[1] Biek, R. and Real, L.A. (2010) The Landscape Genetics of Infectious Disease Emergence and Spread. Molecular Ecology, 19, 3515-3531.
http://dx.doi.org/10.1111/j.1365-294X.2010.04679.x
[2] Zhou, H., Hickford, J.G.H. and Fang, Q. (2005) Polymorphism of the DQA2 Gene in Goats. Journal of Animal Science, 83, 963-968.
[3] Yakubu, A., Salako, A.E., De Donato, M., Takeet, M.I., Peters, S.O., Adefenwa, M.A., Okpeku, M., Wheto, M., Agaviezor, B.O., Sanni, T.M., Ajayi, O.O., Onasanya, G.O., Ekundayo, O.J., Ilori, B.M., Amusan, S.A. and Imumorin, I.G. (2013) Genetic Diversity in Exon 2 at the Major Histocompatibility Complex DQB1 Locus in Nigerian Indigenous Goats. Biochemical Genetics, 51, 954-966.
http://dx.doi.org/10.1007/s10528-013-9620-y
[4] Niranjan, S.K., Deb, S.M., Kumar, S., Mitra, A., Sharma, A., Sakaram, D., Naskar, S., Sharma, D. and Sharma, S.R. (2010) Allelic Diversity at MHC Class 11 DQ Loci in Buffalo (Bubalusbubalis): Evidence for Duplication. Veterinary Immunology and Immunopathology, 138, 206-212.
http://dx.doi.org/10.1016/j.vetimm.2010.07.014
[5] Amills, M., Ramirez, O., Tomas, A., Obexer-Ruff, G. and Vidal, O. (2008) Positive Selection on Mammalian MHC-DQ Genes Revisited from a Multispecies Perspective. Genes and Immunity, 9, 651-658.
http://dx.doi.org/10.1038/gene.2008.62
[6] Ballingall, K.T., Luyai, A. and McKeever, D.J. (1997) Analysis of Genetic Diversity at the DQA Loci in African Cattle: Evidence for a BoLA-DQA3 Locus. Immunogenetics, 46, 237-244.
http://dx.doi.org/10.1007/s002510050268
[7] McKenzie, G.W., Abbott, A., Zhou, H., Fang, Q., Merrick, N., Forrest, R.H., Sedcole, J.R. and Hickford, J.G. (2012) Genetic Diversity of Selected Genes That Are Potentially Economically Important in Feral Sheep of New Zealand. Genetics Selection Evolution, 42, 43.
[8] Vandre, R.K., Gowane, G.R., Sharma, A.K. and Tomar, S.S. (2014) Immune Responsive Role of MHC Class II DQA1 Gene in Livestock. Livestock Research International, 2, 1-7.
[9] Vandre, R.K., Sharma, A.K., Gowane, G.R., Rajoriya, R., Rajoriya, S., Sinha, R.K., Kumar, A., Shivhare, M., Caser, D.D. and Meshram, S.K. (2014) Polymorphism and Disease Resistance Possessions of MHC Class II BoLA Genes. DHR International Journal of Biomedical and Life Sciences, 5.
http://www.doublehelixresearch.com/DHRIJBLS
[10] George, P.D.C., Rajasekaran, R., Sudandiradoss, C., Ramanathan, K., Purohit, R. and Sethumadhavan, R. (2008) A Novel Computational and Structural Analysis of nsSNPs in CFTR Gene. Genomic Medicine, 2, 23-32.
http://dx.doi.org/10.1007/s11568-008-9019-8
[11] Liu, L. and Kumar, S. (2013) Evolutionary Balancing Is Critical for Correctly Forecasting Disease Associated Amino Acid Variants. Molecular Biology and Evolution, 30, 1252-1257.
http://dx.doi.org/10.1093/molbev/mst037
[12] Zemla, D., Kostova, T., Gorchakov, R., Volkova, E., Beasley, D.W.C., Cardosa, J., Weaver, S.C., Vasilakis, N. and Naraghi-Arani, P. (2014) Genesv—An Approach to Help Characterize Possible Variations in Genomic and Protein Sequences. Bioinformatics and Biology Insights, 8, 1-16.
http://dx.doi.org/10.4137/BBI.S13076
[13] Choi, Y., Sims, G.E., Murphy, S., Miller, J.R. and Chan, A.P. (2012) Predicting the Functional Effect of Amino Acid Substitutions and Indels. PLoS ONE, 7, e46688.
http://dx.doi.org/10.1371/journal.pone.0046688
[14] Larkin, M.A., Blackshields G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J. and Higgins, D.G. (2007) Clustal W and Clustal X Version 2.0. Bioinformatics, 23, 2947-2948.
http://dx.doi.org/10.1093/bioinformatics/btm404
[15] Bromberg, Y. and Rost, B. (2007) SNAP: Predicts Effect of Non-Synonymous Polymorphisms on Function. Nucleic Acids Research, 35, 3823-3835.
http://dx.doi.org/10.1093/nar/gkm238
[16] Ng, P.C. and Henikoff, S. (2003) SIFT: Predicting Amino Acid Changes That Affect Protein Function. Nucleic Acids Research, 31, 3812-3814.
http://dx.doi.org/10.1093/nar/gkg509
[17] Bairoch, A. and Apweiler, R. (2000) The SWISS-PROT Protein Sequence Database and Its Supplement TrEMBL in 2000. Nucleic Acids Research, 28, 45-48.
http://dx.doi.org/10.1093/nar/28.1.45
[18] Bromberg, Y., Yachdav, G. and Rost, B. (2008) SNAP Predicts Effect on Protein Function. Bioinformatics Applications Note, 24, 2397-2398.
http://dx.doi.org/10.1093/bioinformatics/btn435
[19] Felsenstein, J. (1985) Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution, 39, 783-791.
http://dx.doi.org/10.2307/2408678
[20] Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2011) MEGA 5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 28, 2731-2739.
http://dx.doi.org/10.1093/molbev/msr121
[21] Zhao, Y., Xu, H., Shi, L. and Zhang, J. (2011) Polymorphisms in Exon 2 of MHC Class II DRB3 Gene of 10 Domestic Goats in Southwest China. Asian-Australasian Journal of Animal Science, 24, 752-756.
http://dx.doi.org/10.5713/ajas.2011.10398
[22] Amills, M. (2014) The Application of Genomic Technologies to Investigate the Inheritance of Economically Important Traits in Goats. Advances in Biology, 2014, Article ID: 904281.
http://dx.doi.org/10.1155/2014/904281
[23] McManus, C., Paim, T.D.P., de Melo, C.B., Brasil, B.S.A.F. and Paiva, S.R. (2014) Selection Methods for Resistance to and Tolerance of Helminths in Livestock. Parasite, 21, Article No.: 56.
http://dx.doi.org/10.1051/parasite/2014055
[24] Hickford, J.G.H., Forrest, R.H.J., Zhou, H., Fang, Q. and Frampton, C.M. (2011) Association between Variation in Faecal Egg Count for a Mixed Field-Challenge of Nematode Parasites and Ovine MHC-DQA2 Polymorphism. Veterinary Immunology and Immunopathology, 144, 312-320.
http://dx.doi.org/10.1016/j.vetimm.2011.08.014
[25] Kemper, K.E., Emery, D.L., Bishop, S.C., et al. (2011) The Distribution of SNP Marker Effects for Faecal Worm Egg Count in Sheep, and the Feasibility of Using These Markers to Predict Genetic Merit for Resistance to Worm Infections. Genetics Research, 93, 203-219.
http://dx.doi.org/10.1017/S0016672311000097
[26] Preston, S.J.M., Sandeman, M., Gonzalez, J. and Piedrafita, D. (2014) Current Status for Gastrointestinal Nematode Diagnosis in Small Ruminants: Where Are We and Where Are We Going? Journal of Immunology Research, 2014, Article ID: 210350.
http://dx.doi.org/10.1155/2014/210350
[27] Ellis, S.A. and Hammond, J.A. (2014) The Functional Significance of Cattle Major Histocompatibility Complex Class I Genetic Diversity. Annual Review of Animal Biosciences, 2, 285-306.
http://dx.doi.org/10.1146/annurev-animal-022513-114234
[28] Wuliji, T., Hickford, J.G.H., Lamberson, W.R., Shanks, B.C. and Azarpajouh, S. (2014) Ovine Footrot Gene Marker Screening in a Katahdin Sheep Flock. Proceedings of Joint Annual Meeting of ASAS, Kansas City, 20-24 July 2014.
[29] Takeshima, S., Chen, S., Miki, M., Kado, M. and Aida, Y. (2008) Distribution and Origin of Bovine Major Histocompatibility Complex Class II DQA1 Genes in Japan. Tissue Antigens, 72, 195-205.
http://dx.doi.org/10.1111/j.1399-0039.2008.01092.x
[30] Sun, Y., Zhang, X., Xi, D., Li, G., Wang, L., Zheng, H., Du, M., Gu, Z., Yang, Y. and Yang, Y. (2015) Isolation and cDNA Characteristics of MHC-DRA Genes from Gayal (Bos frontalis) and Gaytle (Bos frontalis × Bostaurus). Biotechnology & Biotechnological Equipment, 29, 33-39.
http://dx.doi.org/10.1080/13102818.2014.986128
[31] Reche, P.A. and Reinherz, E.L. (2003) Sequence Variability Analysis of Human Class I and Class II MHC Molecules: Functional and Structural Correlates of Amino Acid Polymorphisms. Journal of Molecular Biology, 331, 623-641.
http://dx.doi.org/10.1016/S0022-2836(03)00750-2