Abstract
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.
Highlights
Bovine high density (HD) SNPs assay is a most comprehensive genotyping tool to explore genome variation with high coverage resolution across cattle breeds (Howard et al, 2015). This features more than 777,962 SNPs probes that are distributed across entire bovine genome (Leroy, 2014)
Genotyping of selected samples was performed at USDA platform using Illumina Bovine high density (HD) SNPs bead chip spanning 777, 962 SNPs markers across all bovine genome. 200 ng gDNA quantities were used to genotyped these samples according to manufacture protocol
The overall minor allele frequency (MAF) was observed in this study was higher than previous reported studies in indicine breeds (McKay at el., 2008; Edea et al, 2015; Kim at el., 2015) and lower than the average value reported for Red Chittagong that was 0.28 (Uzzaman at el., 2014)
Summary
Bovine high density (HD) SNPs assay is a most comprehensive genotyping tool to explore genome variation with high coverage resolution across cattle breeds (Howard et al, 2015) This features more than 777,962 SNPs probes that are distributed across entire bovine genome (Leroy, 2014). This array was first time introduced in 2009 (Mbole-Kariuki et al, 2014) Applications of this array include genome wide association studies, quantitative trait loci identification, prediction of genetic merit, linkage disequilibrium and breed characterization (Pryce at el., 2014). The potential of this array has been proven in several studies that identified genomic regions which have strong contribution in phenotypic variation. These genomic regions that are related with feed efficiency and intake traits (Lin at el., 2010; Edea et al, 2014) milk production traits and meat type traits (Howard at el., 2015; Kim at el., 2015)
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