Genetic diversity in global chicken breeds as a function of genetic distance to the wild populations
Migration of populations from their founder population is expected to cause a reduction in genetic diversity and facilitates population differentiation between the populations and their founder population as predicted by the theory of genetic isolation by distance. Consistent with that, a model of expansion from a single founder predicts that patterns of genetic diversity in populations can be well explained by their geographic expansion from the founders, which is correlated to the genetic differentiation. To investigate this in the chicken, we have estimated the relationship between the genetic diversity in 172 domesticated chicken populations and their genetic distances to wild populations. We have found a strong inverse relationship whereby 87.5% of the variation in the overall genetic diversity of domesticated chicken can be explained by the genetic distance to the wild populations. We also investigated if different types of SNPs and genes present similar patterns of genetic diversity as the overall genome. Among different SNP classes, the non-synonymous ones were the most deviating from the overall genome. However, the genetic distances to wild populations still explained more variation in domesticated chicken diversity in all SNP classes ranging from 81.7 to 88.7%. The genetic diversity seemed to change at a faster rate within the chicken in genes that are associated with transmembrane transport, protein transport and protein metabolic processes, and lipid metabolic processes. In general, such genes are flexible to be manipulated according to the population needs. On the other hand, genes which the genetic diversity hardly changes despite the genetic distance to the wild populations are associated with major functions e.g. brain development. Therefore, changes in the genes may be detrimental to the chickens. These results contribute to the knowledge of different evolutionary patterns of different functional genomic regions in the chicken.