Population Structure Analysis of Indigenous Cattle Breeds of Pakistan

Analyses of population structure and breed diversity have provided insight into the origin and evolution of cattle. Previously, these studies have used a low density of microsatellite markers; however, with the large number of single nucleotide polymorphism markers that are now available, it is possible to perform genome wide population genetic analyses in cattle. In this study population structure and diversity among ten Pakistani indigenous cattle breeds (Bos indicus) were examined. These include Achi, Bhagnari, Cholistani, Dhanni, Dajal, Kankaraj, Lohani, RedSindhi, Sahiwal and Tharparkar breeds. 500,939 single nucleotide polymorphisms (SNPs) spanning all of the bovine autosomal genome were genotyped with the Illumina Bovine 777K SNP BeadChip. Population structure was examined using the linkage model in the program STRUCTURE and Fst estimates were used to construct a neighbor-joining tree to represent the phylogenetic relationship among these breeds. The whole-genome SNP panel identified several levels of population substructure in the set of examined cattle breeds. The Tharparkar cattle were identified as the most genetically distinct breed; other breeds were genetically indistinguishable with historical data suggesting individuals were characterized into those breeds based upon usage. Exploration of the number of SNP loci required to differentiate between breeds showed that for 120 SNP loci, individuals could only be correctly clustered into breeds 50% of the time, thus a large number of SNP markers are required to replace the microsatellite markers that are currently commonly used in genetic diversity studies.

Key words: Cattle, population structure, diversity