Pakistan J. Zool., vol. 48(6), pp. 1633-1641, 2016. Microsatellite Markers Based Genetic Evaluation of Pakistani Cattle Breeds Tanveer Hussain, 1,2,* Masroor Ellahi Babar, 1,2 Sunday O. Peters, 3 Abdul Wajid, 1 Akhtar Ali, 2 Amber Azam, 1 Zahoor Ahmad, 1 Muhammad Wasim, 1 Ahmad Ali, 4 Kadir Kizilkaya, 5 Marcos De Donato 6 and Ikhide G. Imumorin 7 1 Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan 2 Department of Molecular Biology, Virtual University of Pakistan, Lahore, 54610, Pakistan 3 Department of Animal Science, Berry College, Mount Berry, GA, 30149, USA 4 Department of Bioscience, COMSATS Institute of Information Technology, Sahiwal, 57000, Pakistan 5 Department of Animal Science, Adnan Menderes University, Aydin, 09100, Turkey 6 Lab. Genetica Molecular, Universidad de Oriente, Cumana, 6101, Venezuela 7 Animal Genetics and Genomics Laboratory, International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA A B S T R A C T Animal Genetic Resource of Pakistan is very diverse. There are 15 distinct breeds of cattle in Pakistan all belonging to zebu (humped type) cattle (Bos indicus) for which very little information on genetic architecture is available. Microsatellite markers are being widely used for breed characterization in animals. In the present study 345 individuals of 11 breeds (10 Pakistani cattle breeds and exotic Holstein Friesian breed) were genotyped using 21 fluorescently–labeled microsatellite markers to assess genetic variation and relationships among them. All markers were polymorphic in all studied breeds and observed number of alleles ranged from 6.28 in Tharparker to 10.66 in Dajal with mean value 8.50±1.552. Average values of observed and expected heterozygosity were calculated as 0.4897±0.1538 and 0.8292±0.0744 respectively. Mean values of Fis, Fit, FST and gene flow were 0.2819, 0.3864 and 0.1456 respectively. The average PIC value was 0.81 showing suitability of these markers for forensic analyses. Nei’s genetic distance estimates indicated relatively close genetic identity between Tharparker and Red-Sindhi breeds of Sindh Province of Pakistan while Tharparker and Dajal breeds of Pakistan were found most distinct. The UPGMA-based phylogenetic tree constructed from the genetic distances also indicated that the cattle breeds of Pakistan can be classified into distinct genetic groups based on these markers. This is the first comprehensive report on molecular characterization of Pakistani cattle breeds using microsatellite markers. This study can be helpful for making breed conservation strategies of cattle in Pakistan in future. INTRODUCTION There is a great animal genetic diversity in Pakistan due to its wide range of geographical ad environmental diversity strengthening its agricultural economy. There are 39.6 million cattle with 15 distinct cattle breeds located across the country raised mainly for milk, meat and draft purposes (Anonymous, 2012). All the indigenous Pakistani cattle belong to zebu (humped type) cattle (Bos indicus). The classification of the native cattle breeds of Pakistan has traditionally been based on differences in phenotypic features but these differences are insufficient to identify them distinctly. Characterization and evaluation of genetic differences among these breeds is necessary for their effective and meaningful __________________________ * Corresponding author: tanveer.hussain@vu.edu.pk 0030-9923/2016/0006-1633 $ 8.00/0 Copyright 2016 Zoological Society of Pakistan improvement and conservation. A number of techniques have been used to study genetic diversity and molecular phylogeny of domestic animals. Microsatellite markers, due to their co-dominant and multi-allelic attributes, have been proven to be useful markers for a variety of purposes, such as genome mapping, determination of genetic variation, parentage, assessment of within and among breeds genetic diversity and inbreeding levels, introgression from other species, admixture among breeds evaluating differences within of cattle and determining population substructure (Ciampolini et al., 1995; Garcia– Moreno et al., 1996; MacHugh et al., 1998; Edwards et al., 2000; Canon et al., 2001; Tapio et al. 2006; Ginja et al. 2009; Li and Kantanen, 2009; Qi et al., 2009). The present study was designed to characterize 9 famous indigenous cattle breeds of Pakistan (Sahiwal, Cholistani, Red-Sindhi, Tharparker, Dhanni, Lohani, Dajal, Bhagnari, Achai) along with Nari-Master breed (a recently developed beef breed by crossing Bhangnari and Australian Drought Master) and exotic Holestein Friesian Article Information Received 10 February 2015 Revised 22 December 2015 Accepted 14 April 2016 Available online 25 September 2016 Authors’ Contribution TH and MEB conceived and designed the study. TH, AW, AA did sampling and genome extraction. TH, AA, ZA amplified the markers. TH, SOP, AW, KK, MDD analyzed the data. TH, MEB, MW, SOP, AA, MDD, IGI wrote the article. Key words Microsatellite markers, Heterozygosity, Pakistani cattle breeds