Indian Journal of Biotechnology Vol 13, July 2014, pp 411-413 Molecular genetic architecture of Hallikar cattle (Bos indicus) revealed through microsatellite markers P Hepsibha, A Gogoi and S M K Karthickeyan* Department of Animal Genetics and Breeding, Madras Veterinary College, Chennai 600 007, India Received10 January 2013 ; revised 23 May 2013; accepted 17 July 2013 Hallikar breed of cattle, popularly known as the ‘champion of draft breeds’, is a typical Mysore type cattle. Molecular characterization of Hallikar cattle through automated genotyping of 22 microsatellite loci revealed a total of 166 alleles with the number of alleles ranging from 3 (ILSTS033) to 16 (TGLA53) with a mean of 7.55±0.65, and the mean effective number of alleles was 3.67±0.31. The sizes of the alleles ranged from 92 (CSRM60) to 302 bp (ILSTS006). The overall mean polymorphic information content value was 0.6367±0.03. The observed (H o ) and expected heterozygosity (H e ) values averaged 0.6068±0.05 and 0.6863±0.03, respectively, measuring high genetic variation in the population. The overall mean deficit of heterozygotes (F IS ) (0.1314±0.05) exhibited existence of a breed structure in Hallikar. Keywords: Hallikar cattle, heterozygosity, genetic architecture, microsatellite markers Hallikar is one of the oldest (around 600-yr-old) breed of cattle in India, popularly known as the ‘champion of draft breeds’, forming a base for many of the present day South Indian cattle breeds. It is a typical Mysore type cattle, found in the southern region of the Indian peninsula of Karnataka state (Mysore, Mandya, Bengaluru, Kolar, Tumkur, Hassan and Chitradurga districts) 1 . It is a medium-sized animal with compact and muscular body, grey to dark grey-coloured coat, long face with small ears, prominent bulgy forehead furrowed in the middle and backward carrying long horns (emerging near each other at the base). As per the Livestock Census (2007), the population of Hallikar was found to be 1.998 million with the breedable females of 0.75 million. In addition to draft purpose, the breed is also used for cart racing. The average speed of the bullock is 3 km/h with the pulling power of 0.91 hp. Being a popular breed in the region, it is essential to understand the genetic architecture of the breed, using molecular markers, to explore the genetic uniqueness in it. Since, microsatellites are short tandem repeats exhibiting high polymorphism and are used as powerful molecular tools in measuring the genetic diversity within a population, this study was taken up to analyse the genetic variation within Hallikar breed of cattle. Blood samples of Hallikar breed of cattle were collected randomly from 48 animals belonging to different farmers’ herds in its breeding tract. Genomic DNA was isolated from each blood samples by phenol-chloroform method 2 . Twenty two bovine-specific microsatellite markers were selected as per the recommendation of FAO (http://www.fao.org/dad-is) considering their size, degree of polymorphism and genome coverage. These markers were amplified by polymerase chain reaction (PCR) from genomic DNA samples of the breed. The PCR mixture consisted of 10× PCR buffer, 1.5 mM MgCl 2 , 10 mM dNTPs, 5 pmoles each of forward and reverse primers, 50-100 ng template DNA and the volume made up to 15 L with milli Q water. The PCR thermal-cycler conditions consisted of initial denaturation at 95°C for 5 min, followed by 35 cycles of denaturation (95°C for 45 sec), annealing (with temperature ranging between 50 and 64°C for 45 sec) and extension (72°C for 45 sec), and final extension (72°C for 7 min). The amplified PCR products were then checked manually on 2% agarose gel electrophoresis at 100 V. Genotyping of the markers were carried out on an automated ABI prism 3730XL genetic analyzer. The chromatogram peaks were then analyzed by GeneMapper software and the data were retrieved in an excel sheet. The scores were then checked and fine tuned manually to avoid errors. The genotypic data were analysed using software (PopGene version 1.31) 3 and the allele diversity were measured by calculating observed and effective number of alleles, allele frequencies, observed and expected heterozygosities, inbreeding estimate (F IS ) or heterozygote deficiency. Polymorphism information content (PIC) was calculated using PIC calculator 4 . Bottleneck analysis was done to check any recent reduction in the population 5 . —————— *Author for correspondence: Tel: +91-44-2538 1506; Mobile: +91-9791103976 Email: kannikarthi@yahoo.co.in