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Online Journal of Veterinary Research©

Volume 20(3):177-182, 2016.



Single nucleotide polymorphisms (SNP) on transcriptome of Holstein cows

shared with Illumina bovine SNP arrays


Mohammad Hossein Banabazi1,  Ardeshir Nejati Javaremi1, Ikhide G. Imumorin2,

Mostafa Ghaderi Zefrei3 and Seyed Reza Miraei Ashtiani1


1Department of Animal Science, Faculty of Agricultural Science and Engineering, College of Agriculture & Natural Resources, University of Tehran, Karaj, 3Department of Animal Science, Faculty of Agriculture, University of Yasouj, Yasouj, Iran. 2Department of Animal Science, Cornell University, College of Agriculture and Life Sciences, Ithaca, New York, USA.




Banabazi MH, Nejati Javaremi A, Imumorin IG, Ghaderi Zefrei M, Miraei Ashtiani SR., Single nucleotide polymorphisms (SNP) on transcriptome of Holstein cows shared with Illumina bovine SNP arrays, Onl J Vet Res., 20(3):177-182, 2016. We report SNP loci determined by RNA-Seq located on transcriptome from 40 Holstein cows shared with Illumina SNP arrays. 53478 SNP loci were found but only 7167 were shared with Illumina bovine high density (HD) array. The low number of SNP’s negate their use in a reduced HD SNP panel. However, 167290 of 777,962 SNP markers located on HD SNP panel were called in the assembled transcriptome. These SNP markers are not necessarily polymorphic but may be reliable since they retained the same distribution as the original HD panel. The discovered SNP loci located in genomic coding regions (mRNA sequences) may improve genome enabled predictions compared with current SNP array



Keywords : Transcriptome, RNA-Seq, SNP discovery, Holstein cow,  Illumina Bovine SNP.