Determination of genetic diversity in hair, honamli, kabakulak and norduz goats using loci associated with major histocompatibility complex (MHC)

The Мajor Histocompatibility Complex (MHC) plays an important role in innate and adaptive immune systems in vertebrates. In this master thesis, the resistance to tuberculosis, the tolerance to heat and genetic diversity in Hair, Honamlı, Kabakulak and Norduz goats raised in Turkey were evaluated using MHC-linked loci. The phylogenetic relation was also investigated between goat populations using MHC-linked loci. PCR-RFLP method was used for the determination of polymorphisms on MHC class II DRB region related to resistance to tuberculosis and tolerance to heat. Five different microsatellite loci on the MHC gene were used to determine the genetic diversity. According to results of PCR-RFLP analysis in the KIL, HNM, KBK and NRD goats reared in Turkey, the genotypes were determined with ranging frequencies on MHC class II DRB gene associated with resistance to tuberculosis (genotype pp - PstI and AluI genotype Tt - TaqI) and heat tolerance (genotype AA - BsaHI). However, GG, GC and CC (AluI) genotypes associated with heat tolerance could not be determined. The obtained results from this study indicate that PstI and TaqI polymorphisms on MHC class II DRB gene in the KIL, HNM, KBK and NRD goats may be used in Marker Assisted Selection (MAS) studies for Tuberculosis. It was concluded that BsaHI polymorphism may be used for heat tolerance but AluI polymorphism are not suitable for MAS studies. In the study, all microsatellite loci were found as polymorphic. The mean number of alleles ranged from 8.20 (NRD) to 8.80 (KIL and KBK), mean observed heterozygosity values varied from 0.68 (NRD) to 0.80 (KBK) and inbreeding coefficient (FIS) ranged from -0.017 (KBK) to 0.13 (HNM). Analyses of Molecular Variance (AMOVA) indicated that 8.62 % of the total genetic variation was due to differences between populations. Genetic differentiation between goat populations (pairwise FST coefficients) ranged from 0.01 (between KIL-KBK and HNM-KBK) to 0.19 (between HNM-NRD and NRD-KBK). According to phylogenetic analysis (UPGMA dendogram, FCA and Structure analysis) goat populations were clustered in two groups. KIL, HNM and KBK were in the first group while second group consist of NRD goats. As a result, high genetic diversity and low inbreeding were determined for MHC-linked loci in KIL, HNM, KBK and NRD goats reared in Turkey. Also, genetic difference could not be determined in KIL, HNM and KBK goats for related loci. The finding obtained from this study show that there is great potential for possible breeding studies for adaptive traits in KIL, HNM, KBK and NRD goats in future.