Brief Summary of Minutes of Annual Meeting

Attendees:

• Technical Committee: Giridhar Athrey, Jack Dekkers, Yvonne Drechsler, Tae Hyun Kim, Susan J. Lamont, Fiona McCarthy, Tom E. Porter, Androniki Psifidi, Kent Reed, Douglas Rhoads, Jiuzhou Song, Roger A. Sunde, Hui Yu, Huaijun Zhou
• Other: Travis Williams

1. Call to Order:

The meeting was called to order by Yvonne Drechsler at 9:08 am.

2. Administrative Advisor Update (Sue Lamont):

• It is important to include a short impact statement in each station’s technical report.
• The governance term for officers (chair, secretary) has been changed from two years to one year, now that there is no NRSP8 poultry officer to participate in workshop organization
• Membership updates (e.g., members who have moved positions or retired) should be communicated by their experiment station administrators and then will be updated by the North Central Regional Association office. There are currently some non-active members.

3. Old Business (Yvonne Drechsler):

• Reminder: Station reports should be circulated through NIMSS to the Technical Committee members before the meeting. Members are encouraged to submit their reports as early as possible.

4. New Business (Yvonne Drechsler):

• Next Year's Chair: Tae Hyun Kim was announced as the next chair.
• Next Secretary Vote: Fiona McCarthy nominated Jiuzhou Song for secretary. Tom E. Porter seconded the nomination. The motion was approved with no opposing votes.
• Discussion of Next Year's Meeting: Alternatives to holding the 2026 meeting in conjunction with the PAG (Plant and Animal Genome) meeting were discussed, including the Annual Poultry Science Association (PSA) meeting.
• PSA Meeting Pros: Could promote membership and attendance of a broader poultry research community that could utilize ‘Advanced Technologies’ from NC1170; lower meeting attendance cost compared to PAG; genuine interest exists in bridging the genetics community and the general poultry science community.
• PSA Meeting Cons: The PSA program is already set; a separate session or symposium would need to be organized (a symposium would require manuscript obligations); only one Technical Committee meeting is authorized per federal fiscal year, meaning the next meeting would be in the summer of 2026.
• Decision: After discussion, a motion was made, seconded, and passed to hold next year’s NC1170 meeting and poultry workshop at PAG2026. The decision to move the meeting location will be made in 2026. Tom Porter will contact PSA leadership regarding future collaboration.
• Student Travel Support for 2026 Poultry Workshop: The following options for student travel support were discussed:

• USDA conference grant
• Research Coordination Network
• PSA support (Note: PSA membership must be current to take advantage of this support. Several members missed out on opportunities this year due to lapsed memberships. Members should ensure their PSA memberships are up-to-date.)
• Industry support

• NC1170 Visibility: Participation in the National Poultry Breeder’s Roundtable was encouraged to increase the visibility of NC1170.

5. Adjournment: The meeting was adjourned at 10:08 am.

Gene Nomenclature and Bioinformatics:

Researchers at the Arizona Agricultural Experiment Station, led by Fiona McCarthy, focused on improving chicken gene nomenclature.  They standardized gene names for 288 gene records and assigned informative names to previously uncharacterized genes.  These genes include 47 Scavenger Receptors, 46 Histidine triad nucleotide-binding proteins, 59 G2E3/PHF7 novel male germline factors, 79 novel ITPRIP genes, 90 protocadherin genes, and 56 nucleoporins.  This work involved collaboration with seven undergraduate students from the University of Arizona and researchers from Western University of Health Sciences, West Virginia University, Hy-Line International, NCBI, and the University of Cambridge.   

Adnan Alrubaye and Doug Rhoads, within the Arkansas station, continued to collaborate on lameness and other bacterial diseases affecting the broiler industry.  The main goal was to develop mitigation measures to reduce BCO lameness in broiler chickens.  Rhoads collaborated with station members in Delaware and Mississippi on bioinformatics of bacterial pathogen genomes.   

Disease Resistance and Immunity:

Iowa State University, led by Sue  Lamont and Jack Dekkers, maintained eight unique chicken genetic research lines.  These lines include highly inbred lines, MHC-congenic pairs of lines, a closed broiler population, and an advanced intercross line.  They collaborated with UC-Davis and Sokoine University in Tanzania to evaluate egg production and egg quality for indigenous chicken ecotypes.  They also conducted research on avian influenza-induced gene expression in diverse chicken lines.   

Researchers led by Yvonne Drechsler focused on generating transcriptome and genome annotation data from 20 tissues.  They also conducted variant calling and allele-specific expression (ASE) analysis, identifying thousands of significant ASE SNPs across intestinal tissues.  Further research focused on histone modification and DNA methylation to annotate candidate cis-regulatory elements.  They also investigated the role of Cluster Homolog Immunoglobulin-like Receptors (CHIRs) in avian immunity, using MHC-defined chicken lines as a model.   

Muscle Development and Meat Quality:

Researchers at the University of Delaware, led by Behnam Abasht and Carl J. Schmidt, focused on Wooden Breast myopathy in broiler chickens. They used spatial transcriptomics and RNA-sequencing to characterize the cell-type-specific expression profile and identify differentially expressed genes associated with Wooden Breast. They also investigated the role of candidate genes CNN1 and PHRF1 in satellite cell function and characterized the metabolic maturation of the post-hatch liver.

Researchers at the University of Minnesota, led by Kent M. Reed, investigated the influence of thermal challenge on turkey muscle development and meat quality.  They also completed the analysis and publication of a small RNAseq dataset examining the expression of hepatic miRNA in domestic and wild turkeys exposed to aflatoxin B1 challenge.  Additionally, they collaborated on projects examining age-dependent fertility loss in laying hens.   

Hui Yu and Ali Nazmi at The Ohio State University conducted research on the molecular characterization of satellite cell populations in the turkey pectoralis major muscle.  They collaborated with Sandra Velleman to perform RNA sequencing and compare the transcriptomic differences between fast-growing and slow-growing satellite cells.   

Genetic Mechanisms and Breeding:

Samuel E. Aggrey and collaborators focused on improving genetic parameter estimation of reproductive traits in poultry.  They investigated the effects of data transformations on heritability estimates and animal re-ranking for fertility, percent egg production, and hatch of fertiles.  They also explored imputation methods and efficient estimators to improve genetic parameter estimation under limited sampling.  Additionally, they incorporated SNP prioritization based on the fixation index (FST) statistic to optimize the genetic relationship matrix for genomic selection.  

Huaijun Zhou and collaborators at the University of California, Davis, focused on several projects, including functional validation of candidate enhancers and regulatory variants in the chicken genome using MPRAS, leveraging multi-tissue allele-specific epigenomic profiling to decipher the genetic architecture of complex traits, uncovering putative causal mechanisms for growth-related traits through comparative epigenomic analysis, and utilizing long-read sequencing to investigate RNA isoform diversity and uncover genetic mechanisms of growth.

Roger A. Sunde at the University of Wisconsin continued research on the effect of selenium (Se) status on the hepatic transcriptome of turkey poults. They also worked on identifying low and high molecular weight Se metabolites in turkeys fed high dietary selenium, collaborating with researchers in France.

Tool Development:

Tae Hyun Kim at Penn State University has developed user-friendly CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) transgenic DF-1, DT40 and LMH cell lines, providing affordable and novel avian research tools. These transgenic lines will facilitate gain- and loss-of-function studies by easily introducing guide RNAs, enabling precise gene modulation in vitro.

Aggrey, S. E. and R. Rekaya, 2024. Genetic factors affecting feed efficiency in meat-type chickens. In: Advances in Poultry Nutrition. (T. J. Applegate, Ed), Burleigh Dodds, Science Publishing, Cambridge, U. K. 17pp http://dx.doi.org/10.19103/AS.2024.0143.06   

Adomako, K., S. Sovi, B. Kyei, J. A. Hamidu, O. S. Olympio and S. E. Aggrey, 2024. Phenotypic characterization and analysis of genetic diversity between commercial crossbred and indigenous chickens from three different agro-ecological zones using DArT-Seq technology. PLoS ONE 19(5): e0297643. https://doi.org/10.1371/journal.pone.0297643   

Ariyo, O. W., J. Kwakye, S. Sovi, B. Aryal, E. Hartono, A. F. A. Ghareed, M. C. Milfort, A. L. Fuller, R. Rekaya and S. E. Aggrey, 2024. mRNA expression of kidney aquaporins and blood composition of meat-type chickens raised with or without glucose supplementation under cyclic heat or thermoneutral condition. Thermal Biology 126, 104003 https://doi.org/10.1016/j.jtherbio.2024.104003   

Asnayanti, A., Do, A., and Alrubaye, A. (2024). Microbiology, induction, and management practices to mitigate lameness caused by bacterial chondronecrosis with osteomyelitis in broiler chickens. Ger. J. Vet. Res 2024. pp:14-30. Doi: https://doi.org/10.51585/gjvr.2024.4.0106.   

Assumpcao, ALFV; K Arsi, A Asnayanti, KS Alharbi, ADT Do, QD Read, R Perera, A Shwani, A Hasan, SD Pillai, RC Anderson. AM Donoghue, DD Rhoads, PRR Jesudhasan, AAK Alrubaye (2024). Electron-Beam-Killed Staphylococcus Vaccine Reduced Lameness in Broiler Chickens. Vaccines 12, 1203. https://doi.org/10.3390/vaccines12111203   

Bierla K, Szpunar J, Lobinski R, Sunde RA. Use of laser-ablation inductively-coupled mass spectroscopy for analysis of selenosugars bound to proteins. Metallomics, 2025 (accepted 1/7/25, in press; submitted 9/26/24; revision submitted 11/4/2024)   

Bordini, M., Wang, Z., Soglia, F., Petracci, M., Schmidt, C.J. and Abasht, B., 2024. RNA-sequencing revisited data shed new light on wooden breast myopathy. Poultry Science, p.103902.   

Botchway, P.K., Amuzu-Aweh, E.N., Naazie, A., Aning, G.K., Otsyina, H.R., Saelao, P., Wang, Y., Zhou, H., Dekkers, J.C., Lamont, S.J. and Gallardo, R.A., 2024. Genotypic and phenotypic characterisation of three local chicken ecotypes of Ghana based on principal component analysis and body measurements. Plos one, 19(8), p.e0308420. https://doi.org/10.1371/journal.pone.0308420   

Chen Y, Kosonsiriluk S, Ehresmann L, Reed KM, Noll S, Wileman B, Studniski M, and Boukherroub K. 2024. Changes in adaptive immune cell count and localization in the reproductive tract of turkey breeder hens in response to artificial insemination throughout their laying cycle. Poultry Science, 2024:104448, https://doi.org/10.1016/j.psj.2024.104448.   

Degalez F, Charles M, Foissac S, Zhou H, Guan D, Fang L, Klopp C, Allain C, Lagoutte L, Lecerf F, Acloque H, Giuffra E, Pitel F, Lagarrigue S. Enriched atlas of IncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues. Sci Rep. 2024 Mar 19;14(1):6588. doi: 10.1038/s41598-024-56705-y.   

Drechsler Y, Ng T, Sparling B, Hawkins RD. 177 Functional Annotation of an Array of Immune Cells and Various Tissues in the Chicken. Journal of Animal Science. 2023 Nov 1;101(Supplement_2):24-5.   

Ghareeb AFA, Foutz JC, Schneiders GH, Richter JN, Milfort MC, Fuller AL, Rekaya R, Aggrey SE, 2024. Host transcriptome response to heat stress and Eimeria maxima infection in meat-type chickens. https://doi.org/10.1371/journal.pone.0296350   

House, LC, A Hasan, A Asnayanti, AAK Alrubaye, J Pummill, DD Rhoads (2024) Phylogenomic analysis of three distinct lineages uniting Staphylococcus cohnii and Staphylococcus urealyticus from diverse hosts. Microorganisms 12:1549.   

Jorud K, Mendoza KM, Kono T, Coulombe RA, and Reed KM. 2024. Differential hepatic expression of miRNA in response to aflatoxin B1 challenge in domestic and wild turkeys. Toxins, 16(11), 453. https://doi.org/10.3390/toxins16110453.   

Kanlisi, R. A. E. N. Amuzu-Aweh, A. Naazie, H. R. Otsyina, T. R. Kelly, R. A. Gallardo, S. J. Lamont, H. Zhou, J. Dekkers and B. B. Kayang. 2024. Genetic architecture of body weight, carcass, and internal organs traits of Ghanaian local chickens. Front. Genet. 15:1297034. doi: 10.3389/fgene.2024.1297034   

Klünemann, M., L. F. Romero, M. Acman, M. C. Milfort, A. L. Fuller, R. Rekaya, S. E. Aggrey, L. M. Payling and A. Lemme, 2024. Multitissue transcriptomics demonstrates the systemic physiology of methionine deficiency in broiler chickens. Animal 18, 101143. https://doi.org/10.1016/j.animal.2024.101143   

Milfort, M. C., A. F. A. Ghareeb, O. W. Ariyo, J. Kwakye, E. Hartono, S. Sovi, B. Aryal, A. L. Fuler, M. I. El Sabry, F. Stino, R. Rekaya and S. E. Aggrey, 2024. Renal Sugar Metabolites and mRNA Expression of Glucose Transporters in Meat-Type Chickens with Differing Residual Water Intake. Animals 2024, 14(19), 2912; https://doi.org/10.3390/ani14192912   

Paez, S., N. Mapholi, L. T. Nesengani, S. J. Lamont, S. E. Aggrey, O. Hanotte, C. Bottema, and C. Gill, 2024. Supporting social justice through equity-based actions for a sustainable future in animal genetics (at the 39th International Society for Animal Genetics Conference). Animal Genetics (Accepted: 12/24/2024)   

Peichel C, Nair DVT, Manjankattil S, Reed KM, Cox RB, Donoghue AM, and Kollanoor Johny A. 2024. Effect of trans-cinnamaldehyde and peracetic 1 acid alone or in combination on multidrug resistant Salmonella Heidelberg on broiler drumsticks under scalding alone or with chilling and storage in sequence. Journal of Applied Poultry Research, https://doi.org/10.1016/j.japr.2024.100508.   

Poku, R. A., E. Agyeman-Dua, S. Donkor, R. A. Ayizanga, R. Osei-Amponsah, R. Rekaya and S. E. Aggrey, 2024. Changes in rectal temperature as a means of assessing heat tolerance and sensitivity in chickens. Tropical Animal Health and Production 56: 391. https://doi.org/10.1007/s11250-024-04242-1

Powell AA, Velleman SG, Strasburg G, Abrahante Lloréns JE, and Reed KM. 2024. Circular RNA expression in turkey skeletal muscle satellite cells is significantly altered by thermal challenge. Frontiers in Physiology, Avian Physiology, 15:1476487.doi: 10.3389/fphys.2024.1476487. Special Issue: Rising Stars in Physiology.

Prabhakaran DM, Nair DVT, Johnson T, Noll S, Dean C, Reed K, and Johny AK. Shotgun metagenomics unveils beneficial cecal microbiome modulation in turkeys exposed to probiotics and vaccine after multidrug-resistant Salmonella Heidelberg challenge. Frontiers in Microbiology, in review.

Rhoads, D.D., J Pummill, and A.A.K. Alrubaye (2024). Molecular Genomic Analyses of Enterococcus cecorum from Sepsis Outbreaks in Broilers. Microorganisms 2024 Vol. 12 Issue 2 Pages 250 https://doi.org/10.3390/microorganisms12020250

Salem, M., Al-Tobasei, R., Ali, A., An, L., Wang, Y., Bai, X.,... & Zhou, H. (2024). Functional annotation of regulatory elements in rainbow trout uncovers roles of the epigenome in genetic selection and genome evolution. GigaScience, 13, giae092.

Santativongchai P, Klaeui C, Kosonsiriluk S, Saqui-Salces M, Reed KM, Wileman BW, Studniski MM, and Boukherroub KS. 2024. Protocol to establish turkey oviductal organoids as a long-term in vitro model. STAR Protocols, 5(4):103384. doi: 10.1016/j.xpro.2024.103384.

Sculley ER, Rice ES, Carroll RA, Driver JP, Smith J, Kaufman J, Hearn C, Balic A, Chen P, Lamont SJ, Kramer S. A single-nucleus census of immune and non-immune cell types for the major immune organ systems of chicken. bioRxiv. 2024:2024-08.

Shwani, A.; B. Zuo, A. Alrubaye, J. Zhao, D.D. Rhoads (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.  

Sovi, S., K. Adomako, B. Kyei, A. W. Kena, O. S. Olympio and S. E. Aggrey, 2024. A comparative study of population structure and genetic diversity of commercial and indigenous chickens from different agro-ecological zones in Ghana using SilicoDArT and SNP markers. Gene 929, 148823. https://doi.org/10.1016/j.gene.2024.148823

Sparling BA, Ng TT, Carlo-Allende A, McCarthy FM, Taylor Jr RL, Drechsler Y. Immunoglobulin-like receptors in chickens: identification, functional characterization, and renaming to cluster homolog of immunoglobulin-like receptors. Poultry Science. 2024 Feb 1;103(2):103292.  

Tsaxra, J.B., Abolnik, C., Chengula, A.A., Mushi, J.R., Msoffe, P.L.M, Muhairwa, A.P. Phiri, T., Jude, R., Chouicha, N., Mollel, E.L., Zhou, H., Gallardo, R. Kelly, T.R. 2024. Spatiotemporal Patterns of Distribution and Risk Factors for Newcastle Disease Virus Among Chickens in a Tanzania Live Bird Market. Transboundary and Emerging Diseases, vol. 2024, Article ID 5597050, 9 pages, 2024. https://doi.org/10.1155/2024/5597050.

Velleman, S.G., Coy, C.S. and Abasht, B., 2024. Research Note: Chicken breast muscle satellite cell function: effect of expression of CNN1 and PHRF1. Poultry Science, 103(7), p.103781.

Wang, Y., P. Saelao, G. Chanthavixay, R. A. Gallardo, A. Wolc, J. E. Fulton, J. C. Dekkers, S. J. Lamont, T. R. Kelly, H. Zhou. 2024. Genomic regions and candidate genes affecting response to heat stress with Newcastle virus infection in commercial layers chicks using chicken 600K SNP array. Int. J. Mol. Sci. 25(5),2640; doi:10.3390/ijms25052640  

Wang, Z., Khondowe, P., Brannick, E. and Abasht, B., 2024. Spatial transcriptomics reveals alterations in perivascular macrophage lipid metabolism in the onset of Wooden Breast myopathy in broiler chickens. Scientific Reports, 14(1), p.3450.  

Yamashita, T., D.D. Rhoads, J. Pummill. (2024) A robust genome assembly with transcriptomic data from the striped scorpion, Centruroides vittatus. G3: Genes | Genomes | Genetics, August 2024, August 2024, jkae120, https://doi.org/10.1093/g3journal/jkae120

Yu. H, Li. Z, Yimiletey. J, Wan. C, Velleman S. Molecular Characterization of the Heterogeneity of Satellite Cell Populations Isolated from an Individual Turkey Pectoralis Major Muscle. (Frontiers in Physiology, under minor revision, 2025)

Zhou, H., E. L. Clark, D. Guan, S. Lagarrigue, L. Fang, et al.. 2024. Comparative Genomics and Epigenomics of Transcriptional Regulation. Annual Review of Animal Biosciences, 14 (1), ff10.1146/annurev-animal-111523-ff. ffhal-04802793

Zhou, H., I. Baltenweck, J. Dekkers, R. Gallardo, B.B. Kayang, T. Kelly, P. L. M. Msoffe, A. Muhairwa, J. Mushi, A. Naazie, H. R. Otsyina, E. Ouma, S. J. Lamont. 2024. Feed the Future Innovation Lab for Genomics to Improve Poultry: A Holistic Approach to Improve Indigenous Chicken Production Focusing on Resilience to Newcastle Disease. World's Poultry Science Journal. 80:2, 273-297, DOI: 10.1080/00439339.2024.2321350