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OJVRTM
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
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.
ABSTRACT
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.
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