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]

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..