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

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.