[
Adeleke M. A., Peters S. O., Ogunmodede D. T., Oni O. O., Ajayi O. L., Wheto M. Adebambo O. A. (2015): Genotype effect on distribution pattern of maternally derived antibody against Newcastle disease in Nigerian local chickens. Tropical Animal Health and Production 47: 391–394. doi: 10.1007/s11250-014-0728-9.10.1007/s11250-014-0728-9
]Search in Google Scholar
[
Alders R. G., Dumas S. E., Rukambile E., Magoke G., Maulaga W., Jong J., Costa R. (2018): Family poultry: Multiple roles, systems, challenges, and options for sustainable contributions to household nutrition security through a planetary health lens. Maternal and Child Nutrition 14(S3), e12668. doi: 10.1111/mcn.12668.10.1111/mcn.12668
]Search in Google Scholar
[
Balloux F., Amos W., Coulson T. (2004): Does heterozygosity estimate inbreeding in real population? Molecular Ecology 13: 3021–3031. doi: 10.1111/j.1365-294X.2004.02318.x.10.1111/j.1365-294X.2004.02318.x
]Search in Google Scholar
[
Bateson Z. W., Hammerly S. C., Johnson J. A., Morrow M. E., Whittingham L. A., Dunn P. O. (2016): Specific alleles at immune genes, rather than genome-wide heterozygosity, are related to immunity and survival in the critically endangered Attwater’s prairie-chicken. Molecular Ecology 25: 4730–4744. doi: 10.1111/mec.13793.10.1111/mec.13793
]Search in Google Scholar
[
Bin Y., Wang X., Zhao L., Wen P. Xia J. (2019): An analysis of mutational signatures of synonymous mutations across 15 cancer types. Biomedical Central Medical Genetics 20: 190. doi: 10.1186/s12881-019-0926-4.10.1186/s12881-019-0926-4
]Search in Google Scholar
[
Botstein D., White R.L., Skolnick M., Davis R. W. (1980): Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32: 314–331.
]Search in Google Scholar
[
Brambilla A., Keller L., Bassano B., Grossen C. (2017): Heterozygosity-fitness correlation at the major histocompatibility complex despite low variation in Alpine ibex (Capra ibex). Evolutionary Applications 11: 631–644. doi: 10.1111/eva.12575.10.1111/eva.12575
]Search in Google Scholar
[
Brock P. M., Hall A. J., Goodman S. J., Cruz M., Acevedo-Whitehouse K. (2013): Applying the tools of ecological immunology to conservation: A test case in the Galapagos sea lion. Animal Conservation 16: 19–31. doi: 10.1111/j.1469-1795.2012.00567.x10.1111/j.1469-1795.2012.00567.x
]Search in Google Scholar
[
Brumfield R. T., Beerli P., Nickerson D. A., Edwards S. V. (2003): The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology and Evolution 18: 249–256. doi: 10.1016/S0169-5347(03)00018-110.1016/S0169-5347(03)00018-1
]Search in Google Scholar
[
Bush S. W., Moore J. H. (2012): Genome-wide association studies. Public Library of Science Computational Biology 8, e1002822. doi: 10.1371/journal.pcbi.100282210.1371/journal.pcbi.1002822353128523300413
]Search in Google Scholar
[
Cartegni L., Chew S. L., Krainer A. R. (2002): Listening to silence and understanding nonsense: Exonic mutations that affect splicing. Nature Reviews Genetics 3: 285–298. doi: 10.1038/nrg775.10.1038/nrg77511967553
]Search in Google Scholar
[
Chamary J. V., Parmley J. L., Hurst L. D. (2006): Hearing silence: Non-neutral evolution at synonymous sites in mammals. Nature Reviews Genetics 7: 98–108. doi: 10.1038/nrg1770.10.1038/nrg177016418745
]Search in Google Scholar
[
Chen R., Davydov E. V., Sirota M., Butte A. J. (2010): Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. Public Library of Science ONE 5, e13574. doi: 10.1371/journal.pone.0013574.10.1371/journal.pone.0013574296264121042586
]Search in Google Scholar
[
Chen W., Hou L., Zhang Z., Pang X., Li Y. (2017): Genetic Diversity, Population Structure, and Linkage Disequilibrium of a Core Collection of Ziziphus jujuba Assessed with Genome-wide SNPs Developed by Genotyping-by-sequencing and SSR Markers. Frontiers in Plant Science 8: 575. doi: 10.3389/fpls.2017.00575.10.3389/fpls.2017.00575539412628458680
]Search in Google Scholar
[
Croze M., Ziukoric D., Stephan W., Hutter S. (2016): Balancing selection on immunity gene: Review of the current literature and new analysis in Drosophila melanogaster. Zoology 119: 322–329. doi: 10.1016/j. zool.2016.03.004.
]Search in Google Scholar
[
Darnell J. E., Kerr I. M., Stark G. R. (1994): Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins. Science 264: 1415–1421. doi: 10.1126/science.8197455.10.1126/science.81974558197455
]Search in Google Scholar
[
De S., Zhang B., Shih T., Singh S., Winkler A., Donnelly R., Barnes B.J. (2018): B cell-intrinsic role for IRF5 in TLR9/BCR-induced human B cell activation, proliferation, and plasmablast differentiation. Frontiers in Immunology 8: 1938. doi: 10.3389/fimmu.2017.01938.10.3389/fimmu.2017.01938576818029367853
]Search in Google Scholar
[
Desjardins P., Conklin D. (2010): Nanodrop microvolume quantification of nucleic acid. Journal of Visualized Experiments 22: 2565. doi: 10.3791/2565.10.3791/2565334630821189466
]Search in Google Scholar
[
Doveri S., Lee, D., Maheswaran M., Powell W. (2008): Principles and Practices of Plant Genomics (Volume 1). USA, Enfield Science Publishers.
]Search in Google Scholar
[
Durosaro S. O., Ilori B. M., Oguntade D. O., Adebambo A. O., Ozoje M. (2019): Evolution of exon 3 region of interferon regulatory factor-5 gene in Nigerian indigenous chickens. The Pacific Journal of Science and Technology 20: 211–216.
]Search in Google Scholar
[
Ensemble chicken Gallus gallus 5.0.www.ensembl.org. Retrieved on August 9, 2017.
]Search in Google Scholar
[
Esmaeili Reykande S., Rezaei A., Sadr M., Sabani M., Najmi Varzaneh F., Rezaei N. (2018): Association of interferon regulatory factor 5 (IRF5) gene polymorphisms with juvenile idiopathic arthritis. Clinical Rheumatology 37: 2661 – 2665. doi: 10.1007/s10067-018-4010-910.1007/s10067-018-4010-929423720
]Search in Google Scholar
[
Felsentein J. (1965): The effect of linkage on directional selection. Genetics 52: 349 – 363.10.1093/genetics/52.2.34912108555861564
]Search in Google Scholar
[
Forcada J., Hoffman J. I. (2014): Climate change selects for heterozygosity in a declining fur seal population. Nature 511: 462–465. doi: 10.1038/nature13542.10.1038/nature1354225056064
]Search in Google Scholar
[
Fuji Y., Shimizu T., Kusumoto M., Kyogoku Y., Taniguchi T., Hakoshima T. (1999): Crystal structure of an IRF-DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences. European Molecular Biology Organisation Journal 18: 5028–5041. doi: 10.1093/emboj/18.18.5028.10.1093/emboj/18.18.5028117157410487755
]Search in Google Scholar
[
Guo X., Elston R. C. (1999): Linkage information content of polymorphic markers. Human Heredity 49: 112–118. doi: 10.1159/000022855.10.1159/000022855
]Search in Google Scholar
[
Hale M. C., McCormick C. R., Jackson J. R., Dewoody J. A. (2009): Next-generation pyrosequencing of gonad transcriptomes in the polyploidy lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery. BioMed Central Genomics 10: 203–213. doi: 10.1186/1471-2164-10-203.10.1186/1471-2164-10-203
]Search in Google Scholar
[
Hall T. A. (1999): BioEdit: A user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98.
]Search in Google Scholar
[
Hansson B., Westerberg L. (2002): Correlation between heterozygosity and fitness in natural populations. Molecular Ecology 11: 2467–2474. doi: 10.1046/j.1365-294X.2002.01644.x.10.1046/j.1365-294X.2002.01644.x
]Search in Google Scholar
[
Hecht M., Bromberg Y., Rost B. (2015): Better prediction of functional effects for sequence variants. Biomedical Central Genomics 16 (Suppl 8): 51, doi: 10.1186/1471-2164-16-S8-S1. http://www.codoncode.com/aligner.10.1186/1471-2164-16-S8-S1
]Search in Google Scholar
[
International HapMap Consortium (2007): A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851–861. doi: 10.1038/nature06258.10.1038/nature06258
]Search in Google Scholar
[
Keller I., Bensasson D., Nichols R. A. (2007): Transition-transversion bias is not universal: A counter example from grasshopper pseudo genes. Public Library of Science Genetics 3, e22. doi: 10.1371/journal.pgen.0030022.10.1371/journal.pgen.0030022
]Search in Google Scholar
[
Keller L. F., Waller D. M. (2002): Inbreeding effects in wild populations. Trends in Ecology and Evolution 17: 230–241. doi: 10.1016/S0169-5347(02)02489-8.10.1016/S0169-5347(02)02489-8
]Search in Google Scholar
[
Krausgruber T. (2011): Interferon regulatory factor-5: An important player in macrophage polarization and TNF regulation. A thesis submitted for the degree of Doctor of Philosophy at the Kennedy Institute of Rheumatology. Faculty of Medicine, Imperial College, London. 225 p.
]Search in Google Scholar
[
Lazzaro B. P., Clark A. G. (2003): Molecular population genetics of inducible antibacterial peptide genes in Drosophila melanogaster. Molecular Biology and Evolution 20: 914–923. doi: 10.1093/molbev/msg109.10.1093/molbev/msg10912716986
]Search in Google Scholar
[
Leache A. D., Oaks J. R. (2017): The utility of single nucleotide polymorphism (SNP) data in phylogenetics. Annual Review of Ecology, Evolution and Systematics 48: 69–84. doi: 10.1146/annurev-ecolsys-110316-022645.10.1146/annurev-ecolsys-110316-022645
]Search in Google Scholar
[
Lesk A. M. (2002): Introduction to Bioinformatics. (2nd edition). Oxford, Oxford University Press.
]Search in Google Scholar
[
Librado P., Rozas J. (2009): DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451–1452. doi: 10.1093/bioinformatics/btp187.10.1093/bioinformatics/btp18719346325
]Search in Google Scholar
[
Lien C., Fang C., Huso D., Livak F., Lu R., Pitha, P. M. (2010): Critical role of IRF-5 in regulation of B-cell differentiation. Proceedings of the National Academy of Science of the United States of America 107: 4664 – 4668. doi: 10.1073/pnas.0911193107.10.1073/pnas.0911193107284205420176957
]Search in Google Scholar
[
Lyons D. M., Lauring A. S. (2017): Evidence for the Selective Basis of Transition-to-Transversion Substitution Bias in Two RNA Viruses. Molecular Biology and Evolution 34: 3205–3215. doi: 10.1093/molbev/msx251.10.1093/molbev/msx251585029029029187
]Search in Google Scholar
[
Maynard S. J., Haigh J. (2007): The hitch-hiking effect of a favourable gene. Genetic Research 89: 391 – 403. doi: doi: 10.1017/S0016672308009579.10.1017/S001667230800957918976527
]Search in Google Scholar
[
Meraro D., Hashmueli S., Koren B., Azriel A., Oumard A., Kirchhoff S. (1999): Protein-protein and DNA-protein interactions affect the activity of lymphoid-specific IFN regulatory factors. Journal of Immunology 163: 6468–6478.
]Search in Google Scholar
[
Miceli M. C., von Hoegen P., Parnes J. R. (1990): Adhesion versus co-receptor function of CD4 and CD8: Role of the cytoplasmic tail in co-receptor activity. Proceedings of the National Academy of Sciences of the United States of America 88: 2623 – 2627. doi: 10.1073/pnas.88.7.262310.1073/pnas.88.7.2623512901901411
]Search in Google Scholar
[
Nackley A. G. (2006): Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science 314: 1930–1933. doi: 10.1126/science.1131262.10.1126/science.113126217185601
]Search in Google Scholar
[
Nehyba J., Hrdličková R., Burnside J., Bose H. R. (2002): A novel interferon regulatory factor (IRF), IRF-10, has a unique role in immune defense and is induced by the v-Reloncoprotein. Molecular and Cellular Biology 22: 3942–3957. doi: 10.1128/MCB.22.11.3942-3957.2002.10.1128/MCB.22.11.3942-3957.200213382411997525
]Search in Google Scholar
[
Ohta T., Kimura M. (1969): Linkage disequilibrium at steady state determined by random genetic drift and recurrent mutation. Genetics 63: 229–238.10.1093/genetics/63.1.22912123345365295
]Search in Google Scholar
[
Oke U. K. (2011): Influence of some major genes on growth traits of local pullets in humid tropical environment. Agriculture and Biology Journal of North America 2: 570 – 576. doi: 10.5251/abjna.2011.2.4.570.576.
]Search in Google Scholar
[
Paun A., Pitha P. M. (2007): The IRF family, revisited. Biochimie 89: 744 – 753. doi: 10.1016/j. biochi.2007.01.014.
]Search in Google Scholar
[
Payne J. L., Menardo F., Trauner A., Borrell S., Gygli S. M., Loiseau C., Gagneux S. Hall A. R. (2019): Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis. Public Library of Science Biology 17, e3000265. doi: 10.1371/journal.pbio.3000265.10.1371/journal.pbio.3000265653293431083647
]Search in Google Scholar
[
Platten J. D., Cobb J. N., Zantua R. E. (2019): Criteria for evaluating molecular markers: Comprehensive quality metrics to improve marker-assisted selection. Public Library of Science ONE 14: e0210529. doi: 10.1371/journal.pone.0210529.10.1371/journal.pone.0210529633333630645632
]Search in Google Scholar
[
Sauna Z. E., Kimchi-Sarfaty C. (2011): Understanding the contribution of synonymous mutations to human disease. Nature Reviews Genetics 12: 683 – 691. doi: 10.1038/nrg3051.10.1038/nrg305121878961
]Search in Google Scholar
[
Singh N., Choudhury D. R., Singh A. K., Kumar S., Srinivasan K., Tyagi R. (2013): Comparison of SSR and SNP markers in estimation of genetic diversity and population structure of Indian rice varieties. Public Library of Science ONE 8, e84136. doi: 10.1371/journal.pone.0084136.10.1371/journal.pone.0084136
]Search in Google Scholar
[
Skittrall J. P., Ingemarsdotter C. K., Gog J. R., Lever A. M. L. (2019): A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance. Public Library of Science Computational Biology 15, e1007345. doi: 10.1371/journal.pcbi.1007345.10.1371/journal.pcbi.1007345
]Search in Google Scholar
[
Slatkin M. (2008): Linkage disequilibrium: Understanding the evolutionary past and mapping the medical future. Nature Reviews Genetics 9: 477 – 485. doi: 10.1038/nrg2361.10.1038/nrg2361
]Search in Google Scholar
[
Sonaiya E. B., Olori V. E. (1990): Family poultry production in south western Nigeria. Proceedings of International workshop (pp. 243 – 247). Ile Ife Nigeria: Obafemi Awolowo University.
]Search in Google Scholar
[
Srinivasan S., Clements J. A., Batra J. (2016): Single nucleotide polymorphisms in clinics: fantasy or reality for cancer? Critical Reviews in Clinical Laboratory Sciences 53: 29–39. doi: 10.3109/10408363.2015.1075469.10.3109/10408363.2015.1075469
]Search in Google Scholar
[
Stein T., Wollschlegel A., Te H., Weiss J., Joshi K., Kinzel B., Billich A., Guntermann C., Lehmann J. C. U. (2018): Interferon regulatory factor 5 and nuclear factor kappa-β exhibit cooperating but also divergent roles in the regulation of pro-inflammatory cytokines important for the development of TH1 and TH17 responses. Federation of European Biomedical Sciences Journal 285: 3097 – 3113. doi: 10.1111/febs.14600.10.1111/febs.14600
]Search in Google Scholar
[
Tamura T., Yanai H., Savitsky D., Taniguchi T. (2008): The IRF family transcription factors in immunity and oncogenesis. Annual Review of Immunology 26: 535 – 584. doi: 10.1146/annurev. immunol.26.021607.090400.
]Search in Google Scholar
[
Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. (2013): MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution 30: 2725 – 2729. doi: 10.1093/molbev/mst197.10.1093/molbev/mst197
]Search in Google Scholar
[
Taniguchi T., Ogasawara K., Takaoka A., Tanaka N. (2001): IRF family or transcription factors as regulators of host defense. Annual Review of Immunology 19: 623–655. doi: 10.1146/annurev. immunol.19.1.623.
]Search in Google Scholar
[
Thompson J. D., Higgins D. G., Gibson T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighing, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673 – 4680. doi: 10.1093/nar/22.22.4673.10.1093/nar/22.22.4673
]Search in Google Scholar
[
Wakeley J. (1996): The excess of transitions among nucleotide substitutions: New methods of estimating transition bias underscore its significance. Trends in Ecological Evolution 11: 158 – 162. doi: 10.1016/0169-5347(96)10009-4.10.1016/0169-5347(96)10009-4
]Search in Google Scholar
[
Wimmers K., Ponsuksili S., Hardge T., Valle-Zarate A., Mathur P. K., Horst P. (2000): Genetic distinctness of African, Asian and South American local chickens. Animal Genetics 31: 159 – 165. doi: 10.1046/j.1365-2052.2000.00605.x10.1046/j.1365-2052.2000.00605.x10895305
]Search in Google Scholar
[
Wong J. T., de Bruyn J., Bagnol B., Grieve H., Li M., Pym R., Alders R. G. (2017): Small-scale poultry and food security in resource-poor settings: A review. Global Food Security 15: 43 – 52. doi: 10.1016/j. gfs.2017.04.003.
]Search in Google Scholar
[
Wright S. (1992): Coefficient of inbreeding and relationship. The American Naturalist 56: 330 – 338.10.1086/279872
]Search in Google Scholar
