Hostname: page-component-586b7cd67f-2plfb Total loading time: 0 Render date: 2024-11-24T02:28:23.788Z Has data issue: false hasContentIssue false
  • English
  • Français

Genomic loci associated with antibody-mediated immune responses in an F2 chicken population

Published online by Cambridge University Press:  19 November 2018

V. Raeesi Open the ORCID record for V. Raeesi [Opens in a new window] ,
A. Ehsani  and
R.V. Torshizi
V. Raeesi
Affiliation:
Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran 14115–336, Iran
A. Ehsani*
Affiliation:
Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran 14115–336, Iran
R.V. Torshizi
Affiliation:
Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran 14115–336, Iran
*
†E-mail: [email protected]
Get access

Abstract

Immunity-related traits are heritable in chicken, therefore, it is possible to improve the inherent immunity by breeding programs. In this study using the Illumina chicken 60K single nucleotide polymorphisms (SNPs) chip, we performed a set of genome-wide association studies to determine candidate genes and loci responsible for primary and secondary antibody-mediated responses against sheep red blood cell. A F2 population descended from a commercial meat-type breed and an Iranian indigenous chicken was used for this study. Statistical analysis was based on a mixed linear model utilizing genomic relationship matrix to prevent spurious associations. Correction for multiple testing was done by applying 5% and 10% chromosomal false discovery rates (FDRs) for significant and suggestive thresholds, respectively. Nine significant and 17 suggestive associated SNPs were identified. Most of the SNPs that were suggestively associated with the primary response of total plasma immunoglobulins were also significantly associated with this trait in secondary response. Three SNPs were located within a narrow region of 23 kb on chromosome 16. Pathway analysis for the genes surrounding the associated SNPs showed that they are involve in antigen processing and presentation, primary immunodeficiency, vitamin digestion and absorption, cell adhesion molecules, phagosome, influenza A, folding, assembly and peptide loading of class I major histocompatibility complex, lipid digestion, mobilization, and transport (FDR < 0.1). Interestingly, there were common regains associated with multiple immune-related traits.

Keywords

Broilerimmunoglobulingenome-wide association studymixed linear modelsingle nucleotide polymorphisms
Type
Research Article
Information
animal , Volume 13 , Issue 7 , July 2019 , pp. 1341 - 1349
Copyright
© The Animal Consortium 2018 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Arango Duque, G and Descoteaux, A 2014. Macrophage cytokines: involvement in immunity and infectious diseases. Frontiers in Immunology 5, 491, https://doi.org/10.3389/fimmu.2014.00491 Google Scholar
Benjamini, Y and Hochberg, Y 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (Methodological) 57, 289–300.Google Scholar
Biscarini, F, Bovenhuis, H, Van Arendonk, J, Parmentier, H, Jungerius, A and Van Der Poel, J 2010. Across‐line SNP association study of innate and adaptive immune response in laying hens. Animal Genetics 41, 26–38.Google Scholar
Boles, KS, Barchet, W, Diacovo, T, Cella, M and Colonna, M 2005. The tumor suppressor TSLC1/NECL-2 triggers NK-cell and CD8+ T-cell responses through the cell-surface receptor CRTAM. Blood 106, 779–786.Google Scholar
Bovenhuis, H, Bralten, H, Nieuwland, M and Parmentier, H 2002. Genetic parameters for antibody response of chickens to sheep red blood cells based on a selection experiment. Poultry Science 81, 309–315.Google Scholar
Campbell-Valois, F-X, Trost, M, Chemali, M, Dill, BD, Laplante, A, Duclos, S, Sadeghi, S, Rondeau, C, Morrow, IC and Bell, C 2012. Quantitative proteomics reveals that only a subset of the endoplasmic reticulum contributes to the phagosome. Molecular & Cellular Proteomics 11, M111. 016378.Google Scholar
Capel, PJ, Gerlag, PG, Hagemann, JF and Koene, RA 1980. The effect of 2-mercaptoethanol on IgM and IgG antibody activity. Journal of Immunological Methods 36, 77–80.Google Scholar
Chang, CC, Chow, CC, Tellier, LC, Vattikuti, S, Purcell, SM and Lee, JJ 2015. Second-generation PLINK. Rising to the challenge of larger and richer datasets. Gigascience 4, 7, https://doi.org/10.1186/s13742-015-0047-8 Google Scholar
Chaturvedi, S, Yuen, DA, Bajwa, A, Huang, Y-W, Sokollik, C, Huang, L, Lam, GY, Tole, S, Liu, G-Y, Pan, J, Chan, L, Sokolskyy, Y, Puthia, M, Godaly, G, John, R, Wang, C, Lee, WL, Brumell, JH, Okusa, MD and Robinson, LA 2013. Slit2 prevents neutrophil recruitment and renal ischemia-reperfusion injury. Journal of the American Society of Nephrology 24, 1274–1287.Google Scholar
Chiang, C-Y, Engel, A, Opaluch, AM, Ramos, I, Maestre, AM, Secundino, I, De Jesus, PD, Nguyen, QT, Welch, G and Bonamy, GM 2012. Cofactors required for TLR7-and TLR9-dependent innate immune responses. Cell Host & Microbe 11, 306–318.Google Scholar
De Morrée, A, Flix, B, Bagaric, I, Wang, J, van den Boogaard, M, Grand Moursel, L, Frants, RR, Illa, I, Gallardo, E, Toes, R and van der Maarel, SM 2013. Dysferlin regulates cell adhesion in human monocytes. Journal of Biological Chemistry 288, 14147–14157.Google Scholar
Dorshorst, BJ, Siegel, PB and Ashwell, CM 2011. Genomic regions associated with antibody response to sheep red blood cells in the chicken. Animal Genetics 42, 300–308.Google Scholar
Durinck, S, Spellman, PT, Birney, E and Huber, W 2009. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nature Protocols 4, 1184–1191.Google Scholar
Fife, MS, Howell, JS, Salmon, N, Hocking, PM, van Diemen, PM, Jones, MA, Stevens, MP and Kaiser, P 2011. Genome-wide SNP analysis identifies major QTL for Salmonella colonization in the chicken. Animal Genetics 42, 134–140.Google Scholar
Furmanski, AL, Saldana, JI, Ono, M, Sahni, H, Paschalidis, N, D’Acquisto, F and Crompton, T 2013. Tissue-derived hedgehog proteins modulate the differentiation and disease. The Journal of Immunology 190, 2641–2649.Google Scholar
Galibert, L, Diemer, GS, Liu, Z, Johnson, RS, Smith, JL, Walzer, T, Comeau, MR, Rauch, CT, Wolfson, MF, Sorensen, RA, Van der Vuurst de Vries, AR, Branstetter, DG, Koelling, RM, Scholler, J, Fanslow, WC, Baum, PR, Derry, JM and Yan, W 2005. Nectin-like protein 2 defines a subset of T-cell zone dendritic cells and is a ligand for class-I-restricted T-cell-associated molecule. Journal of Biological Chemistry 280, 21955–21964.Google Scholar
Gross, WG, Siegel, PB, Hall, RW, Domermuth, CH and DuBoise, RT 1980. Production and persistence of antibodies in chickens to sheep erythrocytes. 2. Resistance to infectious diseases. Poultry Science 59, 205–210.Google Scholar
Huang, DW, Sherman, BT, Tan, Q, Kir, J, Liu, D, Bryant, D, Guo, Y, Stephens, R, Baseler, MW and Lane, HC 2007. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Research 35, W169–W175.Google Scholar
Janeway, CA, Travers, P, Walport, M and Shlomchik, MJ 2001. The humoral immune response. In Immunobiology: the immune system in health and disease (5th edition. pp. 401–453. Garland Science, New York, NY, USA.Google Scholar
Leonhardt, RM, Fiegl, D, Rufer, E, Karger, A, Bettin, B and Knittler, MR 2010. Post-endoplasmic reticulum rescue of unstable MHC class I requires proprotein convertase PC7. Journal of Immunology 184, 2985–2998.Google Scholar
Luo, C, Qu, H, Ma, J, Wang, J, Li, C, Yang, C, Hu, X, Li, N and Shu, D 2013. Genome-wide association study of antibody response to Newcastle disease virus in chicken. BMC Genetics 14, 42.Google Scholar
Prinjha, R and Tarakhovsky, A 2013. Chromatin targeting drugs in cancer and immunity. Genes & Development 27, 1731–1738.Google Scholar
Pyo, C-W, Hur, S-S, Kim, Y-K, Kim, T-G and Kim, T-Y 2003. Association of TAP and HLA-DM genes with psoriasis in Koreans. Journal of Investigative Dermatology 120, 616–622.Google Scholar
Raeesi, V, Ehsani, A, Torshizi, RV, Sargolzaei, M, Masoudi, AA and Dideban, R 2017. Genome-wide association study of cell-mediated immune response in chicken. Journal of Animal Breeding and Genetics 134, 405–411.Google Scholar
Ruiz-Perez, VL, Blair, HJ, Rodriguez-Andres, ME, Blanco, MJ, Wilson, A, Liu, YN, Miles, C, Peters, H and Goodship, JA 2007. Evc is a positive mediator of Ihh-regulated bone growth that localises at the base of chondrocyte cilia. Development 134, 2903–2912.Google Scholar
Solomon, S, Masilamani, M, Rajendran, L, Bastmeyer, M, Stuermer, CA and Illges, H 2002. The lipid raft microdomain-associated protein reggie-1/flotillin-2 is expressed in human B cells and localized at the plasma membrane and centrosome in PBMCs. Immunobiology 205, 108–119.Google Scholar
Szklarczyk, D, Morris, J, Cook, H, Kuhn, M, Wyder, S, Simonovic, M, Santos, A, Doncheva, N, Roth, A and P. Bork “Von mering, C 2017. The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible. Nucleic Acids Research 45, D362–D368.Google Scholar
Uaesoontrachoon, K, Cha, H-J, Ampong, B, Sali, A, Vandermeulen, J, Wei, B, Creeden, B, Huynh, T, Quinn, J, Tatem, K, Rayavarapu, S, Hoffman, EP and Nagaraju, K 2013. The effects of MyD88 deficiency on disease phenotype in dysferlin-deficient A/J mice: role of endogenous TLR ligands. The Journal of Pathology 231, 199–209.Google Scholar
Van der Zijpp, AJ, Frankena, K, Boneschanscher, J and Nieuwland, MG 1983. Genetic analysis of primary and secondary immune responses in the chicken. Poultry Science 62, 565–572.Google Scholar
Wegmann, TG and Smithies, O 1966. A simple hemagglutination system requiring small amounts of red cells and antibodies. Transfusion 6, 67–73.Google Scholar
Wei, S, Moon, H-G, Zheng, Y, Liang, X, An, CH and Jin, Y 2013. Flotillin-2 modulates fas signaling mediated apoptosis after hyperoxia in lung epithelial cells. PLoS One 8, e77519.Google Scholar
Zeidler, R, Eissner, G, Meissner, P, Uebel, S, Tampe, R, Lazis, S and Hammerschmidt, W 1997. Downregulation of TAP1 in B lymphocytes by cellular and Epstein-Barr virus-encoded interleukin-10. Blood 90, 2390–2397.Google Scholar
Zhang, L, Li, P, Liu, R, Zheng, M, Sun, Y, Wu, D, Hu, Y, Wen, J and Zhao, G 2015. The identification of loci for immune traits in chickens using a genome-wide association study. PLoS One 10, e0117269.Google Scholar
Zhao, H, Anand, AR and Ganju, RK 2014. Slit2-Robo4 pathway modulates LPS-induced endothelial inflammation and its expression is dysregulated during endotoxemia. Journal of Immunology 192, 385–393.Google Scholar
Supplementary material: File

Raeesi et al. supplementary material

Tables S1-S2 and Figure S1

Download Raeesi et al. supplementary material(File)
File 1.4 MB