Genome-Wide Survey of Selection Signatures in Pakistani Cattle Breeds.

Selection signatures define a specific genome region, which is considered specific and important functional trait under natural or artificial selection. In this study, we used two different approaches to identify the selection signatures between and within ten different cattle breeds in Pakistan. The first method was used to detect haplotypes fixation on genomic regions within breeds. The second method, population differentiation index (Fst), was used to identify genomic regions having different allele frequencies between these cattle breeds. All selected breeds include Achi (18), Bhagnari (14), Cholistani (13), Dajal (10), Dhanni (10), Kankraj (12), Lohani (19), Red Sindhi (13), Sahiwal (14) and Tharparkar (13), were divided into three populations (A, B & C) based on nucleotide structural analysis. In this study, we identified fifty-three candidate genomic regions using both approaches. Seventeen genomic regions were common among three populations and forty-nine were successfully annotated with identification of some candidate genes. MCIR gene is found on BTA-18 between 14, 757, 332-14, 759, 082 bp. However, a number of putative genes linked with production traits (LAP3, CAPN3, CYP19, SAR1B and RPS6KA2), reproductive traits (PIK3CA, SPERT and IGF1R), nervous system (KIT, FGF5, ASIP and HSPB9) and immune response (IL2, IL4, SERPINA3-8 and BOLA3) are identified as being under selection. The finding of this preliminary selection signatures study in Pakistani cattle breeds provides a new insight for genomic diversity during domestication events and breed development. These results could be used to expedite the genomic assisted breeding selection in these breeds for the improvement of important economic related traits. [ABSTRACT FROM AUTHOR]