ascites and evaluation of correlated production traits. Hereditas 159 article 9 (2022)
Bowman, A.; Fitzgerald, C.; Pummill, J.F.; Rhoads, D.D.; Yamashita, T. (2021). Reduced Toxicity of Centruroides vittatus (Say, 1821) May Result from Lowered Sodium β Toxin Gene Expression and Toxin Protein Production. Toxin, 13: 828. https://doi.org/10.3390/toxins13110828
Ekesi NS, Hasan A, Parveen A, Shwani A, Rhoads D. 2021. Embryo Lethality Assay for Evaluating Virulence of Isolates from Bacterial Chondronecrosis with Osteomyelitis in Broilers. Poultry Science 100:101455
Ekesi NS, Hasan A, Alrubaye A, Rhoads D. 2021. Genomic comparisons of bacterial isolates from lame broilers. Poultry Science 100 (7):101148
Rhoads DD, Wideman RF (2020) Physiological challenges in poultry breeding. In: Advances in poultry genetics and genomics, edited by S. E. Aggrey, H. Zhou, M. Tixier-Boichard and D. Rhoads. Burley Dodds Science Publishing 2020
Alrubaye AAK, Ekesi NS, Hasan A, Elkins E, Ojha S, Zaki S, Dridi S, Wideman RF, Rebollo MA, Rhoads DD (2020) Chondronecrosis with Osteomyelitis in Broilers: Further Defining Lameness-Inducing Models with Wire or Litter Flooring, to Evaluate Protection with Organic Trace Minerals. Poultry Science 99 (11):5422-5429.
Alrubaye A, Ekesi NS, Hasan A, Koltes DA, Wideman Jr R, Rhoads D (2020) Chondronecrosis with osteomyelitis in broilers: Further defining a bacterial challenge model using standard litter flooring and protection with probiotics. Poultry Science 99 (12):6474-6480.
Parveen A, Jackson C, Dey S, Tarrant KJ, Anthony NB, Rhoads DD. 2020. Identification and validation of quantitative trait loci for ascites in broilers using whole genome resequencing. BMC Genetics: 21:54 (online)
Shwani A, PRF Adkins, NS Ekesi, A Alrubaye, MJ Calcutt, JR Middleton, DD Rhoads (2020). Whole genome comparisons of Staphylococcus agnetis isolates from cattle and chickens. Applied and Environmental Microbiology. 86 (12): e00484-20
Rhoads DD, Robert F. Wideman J. 2020. Physiological challenges in poultry breeding, 18pp. In: Advances in poultry genetics and genomics, Editors: Aggrey SE, Zhou H, Tixier-Boichard M, Rhoads D, Burley Dodds Science Publishing, Cambridge, UK.
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
Greene, E., Flees, J., Dhamad, A., Alrubaye, A., Hennigan, S., Pleimann, J., Smeltzer, M., Murray, S., Kugel, J., Goodrich, J., Robertson, A., Wideman, R., Rhoads, D. & Dridi, S. (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.
Yamashita T, DD Rhoads, J Pummill. (2019) Genome Report: Genome Analyses of a New Mycoplasma Species From the scorpion Centruroides vittatus. G3: Genes|Genomes|Genetics 8:993-997 doi.org/10.1534/g3.118.200858
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
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.
Yamashita T, D Rhoads, J Pummill. 2018. The complete mitochondrial genome of the scorpion Centruroides vittatus (Arachnida: Scorpiones). Mitochondrial DNA Part B: Resources (TMDN) doi: 10.1080/23802359.2017.1407685
Emami N.K., A. Golian, M.D. Mesgaran, N.B. Anthony, D.D. Rhoads. 2017. Mitochondrial biogenesis and PGC1α gene expression in male broilers from ascites susceptible and resistant lines. Journal of Animal Physiology and Animal Nutrition doi: 1111/jpn.12706
Albalawi TA, D Rhoads, and R Barabote 2017. Draft genome sequence of Anoxybacillus sp. strain UARK-01, a new thermophilic lignin-utilizing bacterium isolated from soil in Arkansas, USA. Genome Announcements 5: e00588-17
Emami N.K., A. Golian, M.D. Mesgaran, N.B. Anthony, D.D. Rhoads. 2017. Mitochondrial biogenesis and PGC1α gene expression in male broilers from ascites susceptible and resistant lines. Journal of Animal Physiology and Animal Nutrition 10.1111/jpn.12706
Krishna S, KJ Tarrant, DD Rhoads, and NB Anthony. 2017. Effects of a chromosome 9 quantitative trait locus for ascites on economically important traits in broilers. Poultry Science 10.3382/ps/pex154
Tarrant KJ, S Dey, R. Kinney R, NB Anthony and DD Rhoads. 2017. Multi-generational genome wide association studies identify chromosomal regions associated with ascites phenotype. Poultry Science 96:1544-1552.
Kodambashi Emami, N., A. Golian, D.D. Rhoads, M. Danesh Mesgaran. 2017. Interactive effects of temperature and dietary supplementation of arginine or guanidinoacetic acid on nutritional and physiological responses in male broiler chickens. British Poultry Science, 1-8. doi:10.1080/00071668.2016.1257779
Dey S., S. Krishna, N.B. Anthony, D.D. Rhoads. 2017. Further investigation of a quantitative trait locus for ascites on chromosome 9 in broiler chicken lines. Poultry Science 96:788–797 DOI:10.3382/ps/pew380
Al-Rubaye A.A.K., N.S. Ekesi, S. Zaki, N.K. Emami, R.F. Wideman Jr, D.D. Rhoads. 2017. Chondronecrosis with Osteomyelitis in Broilers: Further Defining a Bacterial Challenge Model Using the Wire Flooring Model. Poultry Science 96:332–340. doi: 10.3382/ps/pew299
Lind CM, B. Flack, D.D. Rhoads, and S.J. Beaupre. (2016) The mating system and reproductive life history of female Timber Rattlesnakes in northwestern Arkansas. Copeia 2016(2):518-528
Mandal, R. K., T. Jiang, A. A. Al-Rubaye, D. D. Rhoads, R. F. Wideman, J. Zhao, I. Pevzner, and Y. M. Kwon. 2016. An investigation into blood microbiota and its potential association with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers. Scientific Reports 6:25882. doi 10.1038/srep25882.
Al-Rubaye, A.A.K., M.B. Couger, S. Ojha, J.F. Pummilll, J.A. Koon II, R.F. Wideman, and D.D. Rhoads (2015). Genome analysis of Staphylococcus agnetis, an agent of lameness in broiler chickens. PLoS One 10(11): e0143336.
Schmid, M., J. Smith, D. W. Burt, B. L. Aken, P. B. Antin, A. L. Archibald, C. Ashwell, P. J. Blackshear, C. Boschiero, C. T. Brown, S. C. Burgess, H. H. Cheng, W. Chow, D. J. Coble, A. Cooksey, R. P. M. A. Crooijmans, J. Damas, R. V. N. Davis, D. J. de Koning, M. E. Delany, T. Derrien, T. T. Desta, I. C. Dunn, M. Dunn, H. Ellegren, L. Eöry, I. Erb, M. Farré, M. Fasold, D. Fleming, P. Flicek, K. E. Fowler, L. Frésard, D. P. Froman, V. Garceau, P. P. Gardner, A. A. Gheyas, D. K. Griffin, M. A. M. Groenen, T. Haaf, O. Hanotte, A. Hart, J. Häsler, S. B. Hedges, J. Hertel, K. Howe, A. Hubbard, D. A. Hume, P. Kaiser, D. Kedra, S. J. Kemp, C. Klopp, K. E. Kniel, R. Kuo, S. Lagarrigue, S. J. Lamont, D. M. Larkin, R. A. Lawal, S. M. Markland, F. McCarthy, H. A. McCormack, M. C. McPherson, A. Motegi, S. A. Muljo, A. Münsterberg, R. Nag, I. Nanda, M. Neuberger, A. Nitsche, C. Notredame, H. Noyes, R. O”Connor, E. A. O”Hare, A. J. Oler, S. C. Ommeh, H. Pais, M. Persia, F. Pitel, L. Preeyanon, P. Prieto Barja, E. M. Pritchett, D. D. Rhoads, C. M. Robinson, M. N. Romanov, M. Rothschild, P. F. Roux, C. J. Schmidt, A. S. Schneider, M. Schwartz, S. M. Searle, M. A. Skinner, C. A. Smith, P. F. Stadler, T. E. Steeves, C. Steinlein, L. Sun, M. Takata, I. Ulitsky, Q. Wang, Y. Wang, W. C. Warren, J. M. D. Wood, D. Wragg and H. Zhou (2015). “Third Report on Chicken Genes and Chromosomes 2015.” Cytogenetic and Genome Research 145(2): 79-180.
Zhang, G., C. Li, Q. Li, B. Li, D. M. Larkin, C. Lee, J. F. Storz, A. Antunes, M. J. Greenwold, R. W. Meredith, A. Ödeen, J. Cui, Q. Zhou, L. Xu, H. Pan, Z. Wang, L. Jin, P. Zhang, H. Hu, W. Yang, J. Hu, J. Xiao, Z. Yang, Y. Liu, Q. Xie, H. Yu, J. Lian, P. Wen, F. Zhang, H. Li, Y. Zeng, Z. Xiong, S. Liu, L. Zhou, Z. Huang, N. An, J. Wang, Q. Zheng, Y. Xiong, G. Wang, B. Wang, J. Wang, Y. Fan, R. R. da Fonseca, A. Alfaro-Núñez, M. Schubert, L. Orlando, T. Mourier, J. T. Howard, G. Ganapathy, A. Pfenning, O. Whitney, M. V. Rivas, E. Hara, J. Smith, M. Farré, J. Narayan, G. Slavov, M. N. Romanov, R. Borges, J. P. Machado, I. Khan, M. S. Springer, J. Gatesy, F. G. Hoffmann, J. C. Opazo, O. Håstad, R. H. Sawyer, H. Kim, K.-W. Kim, H. J. Kim, S. Cho, N. Li, Y. Huang, M. W. Bruford, X. Zhan, A. Dixon, M. F. Bertelsen, E. Derryberry, W. Warren, R. K. Wilson, S. Li, D. A. Ray, R. E. Green, S. J. O’Brien, D. Griffin, W. E. Johnson, D. Haussler, O. A. Ryder, E. Willerslev, G. R. Graves, P. Alström, J. Fjeldså, D. P. Mindell, S. V. Edwards, E. L. Braun, C. Rahbek, D. W. Burt, P. Houde, Y. Zhang, H. Yang, J. Wang, A. G. Consortium*, E. D. Jarvis, M. T. P. Gilbert, and J. Wang. 2014. Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346:1311-1320. doi 10.1126/science.1251385. *-D. Rhoads is one of 19 members of the Avian Genome Consortium
Krishanmoorthy, S., C.S. Smith, A.A. Al-Rubaye, G.F. Erf, R.F. Wideman, N.B. Anthony, and D.D. Rhoads. 2014. A quantitative trait locus for ascites on chromosome 9 in broiler chicken lines. Poultry Science93:307-317.
Yamashita, T., and D. D. Rhoads. 2013. Species Delimitation and Morphological Divergence in the Scorpion Centruroides vittatus (Say, 1821): Insights from Phylogeography. PloS ONE 8, e68282.
Wideman, R. F., D. D. Rhoads, G. F. Erf, and N. B. Anthony. 2013. Pulmonary arterial hypertension (ascites syndrome) in broilers: A review. Poultry Sci 92, 64-83.
Froman, D. P., and D. D. Rhoads. 2012. A systems biology definition for chicken semen quality. Journal of Animal Science. Published online before print October 16, 2012, doi: 10.2527/jas.2012-5681
Froman, D. P., and D. D. Rhoads. 2012. Validation of a spectrophotometer-based method for estimating daily sperm production and deferent duct transit. Poultry Science 91: 2621-2627.
DA Kanayeva, R Wang, D Rhoads, GF Erf, MF Slavik, S Tung, Y Li (2012) Efficient separation and sensitive detection of Listeria monocytogenes using an impedance immunosensor based on magnetic nanoparticles, microfluidic chip and interdigitated microelectrode. Journal of Food Protection 75:1951-1959
JR Burks and DD Rhoads. (2011) Sequence Analysis of the Angiotensin II Type 1 Receptor (AGTR1) Gene for Mutations Contributing to Pulmonary Hypertension in the Chicken (Gallus gallus). Inquiry 12:49-59
RF Wideman, KR Hamal, MT Bayona, AG Lorenzoni, D Cross, F Khajali, DD Rhoads, GF Erf, and NB Anthony. (2011) Plexiform Lesions in the Lungs of Domestic Fowl Selected for Susceptibility to Pulmonary Arterial Hypertension: Incidence and Histology. The Anatomical Record 294:739-755
DP Froman, AK Feltmannn, K Pendarvis, AM Cooksey, SC Burgess, and DD Rhoads. (2011) A proteome-based model for sperm mobility phenotype. Journal of Animal Science 89:1330-1337.
M. Hester and D.D. Rhoads (2009) Evolution of Gene Structure in Multicellular Eukaryotes. Inquiry 10:43-48. Supplementary Figures
S. Bailes, J. Devers, J.D. Kirby and D.D. Rhoads. (2007) An Inexpensive, Simple Protocol for DNA Isolation from Blood for High Throughput Genotyping by Polymerase Chain Reaction or Restriction Endonuclease Digestion. Poultry Science 86:102-106.
L.C. Overton, and D.D. Rhoads. (2006) Molecular phylogenetic relationships of Xiphidopicus percussus, Melanerpes, and Sphyrapicus (Aves: Picidae) based on cytochrome b sequence. Molecular Phylogenetics and Evolution 41:288-294.
D.P. Froman, J.D. Kirby, and D.D. Rhoads. (2006) An Expressed Sequence Tag Analysis of the Chicken Reproductive Tract Transcriptome. Poultry Science 85:1438-1441.
L.C. Overton, and D.D. Rhoads (2004) Molecular phylogenetic relationships based on mitochondrial and nuclear gene sequences for the Todies (Todus: Todidae) of the Caribbean. Molecular Phylogenetics and Evolution 32: 524-538.
I. Csiki, I, C. Lam, A. Key, E. Coulter, J.D. Clark, R.M. Pace III, K.G. Smith, and D. D. Rhoads (2003) Analysis of genetic variation in five black bear populations in Arkansas and Louisiana using microsatellite DNA markers. Journal of Mammalogy 84(2):691-701.
J.M. Walker and D.D. Rhoads (2003) The Black Racerunner (Cnemidophorous nigricolor Peters, 1873) in Los Roques Archipelago, Venezuela. Herpetological Review 34(2):105-109.
J.Q. Xia, J.C. Correll, F.N. Lee, W.J. Ross, and D.D. Rhoads (2000) Regional population diversity of Pyricularia grisea in Arkansas and the influence of host selection. Plant Disease 84:877-884.
Kirby, JD, DP Froman and DD Rhoads (2000) Heritable sperm degeneration in the domestic fowl, p 201-212 in The Testis: From Stem Cell to Sperm Function, E Goldberg, ed., Springer, NY.
N. Nakamichi, D. Rhoads, J. Hayashi, Y. Kagawa and T. Matsumura (1998) Detection, Localization and Sequence Analyses of Mitochondrial Regulatory Region RNAs in Several Mammalian Species. Journal of Biochemistry 123:392-398.
M.R. Stevens, J.W. Scott, P.D. Griffiths, D.K. Heiny, and D.D. Rhoads (1996) A linkage map of the tomato spotted wilt virus resistance gene Sw-5 using near isogenic lines and an interspecific cross. Acta Horticulturae 431:385-392.
M.R. Stevens, E.M. Lamb, and D.D. Rhoads (1995). Mapping the Sw-5 locus for tomato spotted wilt virus resistance in tomatoes using RAPD and RFLP analyses. Theoretical and Applied Genetics 90:451-456.
J.C. Correll, D.D. Rhoads, and J.C. Guerber (1993). Examination of mitochondrial DNA restriction fragment length polymorphisms, DNA fingerprints, and randomly amplified polymorphic DNA of Colletotrichum orbiculare. Phytopathology 83:1199-1204.
J.Q. Xia, J.C. Correll, F.N. Lee, M.A. Marchetti, and D.D. Rhoads (1993). DNA fingerprinting to examine microgeographic variation in the Magnaporthe grisea (Pyricularia grisea) population in two rice fields in Arkansas. Phytopathology 83:1029-1035.
P.F. Overman, D.D. Rhoads, E.S. Tasheva, M.M. Pyle, and D.J. Roufa (1993). Multiple regulatory elements ensure accurate transcription of a human ribosomal protein gene. Somatic Cell and Molecular Genetics 19(4):347-362
J.-J. Diaz, D.D. Rhoads, and D.J. Roufa (1991). PCR-mediated chemical (PMC) mutagenesis of cloned duplex DNAs. BioTechniques 11(2):204-211.
D.D. Rhoads and D.J. Roufa (1991). Molecular evolution of the mammalian ribosomal protein gene RPS14. Molecular Biology and Evolution 8(4):503-514.
J.-J. Diaz, D.D. Rhoads and D.J. Roufa (1990). Genetic analysis of a vital mammalian housekeeping locus using CHO cells that express a transfected mutant allele. Somatic Cell and Molecular Genetics 16:517-528.
C.G. Maki, D.D. Rhoads, J.-J. Diaz, and D.J. Roufa (1990). A Drosophila ribosomal protein functions in mammalian cells. Molecular and Cellular Biology 10:4524-4528.