Genome-wide SNPs analysis of indigenous zebu breeds in Pakistan

• Published in: Biotechnology in animal husbandry Vol. 33; no. 1; pp. 13 - 25
• Main Authors: Mustafa, Hamid, Eiusoo, Kim, Heather, Huson, Ajmal, Adeela, Riley, David, Pasha, Nasser, Ali, Afzal, Javed, Khalid, Sonstegard, Tad
• Format: Journal Article
• Language: English
• Published: Institute for Animal Husbandry, Belgrade 2017
• Subjects: cattle; distribution; minor allele frequency; SNPs; variation
• ISSN: 1450-9156; 2217-7140
• DOI: 10.2298/BAH1701013M

Prospects of high throughput technology in animal genetics makes easy to investigate hidden genetic variation in farm animal?s genetic resources. However, many SNPs technologies are currently practicing in animal genetics. In this study, we investigated genome wide SNPs variations and its distribution across the indigenous cattle population in Pakistan using Illumina Bovine HD (777K) SNPs bead chip. A total of 136 individuals from ten different breeds were genotyped and after filtration 500, 939 SNPs markers were used for further analysis. The mean minor allele frequency (MAF) was 0.23, 0.20, 0.22, 0.22, 0.20, 0.18, 0.20, 0.22, 0.21 and 0.18 observed for Achi, Bhagnari, Cholistani, Dhanni, Dajal, Kankraj, Lohani, Red sindi, Sahiwal and Tharparkar cattle, respectively. Significant difference (P<0.001) of MAFs were observed in selected population. A common variants minor allele frequency (?0.10 and? 0.5) was estimated (64%). Across all sampled populations 64% SNPs markers were observed polymorphic (MAF>0.05) within breeds and remaining 36% were considered as monomorphic markers. Average observed (Ho) and expected (HE) heterozygosity values 0.662 and 0.640 were estimated among these breeds. In conclusion, this preliminary study results revealed that these SNPs variation level could potentially be used for genetic characterization of zebu cattle breeds and could also be used to estimate genetic potential of these cattle breeds for livestock improvement in country. nema