NC1170: Advanced Technologies for the Genetic Improvement of Poultry

(Multistate Research Project)

Status: Active

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SAES-422 Reports

Annual/Termination Reports:

[03/04/2024] [02/12/2025] [02/19/2026]

Date of Annual Report: 03/04/2024

Report Information

Annual Meeting Dates: 01/13/2024 - 01/14/2024
Period the Report Covers: 01/01/2023 - 12/31/2023

Participants

Brief Summary of Minutes

NC1170 business meeting minutes

Technical Committee Attendees: Douglas Rhoads, Susan Lamont, Kent Reed, Carl Schmidt, Huaijun Zhou, Fiona McCarthy, Bindu Nanduri, Yvonne Drechsler, Adnan Alrubaye, Tom Porter, Androniki Psifidi, Tae Kim, Gale Strasburg, Roger Sunde, Sammy Aggrey.

Other: Janet Fulton, Travis Williams

9.30 AM Call meeting to order

9.30 AM Adnan Alrubaye welcomes participants, announcing chair Yvonne Drechsler for next year

9.31 AM Susan Lamont:

Overview of NC1170 as coordinator/advisor. NC1170 was renewed for 5 years, and this is first meeting. Documentation of collaboration across stations needed in reports. Email will be sent out for collaborative work. Technical committee reports are to be sent out in advance to be able to engage at meeting. Annual report is due 60 days after meeting.

Two opportunities for awards: Feb 1^st and Feb 28^th. Project award, 15k (Feb 28). Ag innovation award for excellence in multi-state research. Individual award for scientist in multi-state project. Active researcher, employed by land grant university, active research. (Feb 1). Asking for nomination, email Sue Lamont.

9.45 AM Motion to keep NC1170 at PAG, voted to approve, no oppose

9.47 AM Huaijun Zhou nominated Tae Kim as secretary, seconded by Bindu Nanduri, voted to approve, no oppose

9.49 AM Discussion about finances for supporting more student participation at the NC1170 meeting, such as USDA conference grants for students/postdocs. Problem is USDA only gives to one project, so would have to coordinate with other species. Maybe through NRSP8. Specific education grants?

Expand members, reach out to people NC1170. Pending application (James Koltes) Research Coordination Network, might be able to fund students too, Animal Breeding and Genetics. Other options: Trust travel grants, PSA, funds student travel. WPSA. Sponsorship

Look into satellite meeting, have the meeting at PSA? Encourage more genetics researchers to participate at PSA, write a proposal to coordinate a symposium.

Angelica van Goor brought up how to advise new funded PIs to join a multi state. (go on NIMSS and familiarize)

Also, PD meeting is at PAG every year.

Tom Porter will ask for travel support at PSA

10.20 AM Meeting adjouned

Accomplishments

Yvonne Drechsler,Western University of Health Sciences,  Fiona McCarthy, University of Arizona; Wesley Warren, University of Missouri. Immunoglobulin-like receptors were identified and characterized in B2 vs B19 macrophages. Immune cell atlas was further annotated to identify novel and rare subpopulations of immune cells in the chicken. PAG30: Poultry Workshop. Participated in NC1170 workshop as co-chair/secretary PAG30: Poultry Workshop: Wesley C. Warren, Edward Ricemeyer, Ashley Meyer, Elaina Sculley, Christine G Elsik, Susan J. Lamont, Yvonne Drechsler, Melissa S. Monson, Cari J. Hearn, Hans H. Cheng. Progress toward an immune cell atlas in the chicken. Fiona McCarthy AZ, Abasht, Behnam - UDEL, Schmidt, Carl J - UDEL, Sunde, Roger A - WI, Drechsler, Yvonne - Western University of Health Sciences, Miller, Marcia - City of Hope Beckman Research Institute (former member). Participated in the NC1170 annual meeting, held as part of the Poultry Workshop at the Plant & Animal Genome Conference held in San Diego, 13-18 January 2023. Gale Strassburg, MSU; Kent Reed MN. Work is in progress to analyze changes in gene expression (MN) and metabolites (MSU) in breast muscle from turkey hatchlings exposed to heat stress or cold stress in comparison to that of standard industry conditions.  Our research groups meet periodically throughout the year on Zoom to discuss progress. Reed is a project co-director on our USDA project: Turkey Breast Muscle Development: The Biological Response to Thermal Challenge in Production Birds. Project Director: Strasburg, G.M.; Project Co-Directors: Jones, A.D., Velleman, S.V., Reed, K.M.  USDA - National Institute of Food and Agriculture. June 1, 2020 – May 31, 2024. Award Number: 2020-67015-30827. Award Amount: $500,000. Douglas Rhoads, Carl Schmidt (DE), Adnan Alrubaye (AR). Whole Genome Resequencing in Broilers to Map the Genetics for Resistance to Bacterial Chondronecrosis with Osteomyelitis Leading to Lameness. Cobb-Vantress, Inc.; 1/2022-12/2023; $54,735; PI- Alrubaye; coPI: Rhoads, Pummill. Genomic markers for distinguishing pathogenic Enterococcus cecorum in a broiler lameness epidemic model system. Arkansas Biosciences Institute; 7/2022-5/2023; $33792; PI; Rhoads; coPIs: Alrubaye, Pummill. Advancing Molecular Research Using Droplet Digital PCR. Arkansas Biosciences Institute; 7/2022-5/2023; $125,010; PI- Zhang; coPIs Qian, Wang, Savin, Rhoads, Srivastava, Zhao, Nelson, Du, Alrubaye, Kumar. Developing a Multispecies Bacterial Vaccine for protection against Bacterial Chondronecrosis with Osteomyelitis Lameness for broilers. US Poultry and Egg Association; 1/2023-6/2024; $79363; PI-Alrubaye; co PI- Jesudhasan, Rhoads. Further Evaluate Herbonis Feed Additives for protection against lameness and improving the well-being of broilers in a lameness challenge model. Nuproxa Switzerland; 1/2023-12/31/2024; 72,729; PI-Alrubaye; coPI- Rhoads Susan Lamont (IA) Behnam Abasht (DE); Carl Schmidt (DE); Huaijun Zhou (UCD); Hans Cheng (ADOL). Genes, pathways and genomic regions associated with important biological traits in chickens were identified. Unique research populations of chickens were maintained for current and future scientific studies at Iowa State University and elsewhere. Biological materials (chicks, fertile eggs, DNA) were shared for collaborative research on epigenetics, disease resistance and biodiversity. Organized Animal Genomics and Climate Change Workshop at Plant and Animal Genome conference, Jan 2024. Organized Words of Wisdom workshop at International Society of Animal Genetics, July 2023  Roger A Sunde, WI. Collaborators in NC-1170: Kent Reed (MN). Periodic consultant in NC-1170: Fiona McCarthy (AZ). Under NC1170 in collaboration with Kent Reed and Kristelle Mendoza at the U. Minnesota we conducted RNA seq studies in turkeys fed graded levels of selenium (Se) to show that adaptation to high Se is not accomplished by transcription regulation. Prior to this work, with help from Fiona McCarthy at the U. Arizona, we cloned the full selenotranscriptome of the turkey. Using this RNA seq data, we conducted Gene set enrichment analysis (GSEA) because it evaluates transcript expression data at the level of gene sets to detect changes in pathways and biological processes that are coordinated at a more subtle level than found by differential expression analysis of individual genes. Analysis of the turkey poult data set also found no gene sets that were consistently altered by high-Se and supernutritional-Se. Cross-species GSEA comparison of transcript expression in turkeys vs. rats fed graded levels of dietary Se also identified no common gene sets significantly and consistently regulated by high Se in rats and turkeys.

Publications

Sparling BA, Ng TT, Carlo-Allende A, McCarthy FM, Taylor RL Jr, Drechsler Y: Immunoglobulin-like Receptors in Chickens: identification, functional characterization, and renaming to Cluster Homolog of Immunoglobulin-like Receptors. Poultry Science Volume 103, Issue 2, 2024. Schmidt CJ, Kim DK, Pendarvis GK, Abasht B, McCarthy FM. Proteomic insight into human directed selection of the domesticated chicken Gallus gallus. PLoS One. 2023 Aug 7;18(8):e0289648. doi: 10.1371/journal.pone.0289648. 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. doi.org/10.1371/journal.pone.0283914 Pritchett, E.,M., Van Goor, A., Schneider,  B.K., Young, M., Lamont, S.J., Schmidt, C.K. 2023. Chicken pituitary transcriptomic responses to acute heat stress. Mol. Biol. Rep. doi.org/10.1007/s11033-023-08464-8 Warren, W.C., Rice, E.S., Meyer, A., Hearn, C.J., Steep, A., Hunt, H.D., Monson, M.S., Lamont, S.J., Cheng, H.H. 2023. The immune cell landscape and response of Marek’s disease resistant and susceptible chickens infected with Marek’s disease virus. Scientific Rep. 13:5355. doi.org/10.1038/s41598-023-32308-x  Wang, Y., Saelao, P., Kern, C., Zhao, B., Gallardo, R.A., Kelly, T., Dekkers, J.M., Lamont, S.J., Zhou, H. 2023. Distinct hypothalamus and breast muscle transcriptomic response to heat stress under Newcastle Disease virus infection.  Cytogenet. Genome Res. DOI.org/10.1159/000529376  Smith J., Alfieri, J.M., Anthony, N., Arensburger, P., Athrey, G.N., Balacco, J., Balic, A., Bardou, P., Barela, P., Bigot, Y., Blackmon, H., Borodin, P.M., Rachel Carroll, R., Casono, M.C., Charles, M., Cheng, H., Chiodi, M., Cigan, L., Coghill, L.M., Crooijmans, R., Neelabja Das, N., Davey, S., Davidian, A., Degalez, F., Dekkers, J.M., Derks, M., Diack, A.B., Djikeng, A., Drechsler, Y., Dyomin, A., Fedrigo, O., Fiddaman, S.R., Giulio Formenti, G., Frantz, L.A.F., Fulton, J.E., Gaginskaya, E., Galkina, S., Gallardo, R.A., Geibel, J., Gheyas, A., Godinez, C.J.P., Goodell, A., Graves, J.A.M., Griffin, D.K., Haase, B., Han, J.-L., Hanotte, O., Henderson, L.J., Hou, Z.-C., Howe, K., Huynh, L., Ilatsia, E., Jarvis, E., Johnson, S.M., Kaufman, J., Kelly, T., Kemp, S., Kern, C., Keroack, J.H., Klopp, C., Lagarrigue, S., Lamont, S.J., Lange, M., Lanke, A., Larkin, D., Larson, G., Layos, J.K.N., Lebrasseur, O., Malinovskaya, L.P., Martin, R.J., Martin Cerezo, M.L., Mason, A.S., McCarthy, F.M., McGrew, M.J., Mountcastle, J., Kamidi Muhonja, C., Muir, W., Muret, K.,  Murphy, T., Ng’ang’a, I., Nishibori, M., O’Connor, R.E., Ogugo, M., Okimoto, R., Ouko, O., Patel, H.R., Perini, F., María Pigozzi, M., Potter, K.C., Price, P.D., Reimer, C., Rice, E.S., Rocos, N., Rogers, T.F., Saelao, P., Schauer, J., Schnabel, R., Schneider, V., Simianer, H., Smith, A., Stevens, M.P., Stiers, K., Keambou Tiambo, C., Tixier-Boichard, M., Torgasheva, A.A., Tracey, A., Tregaskes, C.A., Vervelde, L., Wang, Y., Warren, W.C., Waters, P., Webb, D., Weigend, S., Wolc, A., Wright, A.E., Wright, D., Wu, Z., Yamagata, M., Yang, C., Yin, Z.-T., Young, M.C., Zhang, G., Zhao, B., Zhou, H.  2023. Fourth Report on Chicken Genes and Chromosomes 2022. Cytogenet. Genome Res. 162:405–527. DOI.org/10.1159/000529376 Reed KM, Mendoza KM, Kono T, Powell AA, Strasburg GM, Velleman SG. Expression of miRNAs in turkey muscle satellite cells and differential response to thermal challenge. Front Physiol. 2023 Nov 23;14:1293264. doi: 10.3389/fphys.2023.1293264.  Xu J, Strasburg GM, Reed KM, Bello NM, Velleman SG. Differential effects of temperature and mTOR and Wnt-planar cell polarity pathways on syndecan-4 and CD44 expression in growth-selected turkey satellite cell populations. PLoS One. 2023 Feb 3;18(2):e0281350. doi: 10.1371/journal.pone.0281350.. Bierla K, Szpunar J, Lobinski R, Sunde RA. Effect of graded levels of selenium supplementation as selenite on expression of selenosugars, selenocysteine, and other selenometabolites in rat liver. Metallomics 2023;15:mfad066. PMID: 37898555 Bierla K, Szpunar J, Lobinski R, Sunde RA. Selenomethionine supplementation and expression of selenosugars, selenocysteine, and other selenometabolites in rat liver. Metallomics 2023;15:mfad067. PMID: 37898557

Impact Statements

Yvonne Drechsler The impact of our collaborative work is the characterization and annotation of immune cells and immunoglobulin-like receptors in the chicken genome that contribute better understand underlying mechanisms of disease resistance and susceptibility. This will lead to enhanced breeding strategies. Fiona McCarthy: With the expertise provided by these collaborators, we improved standardized naming for poultry genes, most notably for approx. 300 genes associated with immune response to infection. This work is distributed to international, online resources which are used by poultry researchers to more easily understand their results and translate their findings into gains for the poultry industry. Douglas Rhoads: Understanding the genomes of bacterial pathogens of chickens will help us develop management strategies for reducing infections without resorting to antibiotics. Susan Lamont: Using specialized research lines of chickens, the gene expression response of various tissues to heat stress alone, or to Newcastle disease virus infection under heat stress was characterized. Response of single immune cell types to Marek’s disease virus was defined. Gale Strasburg: Extreme weather variations associated with climate change pose a serious threat to the poultry industry’s ability to maintain consistent, low-fat, high-quality meat products. Our research is focused on developing a deeper understanding of the physiological response of turkeys to temperature extremes to improve breeding and management strategies that mitigate the detrimental effects of climate change while assuring delivery of high quality poultry products to consumers Roger Sunde: Results from these NC1170 studies were used in 2022 to report the dietary Se requirements in turkeys and chickens, and to compare these requirements across animal species including humans, other domestic animals, and rodents. These results were presented in 2022 in a comprehensive review..

Date of Annual Report: 02/12/2025

Report Information

Annual Meeting Dates: 01/11/2025 - 01/12/2025
Period the Report Covers: 01/01/2024 - 12/31/2024

Participants

Brief Summary of Minutes

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

Call to Order:

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

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.

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.

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.

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

Accomplishments

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.

Publications

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

Impact Statements

The NC1170-organized annual Poultry Workshop, held at the PAG, saw significant international participation. The workshop featured 22 talks and had 61 attendees officially registered, representing 37 institutions. However, actual attendance was likely higher, as many individuals attended sessions without signing in. This event provided a valuable platform for disseminating research findings from project members to a diverse international audience, which included many attendees beyond the NC1170. Invited presentations from both members and external experts fostered valuable interactions with industry scientists and created a crucial venue for establishing new research collaborations. This successful workshop underscores the project's impact in advancing poultry genetics and genomics research on a global scale.
The research conducted across the NC-1170 project has significant implications for poultry production, health, and welfare.
Improved gene nomenclature and bioinformatics resources will facilitate research and communication within the poultry genetics community.
Research on disease resistance and immunity will contribute to the development of strategies to control avian diseases, potentially reducing economic losses and improving animal welfare.
Studies on muscle development and meat quality will lead to a better understanding of the genetic and environmental factors affecting these traits, potentially leading to improved breeding strategies and management practices.
Advances in genetic and genomic technologies will enable more efficient and accurate selection for economically important traits, leading to improved productivity and sustainability of poultry production.
Democratizing access to user-friendly CRISPR technology will empower the research community to explore poultry biology. The standardized, user-friendly system will revolutionize avian research by enhancing experimental efficiency, accessibility, and reproducibility, significantly accelerating the pace of discovery.

Date of Annual Report: 02/19/2026

Report Information

Annual Meeting Dates: 01/10/2026 - 01/11/2026
Period the Report Covers: 01/01/2025 - 12/31/2025

Participants

Brief Summary of Minutes

At the beginning, Advisor Sue Lamont emphasized the importance of including a short impact statement in each station's technical report. When developing a new proposal for the NC1170, the Technical Committee should be formed before the 2027 deadline. Station reports should be circulated via NIMSS to Technical Committee members. Members are encouraged to submit their reports as early as possible. At the PAG 33 Poultry Workshop, 64 participants attended, as shown on the attached sign-in sheets.

After unanimously approving last year's minutes, Dr. Jiuzhou Song was announced as the next chair. Dr. Aditya Dutta was nominated for the secretary position next year. The motion was approved with no opposing votes.

Regarding recruitment members, the meeting discussed identifying potential international members, e.g., INRA, Roslin, and the Netherlands. We need to reach out to the broader avian community, e.g., the Avian Genomics Goes Wild Workshop at PAG and the new poultry and avian hires listing. We also discussed setting up a booth at the Poultry Science Association meeting.

To attract early-career scientists to the NC11770 Poultry Workshop, we need to apply for travel support from the USDA conference grant and encourage them to apply for the PSA travel award.

Regarding the location of the new year meeting, 15 stations participated in the ballot during the voting window (1/29 to 2/10). By a narrow margin, the community selected Motion B (PSA in Fort Worth) over Motion A (PAG in San Diego). Vote Count Summary: Motion B is officially carried.

Motion A (PAG, San Diego, CA - Jan 2027): 7 votes

Motion B (PSA, Fort Worth, TX - July 2027): 8 votes

Accomplishments

Gene Nomenclature and Bioinformatics: Drs. Jack Dekker and Sue Lamont at Iowa State University developed methods and evaluated them to facilitate data sharing while protecting confidential information in poultry genetics and breeding. They also maintained a unique research population of chickens for current and future scientific studies. They also collected biological materials (chicks, fertile eggs, and DNA) for collaborative research on disease resistance and biodiversity. Importantly, they developed strategies to improve selection for layer production under commercial conditions, creating opportunities to balance genetic gains and inbreeding and to target specific markets for layer chickens. Prof. Huaijun Zhou at UC, Davis has established scalable experimental and computational frameworks (MPRA, machine learning, allele-specific analyses) that enable functional annotation of noncoding regulatory elements in the chicken genome, addressing a major gap in poultry genomics. Meanwhile, his lab generated one of the first validated maps of chicken enhancers and regulatory variants, demonstrating that regulatory potential can be predicted from DNA features, enabling genome-wide prioritization of functional variants and accelerating discovery beyond experimental assays alone. Besides, his lab created a multi-tissue atlas of allele-specific regulatory effects across chromatin and transcriptional layers, providing a foundational resource for understanding tissue-specific gene regulation in poultry. Research led by Dr. Fiona McCarthy made significant contributions to chicken gene nomenclature. Based on gene products and their evolutionary relationships, her lab provided standardized gene names, enabling us to understand gene function better and support comparative studies. Data provided by the CGNC are shared with public databases (e.g., NCBI and Ensembl), making it easier for researchers to compare their results with those of other research groups. Disease Resistance and Immunity: Prof. Roger Sunde at the University of Wisconsin generates turkeys with selenium status that ranges from Se-deficient to high-Se by feeding turkey poults, and then analyzes tissues for selenoenzyme activity, transcript expression, and selenosugars. They found the dietary selenium requirement of the young turkey poult should be raised to 0.4 µg Se/g as inorganic selenium, and that the turkey is resistant to high dietary Se, further indicating that the FDA limit of dietary selenium supplementation could be safely raised to 0.5 µg Se/g as inorganic selenium, at least for young turkey poults. Selenosugars may serve as biomarkers of high Se status and help explain how turkeys, as well as other animals, protect against Se toxicity. At UC, Davis, Dr. Huaijun Zhou’s lab demonstrated the power of advanced intercross populations combined with modern genomics to improve mapping resolution of complex traits, supporting more precise identification of causal loci, advancing understanding of genetic and cellular mechanisms underlying avian influenza resistance, providing insights that support precision breeding, improved vaccine strategies, and enhanced poultry resilience. They also delivered broadly shareable datasets, analytical pipelines, and biological insights that strengthen the poultry research community’s capacity to translate genomic information into applied breeding and genetic improvement strategies. Dr. Jiuzhou Song at UMD performed genome-wide gene expression analysis in spleen, thymus, and bursa tissues from the MD-resistant and susceptible lines to elucidate the mechanisms underlying MD resistance and susceptibility. They identified genes and pathways associated with MDV infection. They revealed tissue-specific expression patterns across immune organs and found that MDV infections influenced cytokine-cytokine receptor interactions and cellular development in both resistant and susceptible chicken lines. The research provides new insights into the mechanism of MD progression and motivates further studies of gene function in MD resistance. Muscle Development and Meat Quality: At Ohio State University, Dr. Hui Yu explored the roles of satellite cells in muscle development. She documented increased muscle fiber damage in the pectoralis major of turkeys. Resembling pale, soft, and exudative meat in swine, as well as deep pectoral myopathy and focal myopathy, such abnormalities likely stem from disruptions in normal muscle development. A deeper understanding of SC heterogeneity and function in turkeys will be critical for uncovering the cellular mechanisms underlying these myopathies and improving muscle meat quality in turkey production. Researchers at the University of Minnesota, led by Dr. Kent M. Reed, investigated the influence of thermal challenge on turkey muscle development and meat quality. They also completed an RNA-seq dataset examining hepatic miRNA expression in domestic and wild turkeys exposed to aflatoxin B1. Additionally, they collaborated on projects examining age-dependent fertility loss in laying hens. Genetic Mechanisms and Breeding: In UMD, Drs. Jiuzhou Song and Tom Porter conducted miRNA and long-read transcriptomic analyses of chicken ESCs and PGCs, which are vital for understanding their regulatory mechanisms and differentiation, as well as for sustainable poultry production. These studies provide reference methods for avian species to reprogram cells into iPSCs and establish a network of cell-fate-determination mechanisms. These results provide deep insight into regular mechanisms in avian germline, sex differentiation, and disease resistance. Meanwhile, Porter noted that molecular mechanisms identified through transcriptomic, lipidomic, and proteomic approaches will inform future efforts to improve poultry nutrition, growth, and reproduction through marker-assisted selection. Climate Change: Prof. Samuel Aggrey at the University of Georgia found that as climate change increases the frequency and severity of heat events, poultry producers face growing challenges in maintaining bird health, welfare, and productivity. Glucose supplementation mitigates the negative effects of heat stress by improving energy availability, preserving muscle growth, and maintaining carcass yield. The observed changes in glucose transporter expression provide new insights into metabolic adaptation under thermal stress and may inform future genetic or nutritional strategies to improve heat resilience. Prof. Kent Reed at the University of Minnesota focused on the climate impact on poultry health and production. They identified molecular mechanisms underlying altered muscle development, enabling mitigation strategies by improved genetic selection, nutritional interventions, and other measures to enhance broiler performance. Tool Development: Dr. Tae Hyun Kim at Penn State University has developed user-friendly CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) transgenic cell lines, providing affordable and novel avian research tools. His lab substantially standardized CRISPRa and CRISPRi avian cell lines, reducing technical and financial barriers to functional genomics research in poultry. Importantly, they identified regulatory pathways controlling gonadal development, thereby strengthening understanding of avian reproductive biology, supporting future genetic improvement efforts, and enhancing the NC1170 community's capacity to translate genomic discoveries into biological mechanisms relevant to poultry health, productivity, and sustainability.

Publications

Aryal, B., J. Kwakye, O. W. Ariyo, A. F. A. Ghareeb, M. C., Milfort, A. L., Fuller, S., Khatiwada, R., Rekaya, S. E., and Aggrey, S. E., 2025. Major oxidative and antioxidant mechanisms during heat stress in chickens. Antioxidant 14(4)471 DOI:10.3390/antiox14040471 Bierla K, Szpunar J, Lobinski R, Sunde RA. Use of laser-ablation inductively coupled plasma mass spectrometry for analysis of selenosugars bound to proteins. Metallomics 2025;17:mfaf002. PMID: 39832802 Broadwater, C., J. Guo, J. Liu, I. Tobin, M. A. Whitmore, M. G. Kaiser, S. J. Lamont, G. Zhang. 2025. Breed-specific responses to coccidiosis in chickens: Identification of intestinal bacteria linked to disease resistance. J. Anim. Sci. Biotech. 16:65. <a href="https://doi.org/10.1186/s40104-025-01202-">https://doi.org/10.1186/s40104-025-01202-</a> Ding Y, Dunn J, Zhang H, Zhao K, Song J. Comparative transcriptomic analysis of chicken immune organs affected by Marek's disease virus infection at latency phases. Front Physiol. 2025 Apr 2;16:1520826. doi: 10.3389/fphys.2025.1520826. PMID: 40241721; PMCID: PMC12000659. Elmore, K.A., S.J. Lamont, and E.A. Bobeck. 2025. Genetic line-specific immune profiles and immunometabolic responses to intramuscular lipopolysaccharide. Front. Immunol.16:1608391. <a href="https://doi:10.3389">https://doi:10.3389/fimmu.2025.1608391</a> Hartono, E., O. W. Willems, X, Bai, S. Toghiani, B. Wood, R. Rekaya, and S. E. Aggrey, 2025. Enhancing Genomic Selection for Reproductive Traits in Turkeys Through SNP Prioritization Using the Fixation Index. Poultry Science 105(2):106213. doi: 10.1016/j.psj.2025.106213 Hartono, E., O. W. Willems, X. Bai, B. J. Wood, R. Rekaya and S. E. Aggrey, 2025. Effect of transformation of non-normal fitness data on the estimation of genetic parameters in turkeys. Journal of Animal Breeding and Genetics https://doi.org/10.1111/jbg.12935 Elmore, K.A., S.J. Lamont, and E.A. Bobeck. 2025. Immune cell profile and metabolic preference following intramuscular lipopolysaccharide injection of highly inbred and advanced intercross genetic lines. Front. Vet. Sci. 12:1592021. https://doi:10.3389/fvets.2025.1592021 Guan D, Bai Z, Zhu X, Zhong C, Hou Y, Zhu D; ChickenGTEx Consortium; Li H, Lan F, Diao S, Yao Y, Zhao B, Li X, Pan Z, Gao Y, Wang Y, Zou D, Wang R, Xu T, Sun C, Yin H, Teng J, Xu Z, Lin Q, Shi S, Shao D, Degalez F, Lagarrigue S, Wang Y, Wang M, Peng M, Rocha D, Charles M, Smith J, Watson K, Buitenhuis AJ, Sahana G, Lund MS, Warren W, Frantz L, Larson G, Lamont SJ, Si W, Zhao X, Li B, Zhang H, Luo C, Shu D, Qu H, Luo W, Li Z, Nie Q, Zhang X, Xiang R, Liu S, Zhang Z, Zhang Z, Liu GE, Cheng H, Yang N, Hu X, Zhou H, Fang L. Genetic regulation of gene expression across multiple tissues in chickens. Nat Genet. 2025 May;57(5):1298-1308. doi: 10.1038/s41588-025-02155-9. Epub 2025 Apr 8. PMID: 40200121. Fang L, Teng J, Lin Q, Bai Z, Liu S, Guan D, Li B, Gao Y, Hou Y, Gong M, Pan Z, Yu Y, Clark EL, Smith J, Rawlik K, Xiang R, Chamberlain AJ, Goddard ME, Littlejohn M, Larson G, MacHugh DE, O'Grady JF, Sørensen P, Sahana G, Lund MS, Jiang Z, Pan X, Gong W, Zhang H, He X, Zhang Y, Gao N, He J, Yi G, Liu Y, Tang Z, Zhao P, Zhou Y, Fu L, Wang X, Hao D, Liu L, Chen S, Young RS, Shen X, Xia C, Cheng H, Ma L, Cole JB, Baldwin RL 6th, Li CJ, Van Tassell CP, Rosen BD, Bhowmik N, Lunney J, Liu W, Guan L, Zhao X, Ibeagha-Awemu EM, Luo Y, Lin L, Canela-Xandri O, Derks MFL, Crooijmans RPMA, Gòdia M, Madsen O, Groenen MAM, Koltes JE, Tuggle CK, McCarthy FM, Rocha D, Giuffra E, Amills M, Clop A, Ballester M, Tosser-Klopp G, Li J, Fang C, Fang M, Wang Q, Hou Z, Wang Q, Zhao F, Jiang L, Zhao G, Zhou Z, Zhou R, Liu H, Deng J, Jin L, Li M, Mo D, Liu X, Chen Y, Yuan X, Li J, Zhao S, Zhang Y, Ding X, Sun D, Sun HZ, Li C, Wang Y, Jiang Y, Wu D, Wang W, Fan X, Zhang Q, Li K, Zhang H, Yang N, Hu X, Huang W, Song J, Wu Y, Yang J, Wu W, Kasper C, Liu X, Yu X, Cui L, Zhou X, Kim S, Li W, Im HK, Buckler ES, Ren B, Schatz MC, Li JJ, Palmer AA, Frantz L, Zhou H, Zhang Z, Liu GE; FarmGTEx Consortium. The Farm Animal Genotype-Tissue Expression (FarmGTEx) Project. Nat Genet. 2025 Apr;57(4):786-796. doi: 10.1038/s41588-025-02121-5. Epub 2025 Mar 17. PMID: 40097783. Hou Y, Zou D, Chu Q, Zhan B, Wang R, Guan D, Wang W, Feng X, Li X, Zhu X, Bai Z, Gao Y, Yin H, Xu T, Yuan Z, Hu X, Yang N, Zhou H, Fang L, Zhang Z. The ChickenGTEx portal: a pan-tissue catalogue of regulatory variants shaping transcriptomic and phenotypic diversity. Nucleic Acids Res. 2025 Aug 19:gkaf731. doi: 10.1093/nar/gkaf731 Guan, D., Z. Bai, X. Zhu, C. Zhong, Y. Hou, D. Zhu, H. Li, F. Lan, S. Diao, Y. Yao, B. Zhao, X. Li, Z. Pan, Y. Gao, Y. Wang, D. Zou, R. Wang, T. Xu, C. Sun, H. Yin, J. Teng, Z. Xu, Q. Lin, S. Shi, D. Shao, F. Degalez, S. Lagarrigue, Y. Wang, M. Wang, M. Peng, D. Rocha, M. Charles, J. Smith, K. Watson, A. J. Buitenhuis, G. Sahana, M. S. Lund, W. Warren, L. Frantz, G. Larson, S. J. Lamont, W. Si, X. Zhao, B. Li, H. Zhang, C. Luo, D. Shu, H. Qu, W. Luo, Z. Li, Q. Nie, X. Zhang, R. Xiang, S. Liu, Z. Zhang, Z. Zhang, G. E. Liu, H. Cheng, N. Yang, X. Hu, H. Zhou & L. Fang. 2025. The genetic regulation of multi-tissue transcriptome in chickens. Nature Genetics. https://doi.org/10.1038/s41588-025-02155-9 Kaiser, M.G., Kaufman, S.J. Lamont. 2025. Different MHC class I cell surface expression levels in diverse chicken lines, associations with B blood group, and proposed relationship to antigen-binding repertoire. Poultry Sci. https://doi.org/10.1016/j.psj.2024.104569 Kim J, Han JH, Kim M, Schmidt G, Cho E, Lee JH, Kim TH. From GWAS signal to function: Targeted CRISPR activation enables functional characterization of non-coding SNPs in chickens. Front. Genome Ed. 2025; DOI: 10.3389/fgeed.2025.1662152 Kang TH, Shin SS, Kim TH, Lee SI. Ivangustin alleviates deoxynivalenol-induced apoptosis by regulating FOXO3a translocation in porcine intestinal epithelial cells. Toxins DOI: 10.3390/toxins17040174 Kwakye, J., O. W. Ariyo, A. F. A. Ghareeb, E. Hartono, B. Aryal, S. Sovi, M. C. Milfort, A. L. Fuller, R. Rekaya and S. E. Aggrey, 2025. Effect of glucose supplementation on protein biosynthesis in chickens reared under thermoneutral or heat stress environment. Gene 951, 149408 https://doi.org/10.1016/j.gene.2025.149408 Kirkpatrick C, McCarthy F. Standardized Gene Nomenclature for Chicken Scavenger Receptors. MicroPubl Biol. 2025 Apr 11;2025:10.17912/micropub.biology.001559. PMID: 40291052. Kamkrathok B, Beckford RC, Klug S, Diehl K, Farley L, Porter TE (2025) Effect of early-life thermal conditioning on mRNA expression in tissues under heat stress and non-heat stress conditions in broiler chickens. Poult Sci 105:106244 doi.org/10.1016/j.psj.2025.106244 Liu KL, Porter TE (2025) ScRNAseq analysis of chicken embryonic pituitary reveals cell heterogeneity and a cell type co-expressing Gh and Pomc. Endocrinology 167: bqaf184 doi.org/10.1210/endocr/bqaf184 Lee HJ, Han JH, Chapman B, Jung KM, Rudd I, Han JY, Kim TH. A comprehensive transcriptional profiling of developing gonads reveals the role of TGFβ signaling in female gonadal asymmetry in chickens. Poultry Sci. 2025; DOI: 10.1016/j.psj.2025.104932 Lee CH, Shin S, Kim TH, Lee SI. Nymphoides peltata alleviates patulin-induced glutamine metabolic stress and epithelial toxicity in small intestinal epithelial cells. Toxins 2025; DOI: 10.3390/toxins17070337 Lei XG, Rayman MP, Sunde RA. Selenium. In: Tucker KL, Ross CA, Jensen GL, Torger-Decker R, Duggan CP, editors. Modern Nutrition in Health and Disease (MNHD). 12 ed. 2025. p. 233-56. Li, H., J. Tan, X. Li, S.J. Lamont, H. Sun. 2025. Integrated Transcriptome Analysis Reveals the Lung miRNA–mRNA Regulatory Network Associated with Avian Pathogenic E. coli Infection. Vet. Sci. 2025, 12, 95. https://doi.org/10.3390/vetsci12020095 Lim SJ, Shin S, Kim TH, Lee SI. Euphorbia hypericifolia attenuates citrinin-induced oxidative stress and maintains tight junction integrity in porcine intestinal epithelial cells. Int. J. Mol. Sci. 2025; DOI: 10.3390/ijms26167773 Mandiga, A., G. Li, T. Liu, R. N. Parasuraman, R. M. Pidaparti, V. U. C. Bodempudi, and S. E. Aggrey, 2025. Autonomous Navigation of a Quadruped Robot to Approach Floor Eggs and Path Optimization Analysis for Commercial Feasibility. Applied Engineering in Agriculture 41(6):733-747. doi: 10.13031/aea.16384 Prabhakaran DM, Johny AK, Nair DVT, Manjankattil S, Johnson T, Noll S, and Reed KM. 2025. Beneficial cecal microbiome modulation in turkeys exposed to probiotics and vaccine after multidrug-resistant Salmonella Heidelberg challenge. Microbiology Research, 16:136 https://doi.org/10.3390/microbiolres16070136150. Physiology, 16:1651079. https://doi:10.3389/fphys.2025.1651079.Rauw, W.M., Baumgard, L.H. and Dekkers, J.C.M., 2024. Feed efficiency and metabolic flexibility in livestock. Animal, 101376. <a href="https://doi.org/10.1016/j.animal.2024.101376">https://doi.org/10.1016/j.animal.2024.101376</a> Reed KM, Velleman SG, and Strasburg GM. 2025. Thermal challenge significantly alters gene expression in breast muscle of commercial turkey poults. Frontiers in Physiology, Avian Schmidt, C.J. and S.J. Lamont. 2025. Integrated Genomic Approaches to Characterize and Mitigate Heat Stress in Poultry. Annu. Rev. Anim. Biosci. 2025. 13:121-141. https://doi.org/10.1146/annurev-animal-111523-102021 Sinpru P, Jantasaeng O, Pasri P, Kamkrathok B, Kaewsatuan P, Pengsanthia S, Molee W, Rau A, Porter TE, Tixier-Boichard M, Molee A (2025) Transcriptome profiling of the pituitary gland reveals candidate genes for divergent feed efficiency in slow-growing chickens. Italian Journal of Animal Science 24:2621-2634 doi.org/10.1080/1828051X.2025.2596846 Sinpru S, Diehl K, Ellestad LE, Porter TE (2025) Effect of commercial genetic selection on gene expression in the developing neuroendocrine system of broilers. Poult Sci (in press) Skow, C., L.C. Ott, S.J. Lamont, and M. Mellata. 2025. Host Genetics Regulates Bacterial Plasmid Conjugation Differentially in Avian Ceca Explant Coculture Through Secretory miRNA. npjAntimicrobials and Resistance. https://doi.org/10.1038/s44259-025-00163-7 Tan, J., H. Li, X. Li, S.J. Lamont, and H. Sun. 2025. Integrated transcriptome analysis reveals thelung miRNA-mRNA regulatory network associated with avian pathogenic E. coli infection. Vet.Sci. 2025, 12(2), 95; https://doi.org/10.3390/vetsci12020095. Yimiletey, J., Z. Li, C. Wan, S. Velleman, and H. Yu. 2025. Molecular profiling of satellite cell heterogeneity during differentiation in an individual turkey pectoralis major muscle. Poult Sci 104:105735. doi 10.1016/j.psj.2025.105735 Yu, H., Z. Li, J. Yimiletey, C. Wan, and S. Velleman. 2025. Molecular characterization of the heterogeneity of satellite cell populations isolated from an individual Turkey pectoralis major muscle. Front Physiol 16:1547188. doi 10.3389/fphys.2025.1547188 Zhou, H., F. M. McCarthy, T. H. Kim, W. Warren, G. Zhang. 2026. Emerging technologies in poultry genomics: Unlocking innovation for the future of sustainable production, Poultry Science, Vol 105, Issue 2, https://doi.org/10.1016/j.psj.2025.106240. Zhou H, McCarthy FM, Kim TH, Warren W, Zhang G. Emerging technologies in poultry genomics: Unlocking innovation for the future of sustainable production. Poultry Sci. 2025; DOI: 10.1016/j.psj.2025.106240 Weaver EA, Connolly NP, Kim TH, Ramachandran R. Metformin alters liver metabolism to sustain egg production in reproductively aging broiler breeder hens. Biol. Reprod. 2025; DOI: 10.1093/biolre/ioaf072 Yoon JW, Shin S, Kim TH, Lee SI. Integrated transcriptome and metabolome analysis of the porcine small intestine during weaning. Genes (Basel). 2025; DOI: 10.3390/genes16070727

Impact Statements

The NC1170-organized annual Poultry Workshop, held at the PAG 33, drew significant international participation. The workshop featured 24 talks and had 64 attendees officially registered, representing 43 institutions. However, actual attendance was likely higher, as many individuals attended sessions without signing in. This event provided a valuable platform for project members to disseminate research findings to a diverse international audience, including many attendees beyond NC1170. Invited presentations by both members and external experts fostered valuable interactions with industry scientists and created a crucial venue for establishing new research collaborations. This successful workshop underscores the project's impact in advancing poultry genetics and genomics research globally. Outcomes from the NC1170 project are improving poultry productivity, health, and animal welfare. Standardized gene nomenclature and enhanced bioinformatics resources developed through this project improve data consistency, sharing, and interpretation, strengthening collaboration and research efficiency within the poultry genetics community. Research on disease resistance and immune function informs strategies to control avian diseases, with the potential to reduce economic losses to the poultry industry while improving animal welfare. Project findings on muscle development and meat quality support the development of improved breeding strategies and management practices, thereby enhancing production efficiency and product quality. Advances in genetic and genomic technologies enable more accurate and efficient selection for economically important traits, supporting the long-term sustainability of poultry production systems. Additionally, expanded access to standardized, user-friendly CRISPR technologies increases research capacity across institutions, improves experimental reproducibility, and accelerates the generation of knowledge needed to address current and emerging challenges in poultry genetics and genomics.