Fine Scale Population Structure of Global Cattle Breeds using Dense Haplotype Data

Abstract Text: The International Bovine Haplotype Map Project (Bovine HapMap) has provided an essential database for the study of population structures, breed development and genome-wide associations. Although some of the known relationships among the populations were already described in the data release, the available genotype data provided an opportunity to re-analyze combined datasets and to empirically ascertain previously unknown relationships. We performed a systematic analysis of 72 previously described global cattle breeds using a recently developed network analysis approach (NetView). Using NetView we were able not only to confirm the reported relationships, but also to detect additional sub-structures and numerous, previously unreported close relatives and outliers within the breeds. The inferred sub-structures, relative pairs and outliers make it possible to propose a standardized subset of unrelated cattle for use in future studies in which relatedness and sub-structures can be accounted for.

Keywords:

cattle

population structure

NetView