Non-synonymous Single Nucleotide Polymorphism on TLR1A gene as a candidate for immune function of Indonesian indigenous chicken




Abstract. Indrijani H, Hilmia N, Anang A, Pangestu MSP. 2024. Non-synonymous Single Nucleotide Polymorphism on TLR1A gene as a candidate for immune function of Indonesian indigenous chicken. Biodiversitas 25: 2434-2441. TLR1A is a candidate gene related to the immune system in chickens, which contributes to disease resilience, which could impact their productivity. This study aimed to determine mutations in the TLR1A gene in three indigenous Indonesian chickens namely, Pelung, Black Kedu and Sentul. A total of 127 DNA samples were used and consisted of 38, 41 and 48 respectively for Pelung, Black Kedu and Sentul chickens. DNA was isolated from white blood cells and amplification of TLR1A gene was conducted in part of exon 4 using PCR with specific primer. The sequencing results for the TLR1A gene were analyzed to identify mutations using the BioEdit and MEGA X programs. The results showed genetic polymorphisms in the TLR1A gene in Indonesian indigenous chicken. One synonymous mutation, g.710C>T, in which amino acid coded leusine at 207th, and four non-synonymous mutation, i.e., g.822A>G, altered amino acids coding from threonine to alanine (T245A), g.835C>T, which altered amino acids coding 249th from threonine to methionine (T249M), g.1015G>A that altered amino acids coding 309th from serine to aspargine (S309N) and g.1165T>G that changed amino acid from arginine to proline R359P. All mutation frequencies for the alleles are lower than those for the non-mutation alleles. The non-synonymous mutation of the TLR1A gene might alter the metabolism of this hormone related to the immune system in chickens.


Abbas AK, Lichtman AH, Pillai S. 2021. Cellular and Molecular Immunology, 6th ed. Elsevier Health Science.
Amirdahri SH, Janmohammadi A, Taghizadeh W, Lambert M, Olyayee E, Assadi S. 2023. The optimum ratio of digestible leucine: lysine in wheat-based diets for female broiler chickens from 8 – 21 days of age. J App Poult Res 32: 2. ISSN 1056-6171.
Barjesteh N, Behboudi S, Brisbin JT, Villanueva AI, Nagy É, Sharif S. 2014. TLR ligands induce antiviral responses in chicken macrophages. PLoS One 9:e105713.
Berghof TV, Visker MH, Arts JA, Parmentier HK, Van der Poel JJ, Vereijken AL, Bovenhuis H. 2018. Genomic region containing toll-like receptor genes has a major impact on total IGM antibodies including KLH-binding IGM natural antibodies in chickens. Frontiers in immunology 8: 1879.
Betts MJ, Russell RB. 2003. Amino acid properties and consequences of substitutions. In : John Wiley, Sons. Bioinformatics Genetics, England.
Bhavaniramya S, Vanajothi R, Vishnupriya S, Al-Aboody MS, Vijayakumar R, Baskaran D. 2019. Computational characterization of deleterious SNPs in Toll-like receptor gene that potentially cause mastitis in dairy cattle. Biocatalysis and Agricultural Biotechnology 19: 101151.
Bovenhuis H, Berghof TV, Visker MH, Arts JA, Visscher J, Van Der Poel JJ, Parmentier HK. 2022. Divergent selection for natural antibodies in poultry in the presence of a major gene. Genetics Selection Evolution 54: 1-13.
Dar MA, Urwat U, Ahmad SM, Ahmad R, Kashoo ZA, Dar TA, Bhat S, Mumtaz PJ, Shabir N, Shah RA, Heidari M. 2019. Gene expression and antibody response in chicken against Salmonella Typhimurium challenge. Poultry Science 98: 2008-2013.
Elluru SR, Kaveri SV, Bayry J. 2015. The protective role of immunoglobu- lins in fungal infections and inflammation. Semin Immunopathol 37:187–97.
El-Zayat SR, Sibaii H, Mannaa FA. 2019. Toll-like receptors activation, signaling, and targeting: an overview. Bull Natl Res Cent 43, 187.
Farooq M, Batool M, Kim MS, Choi S. 2021. Toll-Like Receptors as a Therapeutic Target in the Era of Immunotherapies. Front Cell Dev Biol.
Grönwall C, Silverman GJ. (2014). Natural IgM: beneficial autoantibodies for the control of inflammatory and autoimmune disease. J Clin Immunol 34: 12-21.
Hawn TR, Misch EA, Dunstan SJ, Thwaites GE, Lan NT, Quy HT, Chau TH, Rodrigues S, Nachman A, Janer M, Hien TT, Farar JJ, Aderem A. 2007. A common human TLR1 polymorphism regulates the innate immune response to lipopeptides. European Journal of Immunology 37: 2280-2289.
Johnson CM, Lyle EA, Omueti KO, Stepensky VA, Yegin O, Alpsoy E, Hamann L, Schumann RR, Tapping RI. 2007. Cutting edge: A common polymorphism impairs cell surface trafficking and functional responses of TLR1 but protects against leprosy. The Journal of Immunology 178: 7520-7524.
Keestra AM, de Zoete MR, Bouwman LI, Vaezirad MM, van Putten JP. 2013. Unique features of chicken Toll-like receptors. Developmental & Comparative Immunology 41: 316-323.
McGrath, C. 2021. Synonymous but not equal: a special section and virtual issue on phenotypic effects of synonymous mutations. Genome Biol. Evol. 13.
Nei M, Kumar S. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, USA.
Nihashi Y, Ono T, Kagami H, Takaya T. 2019. Toll-like receptor ligand-dependent inflammatory responses in chick skeletal muscle myoblasts. Developmental & Comparative Immunology 91: 115-122.
Palma J, Tokarz-Deptu?a B, Deptu?a J, Deptu?a W. 2018. Natural antibodies facts known and unknown. Cent Eur J Immunol 43: 466–75.
Regar NM, Mutia R, Widhyari DS, Kowel SH. 2013. Pemberian Ransum Kombinasi Herbal dengan Mineral Zink Terhadap Performan Ayam Broiler yang Diinfeksi Escherichia coli. Zootek 33 :35–40.
Rehman MS, Rehman SU, Yousaf W, Hassan FU, Ahmad W, Liu Q, Pan H. 2021. The potential of toll-like receptors to modulate avian immune system: exploring the effects of genetic variants and phytonutrients. Front Genet. doi: 10.3389/fgene.2021.671235.
Ruan WK, Zheng SJ. 2011 Polymorphisms of chicken toll-like receptor 1 type 1 and type 2 in different breeds. Poultry Science 90 : 1941-1947, ISSN 0032-5791,
Tchin BL, Ho WS, Pang SL, Ismail J. 2011. Gene-associated single nucleotide polymorphism (SNP) in cinnamate 4-hydroxylase (C4H) and cinnamyl alcohol dehydrogenase (CAD) genes from acacia mangium superbulk trees. Biotechnology 10:303–315
Velová H, Gutowska-Ding MW, Burt DW, Vinkler M. 2018. Toll-like receptor evolution in birds: gene duplication, pseudogenization, and diversifying selection. Mol Biol Evol.
Wondmeneh EJ, Van Arendonk JA, Van der Waaij EH, Ducro BJ, Parmen-tier HK. 2015. High natural antibody titers of indigenous chickens are related with increased hazard in confinement. Poult Sci 94: 1493–1498.
Yates CM, Sternberg MJ. 2013. Proteins and domains vary in their tolerance of non-synonymous single nucleotide polymorphisms (nsSNPs). Journal of Molecular Biology 425, 1274-1286.
Zhang J, Tan H, Cao Q, Su G, Yang P. 2021. Meta-analysis of miRNA variants associated with susceptibility to autoimmune disease. Disease Markers, 2021.