Evolutionary Relationship And Population Genetic Structure Of Domestic Chicken Using SSR And MHC Markers

Molecular polymorphisms in DNA are an important source of information to characterize andclassify genetic resources. Microsatellites DNA markers have been widely used to assess geneticdiversity within and genetic relationship between populations in all major farm animal species includingchicken in the past20years. Many previous studies used this marker system in a world-wide collectionof chicken breeds originated from various continents and of different management and productionsystems. Using these markers, which are assumed to be neutral to selection, it has been shown that thebreeds cluster according to their geographic location but vary in the degree of genetic diversity independence to their breeding and management histories. The chicken major histocompatibility complex(MHC) is located on the micro-chromosome16and is described as the most variable region in thegenome. The genes of MHC play a central role in the immune system. Particularly, proteins encoded byMHC genes involved in the antigen presentation to T cells. Therefore describing the geneticpolymorphism in this region is crucial in understanding host-pathogen interaction. Although the natureof selection to MHC diversity remains unclear, three major hypotheses have been put forward, such asheterozygote advantage, negative frequency dependence (rare allele advantage) and fluctuating selection.The aim of current study is to quantify different forces that affect the evolution of MHC in chicken byassessing the relationship of MHC diversity in relation to the overall genetic clusters that wereidentified using autosomal microsatellites in chicken. In this study,25populations collected fromdifferent continents, production and management systems were genotyped and the major summary ofresults is as follows:1. Based on seven MHC microsatellites, the genetic diversity of500individuals from domesticchicken and red Jungle fowl were assessed. Totally,94alleles were identified. The most polymorphicmarkers were LEI0258, GAB0001and MHC0371which had43,12and12observed alleles, respectively.Most of markers carried high polymorphism information content (PIC>0.5) except for MCW0312,MHC-D and MHC-T among25populations, indicating rich genetic variation at these loci. A negativecorrelation (R2=-0.9629) was observed between pairwise genetic differentiation (FST) and expectedheterozygosity (HE) at MHC loci.2. In comparison with the genome-wide genetic diversity measured using29autosomalmicrosatellites, MHC region, either at single locus and haplotype level, showed relatively high NA, HOand HEamong most of the populations. However, exceptions were present in some unique lines, such asthe R22that was developed following the directional selection for homozygous B15serotype.3. Pairwise genetic differentiation revealed a lower genetic variation at seven MHC loci than at29genome-wide markers between populations among the continents. There was no correlation betweenthese two sets of FSTestimates (MHC locus-wise vs29SSR, R2=0.4128; MHC haplotype vs29SSR,R2=0.3145).4. Population genetic structuring patterns suggested a rather different evolutionary process of MHCregion compared with the alignment of geographic origin and management history to the genetic differentiation among these populations unveiled using29autosomal markers.5. In order to verify the above observations, we chosen five populations with large number ofsamples, well separated geographic locations and unique managemental histories to analyze theirpopulation genetic structure at MHC loci. A similar picture of genetic variation was eventually obtainedto validate the major findings of this study based on various statistical tests.