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The present investigation was to identify Y chromosome haplogroup using STR markers and to study genetic diversity in Indian breeds of buffalo. A total of 139 semen samples of five different Indian buffalo breeds were collected from different semen station of India for the study. DNA was extracted using standard phenol chloroform method. Based of Y specific microsatellite UMN1113 and UMN0304, the population was divided in 47 haplo groups. Subsequently, analysis of microsatellites revealed that overall haplogroup diversity in whole population of 139 buffalo bulls was (0.798±0.048), Murrah breed had maximum (0.899±0.024) and Surti had minimum (0.600±0.215) diversity. AMOVA showed that between breeds variation was 16.69% and differed significantly among the breeds (P<0.0001). Further, the pair wise genetic distance (FST value) between different breeds showed that Mehsana lies in between Surti and Murrah, which also signifies the fact that Mehsana breed originated as cross of Murrah and Surti, while Nili Ravi and Jaffarabadi were clustered together sharing Y specific signatures.
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