AGRICULTURAL RESEARCH COMMUNICATION CENTRE www.arccjournals.com/www.ijaronline.in *Corresponding author’s e-mail: ranjanashish05@gmail.com 1 Livestock Production and Management Division, ICAR-NDRI, Karnal-132 001, Haryana, India. 2 Artificial Breeding Research Centre, ICAR-NDRI, Karnal-132 001, Hrayana, India. Indian J. Anim. Res., 52(12) 2018: 1680-1683 Print ISSN:0367-6722 / Online ISSN:0976-0555 Sequence characterization and SNP identification of TNP1 gene in Indian cattle breeds Ashish Ranjan*, K.N. Raja, Ranjana Sinha 1 , I. Ganguly, I.D. Gupta, M. Bhakat 2 and T.K. Mohanty 2 Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal-132 001, Haryana, India. Received: 28-04-2017 Accepted: 23-06-2017 DOI: 10.18805/ijar.v0iOF.8492 ABSTRACT Present study was conducted on 50 bulls and 40 male calves of Sahiwal, Tharparkar and Karan Fries cattle maintained at ABRC and LRC, NDRI Karnal (Haryana) to characterize and identify genetic polymorphisms in TNP1 gene. A total of 1568 bp region of TNP-1 gene includes 490 bp of promoter region and two exon and one intron was sequenced and characterized in Bos indicus cattle breeds which are widely distributed in Indian sub-continent. Four sets of primers for TNP1 gene on the basis of Bos Taurus sequence (Acc. No- BK_006511) were designed using Primer3 software and PCR products of 487, 450, 455 and 250 bp were obtained. Amplicons were custom sequenced and subjected to Clustal W analysis which showed no nucleotide changes in coding region and non coding region in Indian cattle breeds as compared to Bos taurus. The 490 bp of promoter region was subjected to transcription factor binding site. Three TATA boxes and two CAAT boxes were identified in the studied fragment. Analysis of SNP was performed using restriction fragment length polymorphism (PCR-RFLP), to detect nucleotide changes in the sequence as reported (g.528G>A, SS1388116558) in Chinese Holstein breed. No polymorphisms were found for tested SNP. Only one genotype GG indicates the absence of variability in the sampled population. Key words: CAAT boxes, Nucleotide sequences, Polymorphism, TATA boxes, TNP1 gene. INTRODUCTION Livestock breeding programmes is an important part of national agricultural policies and its main aim is to improve the food production and income of a country and of livestock keepers. In present scenario the goal of a breeding program is to produce one calf from each cow annually and obtain a high net income for dairymen. In current breeding programs, Semen from few genetically superior bulls is used because more than 60% of genetic improvement occurs through selection of bulls (Rendel and Robertsson, 1950). So, Bull’s DNA is the primary mechanism through which genetic improvements can efficiently be accomplished. In bulls, among the several reasons of infertility and sub-fertility, maturation of spermatozoa is an important factor (Foresta et al., 1992). Subfertility problem was the main reason of culling of Murrah, Sahiwal and KF bulls (Mukhopadhyay et al., 2010). Molecular defects in spermatozoal DNA leads to impairment of interaction with ova and affect embryonic development (Lucy, 2001; Braundmeier and Miller, 2001). Transition nuclear proteins (TNPs) are the most important proteins and involved in histone to protamine substitution during spermatid nuclear transformation for remodelling sperm nuclear chromatin to maintain stability (Mylonis et al., 2005). The TNP1 (Acc. No- BK_006511) gene, which is expressed during spermiogenesis, is located on 2q42-q43 in Bos taurus. TNP1, which appears a day later of TNP2, has been reported to stimulate DNA repair (Kierszenbaum, 2001; Caron et al. , 2001). It decreases the melting temperature of DNA and nucleosomal compaction leading to the suggestion that TNP1 is involved in histone removal (Akama et al., 1998; Singh and Rao, 1988). Therefore, the present study was carried out with the objective to sequence characterize the bovine TNP1 gene in Sahiwal, Tharparkar and Karan Fries breed of Bos indicus cattle and identification of SNP of TNP1 gene. MATERIALS AND METHODS A total of 20 Karan Fries, 20 Sahiwal and 10 Tharparkar bulls giving good as well as poor quality semen were selected from ABRC and from each breed 3 sire were selected who’s male calves were available. About 1-5 male calves from each sire were selected, total 40 calves were selected for study. Ten ml blood was collected aseptically by jugular vein puncture from calves in a sterile vacutainer containing 15% of 0.12 ml EDTA solution. Blood sample were collected after obtaining permission from institute. Genomic DNA from blood and semen were extracted by