Study of MHC polymorphism and its linkage to IGF1 gene in Khorasan indigenous chicken


1 Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran

2 Department of Microbiology and Immunology, School of Veterinary Medicine, University of Tehran, Tehran, Iran


BACKGROUND: Indigenous chickens could serve as precious genetic resources that should be considered in conservation and breeding programs. The Major Histocompatibility Complex (MHC) has a strong association to disease resistance/susceptibility, production and reproduction traits in chicken. Therefore, identifying its polymorphism in populations under selective breeding could be used for selection of disease resistant and higher productive breeds. MHC association with quantitative traits could be  a result of its linkage with causative genes controlling these traits. Insulin-like growth factor 1 (IGF1) is a candidate marker for phenotypic traits in chicken which are associated with important production and reproduction features. Objectives: Based on this hypothesis, MHC polymorphism and its association to IGF1 gene (as a marker for production traits) were investigated in Khorasan indigenous chicken. Methods: In total, 313 DNA samples that belonged to the Khorasan indigenous chicken were analyzed. LEI0258 microsatellite marker and fragment analysis method was used for MHC genotyping. Single nucleotide polymorphism (SNP) of the IGF1 5’-UTR was detected by restriction fragment length polymorphism (PCR-RFLP) and PstI restriction endonuclease enzyme. Linkage disequilibrium between MHC and IGF1 loci were also determined using SAS/Genetics software and likelihood ratio test. Results: Collectively, 25 different alleles (185-493 bp) and 76 genotypes of LEI0258 microsatellite were identified in Khorasan population. Two alleles, A (PstI -) and B (PstI +) and three genotypes (AA, AB and BB) were identified for IGF1 gene. Significant linkage disequilibrium (p=0.0083) was observed between LEI0258 and IGF1 loci in this population. Conclusions: These results indicate a high MHC genetic diversity in Khorasan indigenous chicken as a valuable genetic resource. Results from MHC/IGF1 linkage study confirm the hypothesis that MHC association with production traits could be as a result of MHC linkage with causative genes controlling the traits.


Abbasi, H.A., Kazemi, M. (2011) Detection of polymorphism at the Insulin Like Growth Factor-I gene in Mazandaran native chicken using polymerase chain reaction-restriction fragment length polymorphism method. Am J Vet Sci. 6: 80-83.
Bashalkhanov, S., Pandey, M., Rajora, O. (2009) A simple method for estimating genetic diversity in large populations from finite sample sizes. BMC Genetics. 10: 84.
Bulut, Z., Kurar, E., Ozsensoy, Y., Nizamlioglu, M., Garip, M., Yilmaz, A., Caglayan, T., Dere, S., Kurtoglu, V., Dogan, M. (2013) Determination of chromosomal regions affecting body weight and egg production in Denizli X White Leghorn F2 populations. Eurasian J Vet Sci. 29: 30-38.
Chang, C.S., Chen, C.F., Berthouly-Salazar, C., Chazara, O., Lee, Y.P., Chang, C.M., Chang, K.H., BedHom, B., Tixier-Biochard, M. (2011) A global analysis of molecular markers and phenotypic traits in local chicken breeds in Taiwan. Anim Genet. 43: 172-182.
Chatterjee, R., Sharma, R.P., Bhattacharya, T.K., Niranjan, M., Reddy, B.L. (2010) Microsatellite variability and its relationship with growth, egg production, and immunocompetence traits in chickens. Biochem Genet. 48: 71-82.
Cheng, H.H. (2003) 21 Selection for Disease Resistance: Molecular Genetic Techniques.In: Poultry Genetics, Breeding, and Biotechnology.Muir, W.M., Aggrey, S.E. (eds.). (1st ed.) CABI publishing, UK. p. 385-399.
Dunnington, E.A., Larsen, A.S., O’Sullivan, N.P., Siegel, P.B. (1992) Growth and egg production traits in chickens as influenced by major histocompatibility types and background genomes. J Anim Breed Genet. 109: 188-196.
Ewald, S.J., Ye, X., Avendano, S., McLeod, S., Lamont, S.J., Dekkers, J.C. (2007) Associations of BF2 alleles with antibody titres and production traits in commercial pure line broiler chickens. Anim Genet. 38: 174-176.
Fulton, J.E., Juul-Madsen, H.R., Ashwell, C.M., McCarron, A.M., Arthur, J.A., O’Sullivan, N.P., Taylor Jr, R.L. (2006) Molecular genotype identification of the Gallus gallus major histocompatibility complex. Immunogenetics. 58: 407-421
Hoffmann, I. (2009) The global plan of action for animal genetic resources and the conservation of poultry genetic resources. World Poult Sci J. 65: 286-297.
Hunt, H.D., Jadhao, S., Swayne, D.E. (2010) Major histocompatibility complex and background genes in chickens influence susceptibility to high pathogenicity avian influenza virus. Avian Dis. 54: 572-575.
Izadi, F., Ritland, C., Cheng KM. (2011) Genetic diversity of the major histocompatibility complex region in commercial and noncommercial chicken flocks using the LEI0258 microsatellite marker. Poult Sci. 90: 2711-2717.
Javanrouh Aliabad, A., Seyedabadi, H., Taheri Dezfuli, B. (2011) Association of insulin-like growth factor-I gene with body comosition traits in Iranian commercial broiler lines. World App Sci J. 14: 71-76.
Joiner, K.S., Hoerr, F.J., Van, S.E., Ewald, S.J. (2005) The avian major histocompatibility complex influences bacterial skeletal disease in broiler breeder chickens. Vet Pathol. 42: 275-281.
Kim, M.H., Seo, D.S., Ko, Y. (2004) Relationship between egg productivity and
insulin-like growth factor-I genotypes in Korean native Ogol chickens. Poult Sci. 83: 1203-1208.
Lakshmanan, N., Gavora, J.S., Lamont, S.J. (1997) Major histocompatibility complex class II DNA polymorphisms in chicken strains selected for Marek’s disease resistance and egg production or for egg production alone. Poult Sci. 76: 1517-1523.
Li, H.F., Zhu, W., Chen, K., Song, W., Shu, J., Han, W. (2010) Effect of the polymorphism of GHR gene and IGF-I gene on egg quality in wenchang chicken. Res J Poult Sci. 3: 19-22.
Lima-Rosa, C.A.D.V., Canal, C.W., Fallavena, P.R.V., Freitas, L.B.D., Salzano, F.M. (2005) LEI0258 microsatellite variability and its relationship to B-F haplotypes in Brazilian (blue-egg Caipira) chickens. Genet Mol Biol. 28: 386-389.
Lunden, A., Edfors-Lilja, I., Johansson, K., Liljedahl, L.E. (1993) Associations between major histocompatibility complex genes and production traits in White Leghorns. Poult Sci. 72: 989-999.
Lwelamira, J., Kifaro, G.C., Gwakisa, P.S., Msoffe, P.L.M. (2008) Association of LEI0258 microsatellite alleles with antibody response against Newcastle disease virus vaccine and body weight in two Tanzania chicken ecotypes. Afr J Biotechnol. 7: 714-720.
Malago, J.J., Baitilwake, M.A. (2009) Egg traits, fertility, hatchability and chick survivability of Rhode Island Red, local and crossbred chickens. Tanz Vet J. 26: 24-36.
McConnell, S.K., Dawson, D.A., Wardle, A., Burke, T. (1999) The isolation and mapping of 19 tetranucleotide microsatellite markers in the chicken. Anim Genet. 30: 183-189.
Miller, M.M., Bacon, L.D., Hala, K., Hunt, H.D., Ewald, S.J., Kaufman, J., Zoorob, R., Briles, W.E. (2004) Nomenclature for the chicken major histocompatibility (B and Y) complex. Immunogenetics. 56: 261-279.
Mueller, J. (2004) Linkage disequilibrium for different scales and applications. Brief Bioinform. 5: 355-364.
Muir, W.M., Wong, G.K.S., Zhang, Y., Wang, J.M. Groenen, A., Crooijmans, R.P., Megens, H.J., Zhang, H., Okimoto, R., Vereijken, A., Jungerius, A., Albers, G.A.A., Lawley, C.T., Delany, M.E., MacEachern, S., Cheng, H.H. (2008) Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proc Natl Acad Sci. 105: 17312-17317.
Nagaraja, S.C., Aggrey, S.E., Yao, J., Zadworny, D., Fairfull, R.W., Kuhnlein, U. (2000) Trait association of a genetic marker near the IGFI gene in egg-laying chickens. J Hered. 91: 150-156.
Nikbakht, G., Esmailnejad, A., Barjesteh, N. (2013) LEI0258 Microsatellite Variability in Khorasan, Marandi, and Arian Chickens. Biochem Genet. 51: 341-349.
Notter, D.R. (1999) The importance of genetic diversity in livestock populations of the future. J Anim Sci. 77: 61-69.
Owen, J.P., Delany, M.E., Mullens, B.A. (2008) MHC haplotype involvement in avian resistance to an ectoparasite. Immunogenetics. 60: 621-631.
Safalaoh, C.L. (2001) Village chicken upgrading programme in Malawi. World Poult Sci J. 57: 180-187.
Sander, J.E. (1993) The major histocompatiblity complex and its role in poultry production. World Poult Sci J. 49: 132.
Schou, T.W., Permin, A., Juul-Madsen, H.R., Sorensen, P., Labouriau, R., Nguyen, T.L., Fink, M., Pham, S.L. (2007) Gastrointestinal helminths in indigenous and exotic chickens in Vietnam: association of the intensity of infection with the Major Histocompatibility Complex. Parasitology. 134: 561-573.
Sheldon, B.L. (2000) Research and development in 2000: Directions and priorities for the World’s Poultry Science Community. Poult Sci. 78: 147-158.
Suzuki, K., Matsumoto, T., Kobayashi, E., Uenishi, H., Churkina, I., Plastow, G., Yamashita, H., Hamasima, N., Mitsuhashi, T. (2010) Genotypes of chicken major histocompatibility complex B locus associated with regression of Rous sarcoma virus J-strain tumors. Poult Sci. 89: 651-657.
Tadelle, D., Alemu,Y., Peters, K.J. (2000) Indigenous chickens in Ethiopia: genetic potential and attempts at improvement. World Poult Sci J. 56: 45-54.
Tang, S., Sun, D., Ou, J., Zhang, Y., Xu, G., Zhang, Y. (2010) Evaluation of the IGFs (IGF1 and IGF2) genes as candidates for growth, body measurement, carcass, and reproduction traits in Beijing You and Silkie chickens. Anim Biotech. 21: 104-113.
Vali, N. (2008) Indigenous chicken production in Iran: A Review. Pak J Biol Sci. 11: 2525-2531.
Van der Most, P.J., De Jong, B., Parmentier, H.K., Verhulst, S. (2011) Trade-off between growth and immune function: a meta-analysis of selection experiments. Funct Ecol. 25: 74-80
Weigend, S., Matthes, S., Solkner, J., Lamont, S.J. (2001) Resistance to Marek’s disease virus in White Leghorn chickens: effects of avian leukosis virus infection genotype, reciprocal mating, and major histocompatibility complex. Poult Sci. 80: 1064-1072.
Yeh, F.C., Yang, R.C., Boyle, T.B.J., Mao, J.X. (1997) POPGENE software: Microsoft Windows-based freeware for population genetic analysis. (version 1.32) Center for International Forestry Research, University of Alberta. Edmonton, Canada.